bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)
Authors: Yeaman Sam , Hodgins Kathryn A. , Suren Haktan , Nurkowski Kristin A. , Rieseberg Loren H. , Holliday Jason A. , Aitken Sally N. 
Published: April 2014

Summary

Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change.

By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii).

We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11 658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression.

We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.
Incomplete systemic movement of Xanthomonas campestris pv. musacearum and the occurrence of latent infections in xanthomonas wilt‐infected banana mats
Authors: Ocimati W. , Nakato G. V. , Fiaboe K. M. , Beed F. , Blomme G. 
Published: April 2014

Management of banana xanthomonas wilt (XW) (caused by Xanthomonas campestris pv. musacearum, Xcm) has been impeded by poor adoption of control options that are complex, cumbersome and costly. To improve XW management, this study investigated Xcm survival and latent infections in subsequent generations, survival of latently infected planting materials (suckers), incidence of latent infections in symptomless plants in mats having diseased plants, and XW status across farms and markets in districts previously devastated but currently endemic. On‐station experiments were protected from new infections. Latent bacteria at low levels were detected in up to 20% of the third generation suckers, with a significant (P < 0·05) reduction (43–20%) in subsequent generations. Only 3–6% of latently infected suckers succumbed to XW. Incidence of Xcm in symptomless suckers from farmers' fields (with up to 70% incidence) was low (3%) while it increased (8–25%) with disease severity in mats in controlled experiments. In the surveyed districts, incidence had significantly declined with yields observed to have recovered relative to earlier reports, although latent infections remained high. This study provides evidence that if new infections are prevented, fields with high XW incidence can be rejuvenated. It showed incomplete systemic movement of Xcm in mats coupled to a gradual decline of bacterial load in subsequent generations to levels that cannot initiate disease. These studies explain the current successes in farms practising single diseased plant removal instead of whole mat rouging, and gives hope to farmers lacking access to clean planting material.
Assessing host specialization ofBotrytis cinereaon lettuce and tomato by genotypic and phenotypic characterization
Authors: Leyronas C. , Bryone F. , Duffaud M. , Troulet C. , Nicot P. C. 
Published: April 2014

This study tested the hypothesis thatBotyrtis cinereashows host specialization on tomato and lettuce, using phenotypic and genotypic tools. Strains were isolated from tomato and lettuce grown together in the same greenhouse. Forty‐four lettuce strains and 42 tomato strains were investigated for their genetic diversity and their aggressiveness. Both gene diversity and allelic richness were significantly higher in lettuce strains than in tomato strains (P = 0·01). Cluster analysis revealed a clear division of the strains under study into two clusters. However, this structure did not separate the strains according to their host of origin. Tomato strains were significantly more aggressive than lettuce strains when inoculated on tomatoes (P = 0·001), but no significant differences in aggressiveness were observed when the strains were inoculated on lettuce (P = 0·17) or on apple (P = 0·87). The results suggest an absence of clear host specialization ofB. cinereaon tomato and lettuce.
Loneliness and Suicidal Ideation in Drug‐Using College Students
Authors: Lamis Dorian A. , Ballard Elizabeth D. , Patel Amee B. 
Published: April 2014

The college years are marked by social changes and behavioral experimentation which may increase risk of suicidal ideation. We propose a novel pathway for the development of suicidal thoughts between two established suicide risk factors, loneliness and drug use, which have not been examined in a nonclinical sample. Data were collected from 207 undergraduate drug‐using students at a large southeastern university. As hypothesized, suicidal ideation was positively correlated with both loneliness (r = .40) and drug use (r = .29). After controlling for several demographic variables, social desirability, and anxiety sensitivity, drug use was tested as a potential mediator in the loneliness–suicidal ideation link using a single‐mediator model. Results indicated a significant indirect (mediated) effect of loneliness on suicidal ideation via drug use (ab = 0.09, 95% CI: 0.02–0.18), suggesting that loneliness may contribute to suicidal ideation through increased drug use among college students. Identification of and intervention with students reporting loneliness and drug use may be a promising suicide prevention strategy on college campuses.
Application of a visual soil examination and evaluation technique at site and farm level
Authors: Sonneveld M. P. W. , Heuvelink G. B. M. , Moolenaar S.W. 
Published: April 2014

