bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative plasma and milk dispositions, faecal excretion and efficacy of per os ivermectin and pour‐on eprinomectin in horses
Authors: Gokbulut C. , Ozuicli M. , Aksit D. , Aksoz E. , Korkut O. , Yalcinkaya M. , Cirak V. Y.
Published: March 2016

The horse milk gains increasing interest as a food product for sensitive consumers, such as children with food allergies or elderly people. We investigated the plasma and milk disposition, faecal excretion and efficacy of per os ivermectin (IVM) and pour‐on eprinomectin (EPM) in horses. Ten mares were divided into two groups. The equine paste formulation of IVM and bovine pour‐on formulation of EPM were administered orally and topically at dosage of 0.2 and 0.5 mg/kg bodyweight. Blood, milk and faecal samples were analysed using high‐performance liquid chromatography. The plasma concentration and persistence of IVM were significantly greater and longer compared with those of EPM. Surprisingly, EPM displayed a much higher disposition rate into milk (AUCmilk/plasma: 0.48) than IVM (AUCmilk/plasma: 0.19). IVM exhibited significantly higher faecal excretion (AUCfaeces: 7148.54 ng·d/g) but shorter faecal persistence (MRTfaeces: 1.17 days) compared with EPM (AUCfaeces: 42.43 ng·d/g and MRTfaeces: 3.29 days). Faecal strongyle egg counts (EPG) were performed before and at weekly intervals after treatment. IVM reduced the EPG by 96–100% for up to 8 weeks, whereas the reduction in the EPM group varied from 78 to 99%. In conclusion, due to the relatively low excretion in milk, EPM and IVM may be used safely in lactating mares if their milk is used for human consumption. Nevertheless, much lower plasma and faecal availabilities of EPM could result in subtherapeutic concentrations, which may increase the risk of drug resistance in nematodes after pour‐on EPM administration compared with per os IVM.
Perceptual Particularity
Authors: Schellenberg Susanna
Published: March 2016

Perception grounds demonstrative reference, yields singular thoughts, and fixes the reference of singular terms. Moreover, perception provides us with knowledge of particulars in our environment and justifies singular thoughts about particulars. How does perception play these cognitive and epistemic roles in our lives? I address this question by exploring the fundamental nature of perceptual experience. I argue that perceptual states are constituted by particulars and discuss epistemic, ontological, psychologistic, and semantic approaches to account for perceptual particularity.
The effect of post‐harvest storage conditions on the development of black dot (Colletotrichum coccodes) on potato in crops grown for different durations
Authors: Peters J. C. , Harper G. , Brierley J. L. , Lees A. K. , Wale S. J. , Hilton A. J. , Gladders P. , Boonham N. , Cunnington A. C.
Published: March 2016

The effects of post‐harvest curing and storage temperature on severity of black dot, caused by Colletotrichum coccodes, were investigated for potato crops grown for different crop durations (days from 50% emergence to harvest) in soils that posed a low, medium and high risk of disease. In field trials over four growing seasons (2005–8), black dot severity at harvest increased with increasing crop duration, within the range 103–146 days from 50% emergence to harvest (P < 0.05). In field trials over three growing seasons (2006–8), black dot severity on tubers at harvest increased significantly with increasing soil inoculum in each year, within the range 43–4787 pg C. coccodes DNA/g soil (P < 0.05). Storage trials were conducted to measure the influence of accumulated post‐harvest temperature on black dot. In 2005, no difference in black dot severity was observed on tubers stored for 20 weeks at 2.5 and 3.5 °C. In 2006 (but not 2007), increasing the duration of curing after harvest from 4 to 14 days increased black dot severity on tubers from 8.9 to 11.2% (P < 0.01) in long duration crops (>131 days after 50% emergence) grown under high (>1000 pg C. coccodes DNA/g soil) soil inoculum. The number of days of curing did not affect disease severity for shorter duration crops grown at high soil inoculum, or on crops grown at medium or low (100–1000 and <100 pg C. coccodes DNA/g soil, respectively) soil inoculum concentrations. Soil inoculum and crop duration together provided a reasonable prediction of black dot severity at harvest and after a 20‐week storage period.
Epidemiology and Outcomes of Congenital Diaphragmatic Hernia in Croatia: A Population‐Based Study
Authors: Grizelj Ruža , Bojanić Katarina , Vuković Jurica , Novak Milivoj , Rodin Urelija , Ćorić Tanja , Stanojević Milan , Schroeder Darrell R. , Weingarten Toby N. , Sprung Juraj ,   The Croatian Diaphragmatic Hernia Study Group
Published: March 2016

Background

Outcomes of neonates with congenital diaphragmatic hernia (CDH) are variable; reports are frequently limited to the experience of single tertiary care centres—a possible source of bias. Population‐based studies decrease survivor bias and provide additional insight into this high‐mortality condition. The objective of this study was to examine the incidence and outcomes of CDH in Croatia.

