bluuebunny/crossref_metadata_2025 huggingface dataset:
The locomotory activity rhythm of the spiny mouse,Acomys spinosissimusfrom southernAfrica: light entrainment and endogenous circadian rhythms
Authors: Hoole C. , Oosthuizen M. K. , Chimimba C. T. , Bennett N. C.
Published: August 2012

The circadian rhythm of locomotor activity in the spiny mouseAcomys spinosissimusfromSouthAfrica was investigated under controlled laboratory conditions. Nine individuals were subjected to six successive light cycles of approximately 2 weeks each as follows: (1) a standard light/dark (12:12LD) cycle; (2) a period of constant darkness (DD); (3) a second standard light/dark (12L:12D) cycle; (4) an inverse of theLD(12:12DL) cycle; (5) a short day cycle (8:16LD); and (6) a long day cycle (16:8LD). All the animals exhibited entrainment of their activity to theLDandDLlighting regimes. Locomotor activity ofA. spinosissimusoccurred predominantly during the dark phases of theLD,DL, long day and short day cycles. UnderLD, the mean percentage of activity was 88.7 ± 0.07% during the dark phase. When subjected to constant darkness, all animals expressed free‐running rhythms of locomotor activity (mean ± 1 standard deviation = 23.81 ± 0.33 h; range = 23.2–24.1 h). On the reverseLDcycle, the mean percentage of activity was 81.4 ± 0.09% during the dark phase of the cycle. Mice exhibited significantly more daytime activity during the long day cycle (20.3 ± 5.8%) and no significant change in dark phase activity during the short day cycle (90.1 ± 4.01). The spiny mouse possesses a circadian rhythm of locomotor activity that entrains strongly to light. Locomotory activity occurs predominantly during the dark phase and can therefore be considered a nocturnal mammal.
Mobile hydrocarbon microspheres from >2‐billion‐year‐old carbon‐bearing seams in the South African deep subsurface
Authors: Wanger G. , Moser D. , Hay M. , Myneni S. , Onstott T. C. , Southam G.
Published: August 2012

By ~2.9 Ga, the time of the deposition of the Witwatersrand Supergroup, life is believed to have been well established on Earth. Carbon remnants of the microbial biosphere from this time period are evident in sediments from around the world. In the Witwatersrand Supergroup, the carbonaceous material is often concentrated in seams, closely associated with the gold deposits and may have been a mobile phase 2 billion years ago. Whereas today the carbon in the Witwatersrand Supergroup is presumed to be immobile, hollow hydrocarbon spheres ranging in size from <1 μm to >50 μm were discovered emanating from a borehole drilled through the carbon‐bearing seams suggesting that a portion of the carbon may still be mobile in the deep subsurface. ToF‐SIMS and STXM analyses revealed that these spheres contain a suite of alkane, alkenes, and aromatic compounds consistent with the described organic‐rich carbon seams within the Witwatersrand Supergroup's auriferous reef horizons. Analysis by electron microscopy and ToF‐SIMS, however, revealed that these spheres, although most likely composed of biogenic carbon and resembling biological organisms, do not retain any true structural, that is, fossil, information and were formed by an abiogenic process.
Developmental outcomes of childhood‐onset temporal lobe epilepsy: A community‐based study
Authors: Wilson Sarah J. , Micallef Silvana , Henderson Asawari , Rayner Genevieve , Wrennall Jacquie A. , Spooner Claire , Harvey A. Simon
Published: August 2012

Purpose:  To assess the impact of childhood‐onset temporal lobe epilepsy (TLE) on the attainment of normative developmental tasks and identify predictors of long‐term developmental outcomes.

Methods:  In 1992–1993, a prospective longitudinal cohort study of childhood‐onset TLE was commenced in the State of Victoria, Australia. At review in 2004–2006, we assessed developmental tasks, which are age‐specific individual psychosocial achievements tied to particular phases of the lifespan. The cohort comprised 54 individuals (33 female) with a mean age of 20 years (range 12–29), and mean age at TLE onset of 6 years (range 0.2–15).

Key Findings:  Individuals were clustered into three groups representing distinct developmental trajectories: (1) a Normal group (52%) who achieved most of their developmental tasks, (2) an Altered group (37%) who achieved some, and (3) a Delayed group (11%) who achieved few. The groups showed significant cognitive differences, with the Normal group outperforming the Altered and Delayed groups on a range of measures (p < 0.05). Multiple discriminant function analysis indicated that membership of the groups was independently predicted by the chronicity of seizures, cognitive functioning, having surgically remediable epilepsy, and gender (p < 0.001). Seizure chronicity and cognition discriminated between all three trajectories, while surgical intervention and gender primarily discriminated between the Altered and Delayed trajectories.