AbstractVisual soil examination and evaluation (VSEE) techniques are semi‐quantitative methods that provide rapid and cost‐effective information on soil quality. These are mostly applied at site or field level, but there is an increased need for soil quality indicators at farm level to allow integration with other sustainability indicators. The objectives of this study were to develop and apply a protocol for application of a VSEE technique at site level, to assess the VSEE observations against standardized laboratory analyses and to aggregate VSEE observations to farm level using an appropriate sampling design. The study was conducted at ten dairy farms in a reclaimed polder in the Netherlands with clay and organic soils. A stratified random sampling design was used to account for spatial variability in land use and soil series. VSEE was carried out using the Visual Soil Assessment approach. Results show that 81% of sites were assessed as good and the remainder as moderate to poor. For the clay soils, field observations of soil structure were significantly correlated with pH, bulk density, soil organic matter (SOM) and mean weight diameter of aggregates, whereas for organic soils, soil structure significantly correlated with pH, bulk density, organic C and SOM. The range in overall scores calculated at farm level was smaller than at site level, and most farms were assessed as good.
Distance to emergency obstetric services and early neonatal mortality in Ethiopia
Authors: McKinnon Britt , Harper Sam , Kaufman Jay S. , Abdullah Muna 
Published: April 2014

AbstractObjectivesTo assess the effect of distance to emergency obstetric and newborn care (EmONC) services on early neonatal mortality in rural Ethiopia and examine whether proximity to services contributes to socio‐economic inequalities in early neonatal mortality.MethodsWe linked data from the 2011 Ethiopian Demographic and Health Survey with facility data from the 2008 Ethiopian National EmONC Needs Assessment based on geographical coordinates collected in both surveys. Health facilities were classified based on the performance of nine EmONC signal functions (e.g. neonatal resuscitation, Caesarean section). We used multivariable logistic regression to assess the relationship between distance to services and early neonatal mortality. A decomposition approach was used to quantify the relative contributions of distance to EmONC services and other determinants to overall and socio‐economic inequality in early neonatal mortality.ResultsIn general, closer proximity to EmONC services and higher level of care were associated with lower early neonatal mortality. Living more than 80 km from the nearest comprehensive EmONC facility able to perform all nine signal functions compared to living within 10 km was associated with an increase of 14.4 early neonatal deaths per 1000 live births (95% CI: 0.1, 28.7). Closer proximity to a substandard EmONC facility compared with no facility was not associated with lower early neonatal mortality. Distance to EmONC services was an important determinant of early neonatal mortality, although it did not make a significant contribution to explaining socio‐economic inequality.ConclusionsOur results suggest that recent initiatives by the Ethiopian government to improve geographical access to EmONC services have the potential to reduce early neonatal mortality but may not affect inequalities.
Antibiotic prescribing practice for acute, uncomplicated respiratory tract infections in primary care settings in New Delhi, India
Authors: Kotwani Anita , Holloway Kathleen 
Published: April 2014