Methods

All cases of CDH in Croatia from 2001 through 2013 were ascertained from public health records. Overall and sex‐ and region‐specific incidence rates were calculated, and characteristics associated with 1‐year survival were assessed.

Results

We identified 145 cases of CDH during the study period, for an incidence of 2.67 per 10 000 total births. The incidence did not differ by calendar year (P = 0.38) or geographic region (P = 0.67). There was a slightly higher incidence among males (rate ratio, 1.37, 95% CI 0.99, 1.91). The 1‐year survival rate was 33.1% for the entire cohort and 47.9% for liveborns who received any treatment at an intensive care unit. From multivariable analysis, survival was decreased in neonates with left CDH, liver up (odds ratio 0.1, 95% CI, 0.03, 0.4) and increased when treated in a centre with higher case volume (odds ratio 12.8, 95% CI, 2.2, 72.1).

Conclusions

The incidence of CDH in Croatia is within the range of previous reports. Survival was substantially higher in neonates treated in a centre with higher case volume, which suggests that centralisation of medical care for CDH may be warranted in Croatia.
Body Mass Index, Overweight, and Obesity in Swedish Women Born Post‐term
Authors: Derraik José G. B. , Lundgren Maria , Cutfield Wayne S. , Ahlsson Fredrik
Published: March 2016

Background

There is increasing evidence that post‐term birth (≥42 weeks of gestation) is associated with adverse long‐term outcomes. We assessed whether women born post‐term displayed increased risk of overweight and obesity in adulthood.

Methods

Data were collected at first antenatal visit (~10–12 weeks of gestation) on singleton Swedish women aged ≥18 years in 1991–2009 (mean age 26.1 years), who were born post‐term (n = 27 153) or at term (37–41 weeks of gestation; n = 184 245). Study outcomes were evaluated for continuous associations with gestational age. Stratified analyses were carried out comparing women born post‐term or at term. Analyses were also run with a 2‐week buffer between groups to account for possible errors in gestational age estimation, comparing women born very post‐term (≥43 weeks of gestation; n = 5761) to those born within a narrower term window (38–40 weeks of gestation; n = 130 110).

Results

Increasing gestational age was associated with greater adult weight and body mass index (BMI). Stratified analyses showed that women born post‐term were 0.5 kg heavier and had BMI 0.2 kg/m2 greater than those born at term. Differences were more marked between women born very post‐term (≥43 weeks) vs. a narrower term group (38–40 weeks): 1.0 kg and 0.3 kg/m2. The adjusted relative risks of overweight/obesity and obesity in women born very post‐term were 1.13 and 1.12 times higher, respectively, than in those born at term.

Conclusions

Post‐term birth is associated with greater BMI and increased risk of overweight and obesity in adulthood, particularly among women born ≥43 weeks of gestation.
Lapses in skin conductance responding across anatomical sites: Comparison of fingers, feet, forehead, and wrist
Authors: Payne Andrew F. H. , Schell Anne M. , Dawson Michael E.
Published: March 2016

The fingers are widely accepted as the gold standard for skin conductance (SC) recording, with the feet as a strong alternative. However, there are gaps in the current literature comparing these sites. There is also a great deal of interest in alternative recording sites to permit mobility, but data evaluating these are few and inconsistent. The present report compared multiple sites (fingers, abductor hallucis of the foot, arch of the foot, toes, forehead, and wrist) from 45 college student participants in a short‐term sedentary laboratory setting and found large variation in both tonic and phasic SC responses, as well as crucial lapses in responding at nonpalmar sites. Across‐site correlations between participants and within participants were also examined. The present data show that, in the laboratory setting employing commonly used recording techniques and stimuli, the nonpalmar sites are generally less responsive than the fingers, and the wrist in particular is the lowest in responding, whereas the toes are most similar to the fingers in responding. Within‐participant correlations between the fingers and other sites were greatest for the plantar sites and least for the forehead.
Sequence stratigraphic framework for mixed aeolian, peritidal and marine environments: Insights from the Pennsylvanian subtropical record of Western Pangaea
Authors: Blanchard Sébastien , Fielding Christopher R. , Frank Tracy D. , Barrick James E.
Published: March 2016

Due to difficulties in correlating aeolian deposits with coeval marine facies, sequence stratigraphic interpretations for arid coastal successions are debated and lack a unifying model. The Pennsylvanian record of northern Wyoming,USA, consisting of mixed siliciclastic–carbonate sequences deposited in arid, subtropical conditions, provides an ideal opportunity to study linkages between such environments. Detailed facies models and sequence stratigraphic frameworks were developed for the Ranchester Limestone Member (Amsden Formation) and Tensleep Formation by integrating data from 16 measured sections across the eastern side of the Bighorn Basin with new conodont biostratigraphic data. The basal Ranchester Limestone Member consists of dolomite interbedded with thin shale layers, interpreted to represent alternating deposition in shallow marine (fossiliferous dolomite) and supratidal (cherty dolomite) settings, interspersed with periods of exposure (pedogenically modified dolomites and shales). The upper Ranchester Limestone Member consists of purple shales, siltstones, dolomicrites and bimodally cross‐bedded sandstones in the northern part of the basin, interpreted as deposits of mixed siliciclastic–carbonate tidal flats. The Tensleep Formation is characterized by thick (3 to 15 m) aeolian sandstones interbedded with peritidal heteroliths and marine dolomites, indicating cycles of erg accumulation, preservation and flooding. Marine carbonates are unconformably overlain by peritidal deposits and/or aeolian sandstones interpreted as lowstand systems tract deposits. Marine transgression was often accompanied by the generation of sharp supersurfaces. Lags and peritidal heteroliths were deposited during early stages of transgression. Late transgressive systems tract fossiliferous carbonates overlie supersurfaces. Highstand systems tract deposits are lacking, either due to non‐deposition or post‐depositional erosion. The magnitude of inferred relative sea‐level fluctuations (>19 m), estimated by comparison with analogous modern settings, is similar to estimates from coeval palaeotropical records. This study demonstrates that sequence stratigraphic terminology can be extended to coastal ergs interacting with marine environments, and offers insights into the dynamics of subtropical environments.
Failure of primary atovaquone prophylaxis for prevention of toxoplasmosis in hematopoietic cell transplant recipients
Authors: Gajurel K. , Gomez C.A. , Dhakal R. , Vogel H. , Montoya J.G.
Published: March 2016

The efficacy of primary prophylaxis with atovaquone in preventing Toxoplasma reactivation and disease in hematopoietic cell transplant (HCT) recipients is unknown. We describe 2 cases of atovaquone prophylaxis failure in pre‐HCT Toxoplasma‐seropositive (pre‐HCTSP) recipients who underwent allogeneic HCT (allo‐HCT) and review the literature on atovaquone prophylaxis in HCT recipients.
Primary Epstein–Barr virus infection, seroconversion, and post‐transplant lymphoproliferative disorder in seronegative renal allograft recipients: a prospective cohort study
Authors: Hosseini‐Moghaddam S.M. , Alhomayeed B. , Soliman N. , Weir M.A. , House A.A.
Published: March 2016

Background

Epstein–Barr virus (EBV)‐seronegative renal transplant recipients are at risk of post‐transplant lymphoproliferative disorder (PTLD). We compared primary EBV infection, seroconversion, and PTLD in EBV‐seronegative patients who received renal allograft from seropositive or seronegative donors (D+/R− and D−/R−, respectively).

Methods

We prospectively followed 25 D+/R− and 8 D−/R− recipients. We followed patients from January 1999 to June 2009 with clinical visits, monthly EBV polymerase chain reaction tests, and serologic tests for a period of 1 year after kidney transplantation and on an individual basis thereafter.

Results

Three patients (9%) developed PTLD including 2 early‐onset (<12 months) and 1 late‐onset (>12 months) disease. In D+/R− and D−/R− patients, the frequencies of PTLD (8% vs. 12.5%, P = 0.7), EBV seroconversion (64% vs. 50%, P = 0.4), and EBV viremia (40% vs. 25%, P = 0.6) were not significantly different. Clinical, serologic, and virologic surveillance as well as reduction in immunosuppression after evidence of primary EBV infection resulted in a PTLD rate of 9%, despite a seroconversion rate of 60.6%. Rate of graft loss after reduction in immunosuppression was 10% (2 of 20), which was not significantly different from 13 patients without EBV seroconversion (no graft loss, P = 0.5). Rates of viremia, seroconversion, and PTLD in D+/R− and D−/R− patients appear to be similar.