AbstractObjectiveTo obtain information on prescribing rates and choice of antibiotics for acute, uncomplicated respiratory tract infections (RTIs) in the community.MethodsAntibiotic use in acute, uncomplicated RTIs consisting of common cold/sore throat/cough for not more than five days was surveyed in the community (December 2007–November 2008) using patient exit interviews at public and private facilities from four localities in New Delhi. Data were collected from 10 public sector facilities and 20 private clinics over one year. The percentage of acute, uncomplicated RTIs patients receiving antibiotics in general and using the Anatomical Therapeutic Chemical classification and the Defined Daily Dose (ATS/DDD) were analysed.ResultsAt public and private facilities, 45% (746/1646) and 57% (259/457) of acute, uncomplicated RTI patients were prescribed at least one antibiotic, respectively. The main antibiotic class calculated as percentage of total antibiotics DDDs/1000 prescribed to acute, uncomplicated RTI patients at private clinics was cephalosporins, J01DA (39%), followed by fluoroquinolones, J01MA (24%), penicillins, J01C (19%) and macrolides, J01FA (15%). Newer members from each class were prescribed; older antibiotics such as co‐trimoxazole or tetracyclines were rarely prescribed. At public facilities, the main class of antibiotic prescribed was penicillins (31%), followed by macrolides (25%), fluoroquinolones (20%) and cephalosporins (10%).ConclusionsStudy clearly shows overuse and inappropriate choice of antibiotics for the treatment of acute, uncomplicated RTIs which are mainly due to virus and do not require antibiotic treatment. Results of the study warrant interventional strategies to promote rational use of antibiotics to decrease the overgrowing threat of antibiotic resistance.
In Vitro
Amphotericin B Susceptibility of Malassezia pachydermatis Determined by the CLSI Broth Microdilution Method and Etest Using Lipid-Enriched Media
Authors: Álvarez-Pérez Sergio , Blanco José L. , Peláez Teresa , Cutuli Maite , García Marta E. 
Published: April 2014

ABSTRACT

We determined the
in vitro
amphotericin B susceptibility of 60
Malassezia pachydermatis
isolates by the CLSI broth microdilution method and the Etest using lipid-enriched media. All isolates were susceptible at MICs of ≤1 μg/ml, confirming the high activity of amphotericin B against this yeast species. Overall, the essential agreement between the tested methods was high (80% and 96.7% after 48 h and 72 h, respectively), and all discrepancies were regarded as nonsubstantial.
Lack of Antimicrobial Bactericidal Activity in Mycobacterium abscessus
Authors: Maurer Florian P. , Bruderer Vera L. , Ritter Claudia , Castelberg Claudio , Bloemberg Guido V. , Böttger Erik C. 
Published: April 2014

ABSTRACT

Antibiotic therapy of infections caused by the emerging pathogen
Mycobacterium abscessus
is challenging due to the organism's natural resistance toward most clinically available antimicrobials. We investigated the bactericidal activity of antibiotics commonly administered in
M. abscessus
infections in order to better understand the poor therapeutic outcome. Time-kill curves were generated for clinical
M. abscessus
isolates,
Mycobacterium smegmatis
, and
Escherichia coli
by using antibiotics commonly categorized as bactericidal (amikacin and moxifloxacin) or bacteriostatic (tigecycline and linezolid). In addition, the impact of aminoglycoside-modifying enzymes on the mode of action of substrate and nonsubstrate aminoglycosides was studied by using
M. smegmatis
as a model organism. While amikacin and moxifloxacin were bactericidal against
E. coli
, none of the tested compounds showed bactericidal activity against
M. abscessus
. Further mechanistic investigations of the mode of action of aminoglycosides in
M. smegmatis
revealed that the bactericidal activity of tobramycin and gentamicin was restored by disruption of the chromosomal
aac(2
′) gene in the mycobacterial genome. The lack of bactericidal antibiotics in currently recommended treatment regimens provides a reasonable explanation for the poor therapeutic outcome in
M. abscessus
infection. Our findings suggest that chromosomally encoded drug-modifying enzymes play an important role in the lack of aminoglycoside bactericidal activity against rapidly growing mycobacteria.
Cohort Study of the Impact of Time to Antibiotic Administration on Mortality in Patients with Febrile Neutropenia
Authors: Rosa Regis G. , Goldani Luciano Z. 
Published: April 2014