Conclusions

The incidence of PTLD in renal transplants ranges from 0.5% to 2.9%. Our data show a significantly higher rate in EBV‐seronegative renal allograft recipients, suggesting the need for close surveillance. Our data also suggest that donors for EBV‐seronegative recipients may be accepted irrespective of positive or negative serostatus, with ongoing surveillance important in either circumstance.
Nutritional input from dinoflagellate symbionts in reef-building corals is minimal during planula larval life stage
Authors: Kopp Christophe , Domart-Coulon Isabelle , Barthelemy Dominique , Meibom Anders
Published: March 2016

During their early life stage as planktonic larvae, reef-building corals do not rely on their photosynthesizing symbionts for nutrition.
Deterministic reshaping of single-photon spectra using cross-phase modulation
Authors: Matsuda Nobuyuki
Published: March 2016

With an ultrafast refractive index change in an optical fiber, frequency entanglement of twin photons is modulated on the fly.
Regulation of protein-ligand binding affinity by hydrogen bond pairing
Authors: Chen Deliang , Oezguen Numan , Urvil Petri , Ferguson Colin , Dann Sara M. , Savidge Tor C.
Published: March 2016

Receptor-ligand H-bond pairings have evolved to promote high-affinity binding by reducing competitive interference with water.
Obesity-induced DNA released from adipocytes stimulates chronic adipose tissue inflammation and insulin resistance
Authors: Nishimoto Sachiko , Fukuda Daiju , Higashikuni Yasutomi , Tanaka Kimie , Hirata Yoichiro , Murata Chie , Kim-Kaneyama Joo-ri , Sato Fukiko , Bando Masahiro , Yagi Shusuke , Soeki Takeshi , Hayashi Tetsuya , Imoto Issei , Sakaue Hiroshi , Shimabukuro Michio , Sata Masataka
Published: March 2016

DNA released from obesity-induced degenerated adipocytes stimulates inflammation in adipose tissue and insulin resistance.
Climate, CO
2
, and the history of North American grasses since the Last Glacial Maximum
Authors: Cotton Jennifer M. , Cerling Thure E. , Hoppe Kathryn A. , Mosier Thomas M. , Still Christopher J.
Published: March 2016

Bisoscapes: Bison isotopes show that temperature and precipitation outweigh CO
2
changes for North American grass landscapes.
Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein
Authors: Kimura Shoko , Suzuki Tateki , Chen Meirong , Kato Koji , Yu Jian , Nakamura Akiyoshi , Tanaka Isao , Yao Min
Published: March 2016

Structures of Thg1-like proteins provide insight into the template-dependent nucleotide addition in the reverse (3′-5′) direction.
Direct and cost-efficient hyperpolarization of long-lived nuclear spin states on universal
15
N
2
-diazirine molecular tags
Authors: Theis Thomas , Ortiz Gerardo X. , Logan Angus W. J. , Claytor Kevin E. , Feng Yesu , Huhn William P. , Blum Volker , Malcolmson Steven J. , Chekmenev Eduard Y. , Wang Qiu , Warren Warren S.
Published: March 2016

More than 10,000-fold enhanced magnetic resonance signals with >20-min signal lifetimes on universal biomolecular markers.
A quantum Fredkin gate
Authors: Patel Raj B. , Ho Joseph , Ferreyrol Franck , Ralph Timothy C. , Pryde Geoff J.
Published: March 2016

A quantum controlled-SWAP gate is demonstrated and used to implement small-scale algorithms and produce high-fidelity GHZ states.
Intrinsically core-shell plasmonic dielectric nanostructures with ultrahigh refractive index
Authors: Yue Zengji , Cai Boyuan , Wang Lan , Wang Xiaolin , Gu Min
Published: March 2016

A new type of plasmonic nanostructures with topologically protected metallic shells and high–refractive index dielectric cores.
Nanoscale chemical imaging by photoinduced force microscopy
Authors: Nowak Derek , Morrison William , Wickramasinghe H. Kumar , Jahng Junghoon , Potma Eric , Wan Lei , Ruiz Ricardo , Albrecht Thomas R. , Schmidt Kristin , Frommer Jane , Sanders Daniel P. , Park Sung
Published: March 2016

Photoinduced force microscopy resolves nanometer-scale topology with chemical recognition based on material absorption.
Boundary lubrication of heterogeneous surfaces and the onset of cavitation in frictional contacts
Authors: Savio Daniele , Pastewka Lars , Gumbsch Peter
Published: March 2016

Molecular dynamics simulations show that cavitation occurs when liquids flow over surfaces with sticking and slipping domains.
Discovery of natural MgSiO
3
tetragonal garnet in a shocked chondritic meteorite
Authors: Tomioka Naotaka , Miyahara Masaaki , Ito Motoo
Published: March 2016

A high-pressure phase is discovered in a shocked, stony meteorite.
Relating Carbon and Nitrogen Isotope Effects to Reaction Mechanisms during Aerobic or Anaerobic Degradation of RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine) by Pure Bacterial Cultures
Authors: Fuller Mark E. , Heraty Linnea , Condee Charles W. , Vainberg Simon , Sturchio Neil C. , Böhlke J. K. , Hatzinger Paul B.
Published: March 2016

Kinetic isotopic fractionation of carbon and nitrogen during RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation was investigated with pure bacterial cultures under aerobic and anaerobic conditions. Relatively large bulk enrichments in
15
N were observed during biodegradation of RDX via anaerobic ring cleavage (ε
15
N = −12.7‰ ± 0.8‰) and anaerobic nitro reduction (ε
15
N = −9.9‰ ± 0.7‰), in comparison to smaller effects during biodegradation via aerobic denitration (ε
15
N = −2.4‰ ± 0.2‰).
13
C enrichment was negligible during aerobic RDX biodegradation (ε
13
C = −0.8‰ ± 0.5‰) but larger during anaerobic degradation (ε
13
C = −4.0‰ ± 0.8‰), with modest variability among genera. Dual-isotope ε
13
C/ε
15
N analyses indicated that the three biodegradation pathways could be distinguished isotopically from each other and from abiotic degradation mechanisms. Compared to the initial RDX bulk δ
15
N value of +9‰, δ
15
N values of the NO
2
−
released from RDX ranged from −7‰ to +2‰ during aerobic biodegradation and from −42‰ to −24‰ during anaerobic biodegradation. Numerical reaction models indicated that N isotope effects of NO
2
−
production were much larger than, but systematically related to, the bulk RDX N isotope effects with different bacteria. Apparent intrinsic ε
15
N-NO
2
−
values were consistent with an initial denitration pathway in the aerobic experiments and more complex processes of NO
2
−
formation associated with anaerobic ring cleavage. These results indicate the potential for isotopic analysis of residual RDX for the differentiation of degradation pathways and indicate that further efforts to examine the isotopic composition of potential RDX degradation products (e.g., NO
x
) in the environment are warranted.

IMPORTANCE
This work provides the first systematic evaluation of the isotopic fractionation of carbon and nitrogen in the organic explosive RDX during degradation by different pathways. It also provides data on the isotopic effects observed in the nitrite produced during RDX biodegradation. Both of these results could lead to better understanding of the fate of RDX in the environment and help improve monitoring and remediation technologies.
Differences in the Vulnerability of Waterbird Species to Botulism Outbreaks in Mediterranean Wetlands: an Assessment of Ecological and Physiological Factors
Authors: Anza I. , Vidal D. , Feliu J. , Crespo E. , Mateo R.
Published: March 2016

Avian botulism kills thousands of waterbirds every year, including endangered species, but information about the differences between species in vulnerability to botulism outbreaks and the capacity to act as carriers of
Clostridium botulinum
is still poorly known. Here, we estimated the vulnerability to botulism of 11 waterbird species from Mediterranean wetlands by comparing the number of affected birds with the census of individuals at risk. The capacity of different species to act as carriers was studied by detecting the presence of the
C. botulinum
type C/D botulinum neurotoxin (BoNT) gene in fecal samples and prey items of waterbirds in the wild and by the serial sampling of cloacal swabs of birds affected by botulism. We found differences among species in their vulnerabilities to botulism, probably related to feeding habits, season of arrival, turnover, and, possibly, phylogenetic resilience. The globally endangered white-headed duck (
Oxyura leucocephala
) showed mortality rates in the studied outbreaks of 7% and 17% of the maximum census, which highlights botulism as a risk factor for the conservation of the species. Invasive water snails, such as
Physa acuta
, may be important drivers in botulism epidemiology, because 30% of samples tested positive for the BoNT gene during outbreaks. Finally, our results show that birds may excrete the pathogen for up to 7 days, and some individuals can do it for longer periods. Rails and ducks excreted
C. botulinum
more often and for longer times than gulls, which could be related to their digestive physiology (i.e., cecum development).