ABSTRACT

The time to antibiotic administration (TTA) has been proposed as a quality-of-care measure in febrile neutropenia (FN); however, few data regarding the impact of the TTA on the mortality of adult cancer patients with FN are available. The objective of this study was to determine whether the TTA is a predictor of mortality in adult cancer patients with FN. A prospective cohort study of all consecutive cases of FN, evaluated from October 2009 to August 2011, at a single tertiary referral hospital in southern Brazil was performed. The TTA was assessed as a predictive factor for mortality within 28 days of FN onset using the Cox proportional hazards model. Kaplan-Meier curves were used for an assessment of the mortality rates according to different TTAs; the log-rank test was used for between-group comparisons. In total, 307 cases of FN (169 subjects) were evaluated. During the study period, there were 29 deaths. In a Cox regression analysis, the TTA was independently associated with mortality within 28 days (hazard ratio [HR], 1.18; 95% confidence interval [CI], 1.10 to 1.26); each increase of 1 h in the TTA raised the risk of mortality within 28 days by 18%. Patients with FN episodes with a TTA of ≤30 min had lower 28-day mortality rates than those with a TTA of between 31 min and 60 min (3.0% versus 18.1%; log-rank
P
= 0.0002). Early antibiotic administration was associated with higher survival rates in the context of FN. Efforts should be made to ensure that FN patients receive effective antibiotic therapy as soon as possible. A target of 30 min to the TTA should be adopted for cancer patients with FN.
Amikacin-Fosfomycin at a Five-to-Two Ratio: Characterization of Mutation Rates in Microbial Strains Causing Ventilator-Associated Pneumonia and Interactions with Commonly Used Antibiotics
Authors: Montgomery A. Bruce , Rhomberg Paul R. , Abuan Tammy , Walters Kathie-Anne , Flamm Robert K. 
Published: April 2014

ABSTRACT

The amikacin-fosfomycin inhalation system (AFIS), a combination of antibiotics administered with an in-line nebulizer delivery system, is being developed for adjunctive treatment of ventilator-associated pneumonia (VAP). The
in vitro
characterization of amikacin-fosfomycin (at a 5:2 ratio) described here included determining resistance selection rates for pathogens that are representative of those commonly associated with VAP (including multidrug-resistant strains) and evaluating interactions with antibiotics commonly used intravenously to treat VAP. Spontaneous resistance to amikacin-fosfomycin (5:2) was not observed for most strains tested (
n
, 10/14). Four strains had spontaneously resistant colonies (frequencies, 4.25 × 10
−8
to 3.47 × 10
−10
), for which amikacin-fosfomycin (5:2) MICs were 2- to 8-fold higher than those for the original strains. After 7 days of serial passage, resistance (>4-fold increase over the baseline MIC) occurred in fewer strains (
n
, 4/14) passaged in the presence of amikacin-fosfomycin (5:2) than with either amikacin (
n
, 7/14) or fosfomycin (
n
, 12/14) alone. Interactions between amikacin-fosfomycin (5:2) and 10 comparator antibiotics in checkerboard testing against 30 different Gram-positive or Gram-negative bacterial strains were synergistic (fractional inhibitory concentration [FIC] index, ≤0.5) for 6.7% (
n
, 10/150) of combinations tested. No antagonism was observed. Synergy was confirmed by time-kill methodology for amikacin-fosfomycin (5:2) plus cefepime (against
Escherichia coli
), aztreonam (against
Pseudomonas aeruginosa
), daptomycin (against
Enterococcus faecalis
), and azithromycin (against
Staphylococcus aureus
). Amikacin-fosfomycin (5:2) was bactericidal at 4-fold the MIC for 7 strains tested. The reduced incidence of development of resistance to amikacin-fosfomycin (5:2) compared with that for amikacin or fosfomycin alone, and the lack of negative interactions with commonly used intravenous antibiotics, further supports the development of AFIS for the treatment of VAP.
Potentiation Effects of Amikacin and Fosfomycin against Selected Amikacin-Nonsusceptible Gram-Negative Respiratory Tract Pathogens
Authors: Montgomery A. Bruce , Rhomberg Paul R. , Abuan Tammy , Walters Kathie-Anne , Flamm Robert K. 
Published: April 2014