IMPORTANCE
Botulism is an important cause of mortality in waterbirds, including some endangered species. The global climate change may have consequences in the ecology of wetlands that favor the occurrence of botulism outbreaks. Here, we offer some information to understand the ecology of this disease that can be useful to cope with these global changes in the future. We have found that some species (i.e., coots and dabbling ducks) are more vulnerable to botulism and have a more relevant role in the onset and amplification of the outbreaks than other species (i.e., flamingos and grebes). Feeding habits can explain these differences in part; in addition to the well-known role of necrophagous fly maggots, we found here that water snails are frequent carriers of
Clostridium botulinum
. This is relevant, because these water snails can thrive in eutrophic and polluted wetlands, exacerbating other changes driven by climate change in wetlands.
Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea
Authors: Mellbye Brett L. , Giguere Andrew , Chaplen Frank , Bottomley Peter J. , Sayavedra-Soto Luis A.
Published: March 2016

Nitrosomonas europaea
is a chemolithoautotrophic bacterium that oxidizes ammonia (NH
3
) to obtain energy for growth on carbon dioxide (CO
2
) and can also produce nitrous oxide (N
2
O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of
N. europaea
to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na
2
CO
3
) supplemented with atmospheric CO
2
. IC-limited cultures oxidized 25 to 58% of available NH
3
to nitrite, depending on the dilution rate and Na
2
CO
3
concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH
3
-limited cultures. Rates of N
2
O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH
3
-N that was transformed to N
2
O-N from 0.5% (replete) up to 4.4% (0.2 mM Na
2
CO
3
). Transcriptome analysis showed differential expression (
P
≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C
1
metabolism, including the genes for RuBisCO (
cbb
gene cluster), carbonic anhydrase, folate-linked metabolism of C
1
moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N
2
O. Together, these data suggest that
N. europaea
adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH
3
oxidation from growth and increased N
2
O production.

IMPORTANCE
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO
2
) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of
Nitrosomonas europaea
, a model ammonia-oxidizing bacterium, and report on increased production of N
2
O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N
2
O emissions from nitrification in soils and wastewater treatment.
Culturing and Characterization of Gut Symbiont Burkholderia spp. from the Southern Chinch Bug, Blissus insularis (Hemiptera: Blissidae)
Authors: Xu Yao , Buss Eileen A. , Boucias Drion G.
Published: March 2016

The phloem-feeding Southern chinch bug,
Blissus insularis
, harbors a high density of the exocellular bacterial symbiont
Burkholderia
in the lumen of specialized midgut crypts. Here we developed an organ culture method that initially involved incubating the
B. insularis
crypts in osmotically balanced insect cell culture medium. This approach enabled the crypt-inhabiting
Burkholderia
spp. to make a transition to an
in vitro
environment and to be subsequently cultured in standard bacteriological media. Examinations using ribotyping and BOX-PCR fingerprinting techniques demonstrated that most
in vitro
-produced bacterial cultures were identical to their crypt-inhabiting
Burkholderia
counterparts. Genomic and physiological analyses of gut-symbiotic
Burkholderia
spp. that were isolated individually from two separate
B. insularis
laboratory colonies revealed that the majority of individual insects harbored a single
Burkholderia
ribotype in their midgut crypts, resulting in a diverse
Burkholderia
community within each colony. The diversity was also exhibited by the phenotypic and genotypic characteristics of these
Burkholderia
cultures. Access to cultures of crypt-inhabiting bacteria provides an opportunity to investigate the interaction between symbiotic
Burkholderia
spp. and the
B. insularis
host. Furthermore, the culturing method provides an alternative strategy for establishing
in vitro
cultures of other fastidious insect-associated bacterial symbionts.

IMPORTANCE
An organ culture method was developed to establish
in vitro
cultures of a fastidious
Burkholderia
symbiont associated with the midgut crypts of the Southern chinch bug,
Blissus insularis
. The identities of the resulting cultures were confirmed using the genomic and physiological features of
Burkholderia
cultures isolated from
B. insularis
crypts, showing that host insects maintained the diversity of
Burkholderia
spp. over multiple generations. The availability of characterized gut-symbiotic
Burkholderia
cultures provides a resource for genetic manipulation of these bacteria and for examination of the mechanisms underlying insect-bacterium symbiosis.
Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing
Authors: Van Vliet Danielle , Wiens Gregory D. , Loch Thomas P. , Nicolas Pierre , Faisal Mohamed
Published: March 2016

The use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S.
Flavobacterium psychrophilum
, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S.
F. psychrophilum
genetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96
F. psychrophilum
isolates recovered from rainbow trout (
Oncorhynchus mykiss
), coho salmon (
Oncorhynchus kisutch
), and Chinook salmon (
Oncorhynchus tshawytscha
) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (
n
= 63) or were singletons (
n
= 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity of
F. psychrophilum
within the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution of
F. psychrophilum
genotypes.