ABSTRACT

The amikacin-fosfomycin inhalation system (AFIS) is a combination of 2 antibiotics and an in-line nebulizer delivery system that is being developed for adjunctive treatment of pneumonia caused by Gram-negative organisms in patients on mechanical ventilation. AFIS consists of a combination of amikacin and fosfomycin solutions at a 5:2 ratio (amikacin, 3 ml at 100 mg/ml; fosfomycin, 3 ml at 40 mg/ml) and the PARI Investigational eFlow Inline System. In this antibiotic potentiation study, the antimicrobial activities of amikacin and fosfomycin, alone and in a 5:2 combination, were assessed against 62 Gram-negative pathogens from a worldwide antimicrobial surveillance collection (SENTRY). The amikacin MICs for 62 isolates of
Acinetobacter baumannii
,
Pseudomonas aeruginosa
, and
Klebsiella pneumoniae
were ≥32 μg/ml (intermediate or resistant according to the Clinical and Laboratory Standards Institute [CLSI]; resistant according to the European Committee on Antimicrobial Susceptibility Testing [EUCAST]). Each isolate was tested against amikacin (0.25 to 1,024 μg/ml), fosfomycin (0.1 to 409.6 μg/ml), and amikacin-fosfomycin (at a 5:2 ratio) using CLSI reference agar dilution methods. The median MIC values for amikacin and fosfomycin against the 62 isolates each decreased 2-fold with the amikacin-fosfomycin (5:2) combination from that with either antibiotic alone. Interactions between amikacin and fosfomycin differed by isolate and ranged from no detectable interaction to high potentiation. The amikacin-fosfomycin (5:2) combination reduced the amikacin concentration required to inhibit all 62 isolates from >1,024 to ≤256 μg/ml and reduced the required fosfomycin concentration from 204.8 to 102.4 μg/ml. These results support continued development of the amikacin-fosfomycin combination for aerosolized administration, where high drug levels can be achieved.
VCAM-1/α4β1 Integrin Interaction Is Crucial for Prompt Recruitment of Immune T Cells into the Brain during the Early Stage of Reactivation of Chronic Infection with Toxoplasma gondii To Prevent Toxoplasmic Encephalitis
Authors: Sa Qila , Ochiai Eri , Sengoku Tomoko , Wilson Melinda E. , Brogli Morgan , Crutcher Stephen , Michie Sara A. , Xu Baohui , Payne Laura , Wang Xisheng , Suzuki Yasuhiro 
Published: April 2014

ABSTRACTReactivation of chronic infection withToxoplasma gondiican cause life-threatening toxoplasmic encephalitis in immunocompromised individuals. We examined the role of VCAM-1/α4β1 integrin interaction in T cell recruitment to prevent reactivation of the infection in the brain. SCID mice were infected and treated with sulfadiazine to establish a chronic infection. VCAM-1 and ICAM-1 were the endothelial adhesion molecules detected on cerebral vessels of the infected SCID and wild-type animals. Immune T cells from infected wild-type mice were treated with anti-α4 integrin or control antibodies and transferred into infected SCID or nude mice, and the animals received the same antibody every other day. Three days later, sulfadiazine was discontinued to initiate reactivation of infection. Expression of mRNAs for CD3δ, CD4, CD8β, gamma interferon (IFN-γ), and inducible nitric oxide synthase (NOS2) (an effector molecule to inhibitT. gondiigrowth) and the numbers of CD4+and CD8+T cells in the brain were significantly less in mice treated with anti-α4 integrin antibody than in those treated with control antibody at 3 days after sulfadiazine discontinuation. At 6 days after sulfadiazine discontinuation, cerebral tachyzoite-specific SAG1 mRNA levels and numbers of inflammatory foci associated with tachyzoites were markedly greater in anti-α4 integrin antibody-treated than in control antibody-treated animals, even though IFN-γ and NOS2 mRNA levels were higher in the former than in the latter. These results indicate that VCAM-1/α4β1 integrin interaction is crucial for prompt recruitment of immune T cells and induction of IFN-γ-mediated protective immune responses during the early stage of reactivation of chronicT. gondiiinfection to control tachyzoite growth.