IMPORTANCE
Flavobacterium psychrophilum
is the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity of
F. psychrophilum
from the United States, as this region remains important in salmonid aquaculture.
Type III-Dependent Translocation of HrpB2 by a Nonpathogenic
hpaABC
Mutant of the Plant-Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria
Authors: Scheibner Felix , Schulz Steve , Hausner Jens , Marillonnet Sylvestre , Büttner Daniela
Published: March 2016

The plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria employs a type III secretion (T3S) system to translocate effector proteins into plant cells. The T3S apparatus spans both bacterial membranes and is associated with an extracellular pilus and a channel-like translocon in the host plasma membrane. T3S is controlled by the switch protein HpaC, which suppresses secretion and translocation of the predicted inner rod protein HrpB2 and promotes secretion of translocon and effector proteins. We previously reported that HrpB2 interacts with HpaC and the cytoplasmic domain of the inner membrane protein HrcU (C. Lorenz, S. Schulz, T. Wolsch, O. Rossier, U. Bonas, and D. Büttner, PLoS Pathog
4:
e1000094, 2008,
http://dx.doi.org/10.1371/journal.ppat.1000094
). However, the molecular mechanisms underlying the control of HrpB2 secretion are not yet understood. Here, we located a T3S and translocation signal in the N-terminal 40 amino acids of HrpB2. The results of complementation experiments with HrpB2 deletion derivatives revealed that the T3S signal of HrpB2 is essential for protein function. Furthermore, interaction studies showed that the N-terminal region of HrpB2 interacts with the cytoplasmic domain of HrcU, suggesting that the T3S signal of HrpB2 contributes to substrate docking. Translocation of HrpB2 is suppressed not only by HpaC but also by the T3S chaperone HpaB and its secreted regulator, HpaA. Deletion of
hpaA
,
hpaB
, and
hpaC
leads to a loss of pathogenicity but allows the translocation of fusion proteins between the HrpB2 T3S signal and effector proteins into leaves of host and non-host plants.

IMPORTANCE
The T3S system of the plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria is essential for pathogenicity and delivers effector proteins into plant cells. T3S depends on HrpB2, which is a component of the predicted periplasmic inner rod structure of the secretion apparatus. HrpB2 is secreted during the early stages of the secretion process and interacts with the cytoplasmic domain of the inner membrane protein HrcU. Here, we localized the secretion and translocation signal of HrpB2 in the N-terminal 40 amino acids and show that this region is sufficient for the interaction with the cytoplasmic domain of HrcU. Our results suggest that the T3S signal of HrpB2 is required for the docking of HrpB2 to the secretion apparatus. Furthermore, we provide experimental evidence that the N-terminal region of HrpB2 is sufficient to target effector proteins for translocation in a nonpathogenic
X. campestris
pv. vesicatoria strain.
Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites
Authors: Liu Xikun , Mattes Timothy E.
Published: March 2016

Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating
Mycobacterium
strains and
Nocardioides
sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to
Mycobacterium
and
Nocardioides
strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating
Gordonia rubripertincta
strain B-276 and
Xanthobacter autotrophicus
strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied.

IMPORTANCE
The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.
Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses
Authors: Bennke Christin M. , Reintjes Greta , Schattenhofer Martha , Ellrott Andreas , Wulf Jörg , Zeder Michael , Fuchs Bernhard M.
Published: March 2016

In the age of ever-increasing “-omics” studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescence
in situ
hybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3 m and pitch and roll angles of up to 6.3°. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (
r
2
> 0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.

IMPORTANCE
In this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glöckner, T. Schweder, and R. Amann, Science 336:608–611, 2012,
http://dx.doi.org/10.1126/science.1218344
). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.
Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils
Authors: Alguacil Maria del Mar , Torres Maria Pilar , Montesinos-Navarro Alicia , Roldán Antonio
Published: March 2016

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil ofBrachypodium retusumin six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations.

IMPORTANCECommunities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions.
Permanent congenital hypothyroidism with blood spot thyroid stimulating hormone <10 mU/L
Authors: Jones Jeremy H , Smith Sarah , Dorrian Catherine , Mason Avril , Shaikh M Guftar
Published: March 2016

Background

The UK recommended lower threshold for neonatal blood spot thyroid stimulating hormone (TSH) screening for congenital hypothyroidism (CHT) is 10.0 mU/L. Some laboratories use lower thresholds. This will lead to referral of mildly or unaffected infants but some will require thyroxine therapy.

Methods

Laboratory referrals with a first or repeat capillary TSH between 8.0 and <10.0 mU/L were identified (January 2004 to March 2014). The outcome of these cases was examined.

Results

26 infants had one or more blood spot TSH values between 8.0 and 9.99 mU/L; 65% had transient elevated neonatal TSH while one is awaiting diagnostic challenge. The remaining eight (31%) have permanent CHT; three with dyshormonogenesis, two with thyroid ectopia and the others met the criteria for definite CHT. Two out of three with dyshormonogenesis presented with decompensated hypothyroidism.

Conclusions

Infants with permanent and occasionally severe CHT may have a screening TSH below the UK recommended lower cut-off.
Patterns of orodental injury and mouthguard use in Dutch field hockey
Authors: Vucic Strahinja , Drost Rosalin W , van Wijk Arjen J , Wesselink Paul R , Wolvius Eppo B
Published: March 2016

Background

Orodental injuries in field hockey are a growing cause of concern that requires attention.

Objective

The objective of this cross-sectional study was to investigate the patterns of orodental injury, and the use of mouthguards in Dutch national field hockey.

Materials and methods

In the period from 1 May to 31 July 2014, a 33-item questionnaire about orodental injury and mouthguard use was sent to 7 field hockey clubs in the Netherlands. Data were analysed using 2 multivariable logistic (non-)linear regression per outcome measurement: (1) orodental injury and (2) type of mouthguard.

Results

Out of 6585 players, 1299 (20%) responded sufficiently and were eligible for the study. In total, 214 hockey players (16%) experienced at least 1 orodental injury in their career. The injuries were less severe in athletes who wore a mouthguard during an accident than in those who did not, OR=2.1 to 3.3, p≤0.05. Players without mouthguard sustained broken and knocked out teeth more frequently, while players with a mouthguard had more lip cuts (p≤0.05). Players complained less about custom-made than about mouth-moulded mouthguards (p≤0.05). Also, males were more at risk for an orodental injury, OR=1.4 (95% CI 1.0 to 1.9), and were less likely to have a custom-made mouthguard, OR=0.7 (95% CI 0.6 to 0.9), than females.

Conclusions

A substantial number of field hockey players suffers from orodental injury. Mouthguards should be included in prevention strategies as they are associated with less severe injuries and patterns of injury are to be taken into account when targeting specific groups.
Physiotherapy for pain: a meta-epidemiological study of randomised trials
Authors: Ginnerup-Nielsen Elisabeth , Christensen Robin , Thorborg Kristian , Tarp Simon , Henriksen Marius
Published: March 2016

Objectives

To empirically assess the clinical effects of physiotherapy on pain in adults.

Design

Using meta-epidemiology, we report on the effects of a ‘physiotherapy’ intervention on self-reported pain in adults. For each trial, the group difference in the outcome ‘pain intensity’ was assessed as standardised mean differences (SMD) with 95% CIs. Stratified analyses were conducted according to patient population (International Classification of Diseases-10 classes), type of physiotherapy intervention, their interaction, as well as type of comparator group and risks of bias. The quality of the body of evidence was assessed based on GRADE methodology.

Data sources

Systematic searches were carried out in MEDLINE and PEDro from 1 January 2004–31 December 2013. 174 trials (224 comparisons) met the inclusion criteria for the meta-analysis.

Eligibility criteria for selecting studies

Randomised trials using ‘no intervention’ or of a sham-controlled design were selected. Only articles written in English were eligible.

Results

An overall moderate effect of physiotherapy on pain corresponding to 0.65 SD-units (95% CI 0.57 to 0.73) was found based on a moderate inconsistency (I2=51%). Stratified exploration showed that therapeutic exercise for musculoskeletal diseases tended to be more beneficial than multimodal interventions (difference 0.30 95% CI 0.03 to 0.57; p=0.03). Trials with a ‘no intervention’ comparator tended to have a higher overall effect size than trials with a sham comparator (difference 0.25; 95% CI 0.09 to 0.41; p=0.004). In general, our confidence in the estimates was low, mainly due to high risk of performance biases and between-study heterogeneity.

Conclusions

Physiotherapy reduces pain in adults, but standardisation of interventions and focus on trial research with low risks of bias and reproducible treatment modalities are needed.

Trial registration number

CRD42014008754.