Significance:  Childhood‐onset TLE can disrupt achievement of normative developmental tasks that is independently predicted by medical, biologic, and cognitive factors. Assessment of developmental tasks across the lifespan provides a practical framework for guiding prognostic counseling of patients and families.
Blood–brain barrier dysfunction and epilepsy: Pathophysiologic role and therapeutic approaches
Authors: Marchi Nicola , Granata Tiziana , Ghosh Chaitali , Janigro Damir
Published: August 2012

The blood–brain barrier (BBB) is located within a unique anatomic interface and has functional ramifications to most of the brain and blood cells. In the past, the BBB was considered a pharmacokinetic impediment to antiepileptic drug penetration into the brain; nowadays it is becoming increasingly evident that targeting of the damaged or dysfunctional BBB may represent a therapeutic approach to reduce seizure burden. Several studies have investigated the mechanisms linking the onset and sustainment of seizures to BBB dysfunction. These studies have shown that the BBB is at the crossroad of a multifactorial pathophysiologic process that involves changes in brain milieu, altered neuroglial physiology, development of brain inflammation, leukocyte–endothelial interactions, faulty angiogenesis, and hemodynamic changes leading to energy mismatch. A number of knowledge gaps, conflicting points of view, and discordance between clinical and experimental data currently characterize this field of neuroscience. As more pieces are added to this puzzle, it is apparent that each mechanism needs to be validated in an appropriate clinical context. We now offer a BBB‐centric view of seizure disorders, linking several aspects of seizures and epilepsy physiopathology to BBB dysfunction. We have reviewed the therapeutic, antiseizure effect of drugs that promote BBB repair. We also present BBB neuroimaging as a tool to correlate BBB restoration to seizure mitigation. Add‐on cerebrovascular drug could be of efficacy in reducing seizure burden when used in association with neuronal antiepileptic drugs.
Exploring Predictors of Complication in Older Surgical Patients: A Deficit Accumulation Index and the Braden Scale
Authors: Cohen Rachel‐Rose , Lagoo‐Deenadayalan Sandhya A. , Heflin Mitchell T. , Sloane Richard , Eisen Irvin , Thacker Julie M. , Whitson Heather E.
Published: August 2012

Objectives

To determine whether readily collected perioperative information might identify older surgical patients at higher risk of complications.

Design

Retrospective cohort study.

Setting

Medical chart review at a single academic institution.

Participants

One hundred two individuals aged 65 and older who underwent abdominal surgery between January 2007 and December 2009.

Measurements

Primary predictor variables were first postoperative Braden Scale score (within 24 hours of surgery) and a Deficit Accumulation Index (DAI) constructed based on 39 available preoperative variables. The primary outcome was presence or absence of complication within 30 days of surgery.

Results

Of 102 patients, 64 experienced at least one complication, with wound infection being the most common. In models adjusted for age, race, sex, and open versus laparoscopic surgery, lower Braden Scale scores were predictive of 30‐day postoperative complication (odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.06–1.60), longer length of stay (β = 1.44 (0.25) days; P ≤ .001), and discharge to an institution rather than home (OR = 1.23, 95% CI = 1.02–1.48). The cut‐off value for the Braden score with the highest predictive value for complication was ≤ 18 (OR = 3.63, 95% CI = 1.43–9.19; c statistic 0.744). The DAI and several traditional surgical risk factors were not significantly associated with 30‐day postoperative complications.

Conclusion

This is the first study to identify the perioperative Braden Scale score, a widely used risk‐stratifier for pressure ulcers, as an independent predictor of other adverse outcomes in geriatric surgical patients. Further studies are needed to confirm this finding and to investigate other uses for this tool, which correlates well to phenotypic models of frailty.
Straight and Offset Implant Placement under Axial and Nonaxial Loads in Implant‐Supported Prostheses: Strain Gauge Analysis
Authors: Abreu Celina Wanderley , Nishioka Renato Sussumu , Balducci Ivan , Consani Rafael Leonardo Xediek
Published: August 2012

Purpose: The aim of this in vitro study was to quantify strain development during axial and nonaxial loading using strain gauge analysis for three‐element implant‐supported FPDs, varying the arrangement of implants: straight line (L) and offset (O).

Materials and Methods: Three Morse taper implants arranged in a straight line and three implants arranged in an offset configuration were inserted into two polyurethane blocks. Microunit abutments were screwed onto the implants, applying a 20 Ncm torque. Plastic copings were screwed onto the abutments, which received standard wax patterns cast in Co‐Cr alloy (n = 10). Four strain gauges were bonded onto the surface of each block tangential to the implants. The occlusal screws of the superstructure were tightened onto microunit abutments using 10 Ncm and then axial and nonaxial loading of 30 Kg was applied for 10 seconds on the center of each implant and at 1 and 2 mm from the implants, totaling nine load application points. The microdeformations determined at the nine points were recorded by four strain gauges, and the same procedure was performed for all of the frameworks. Three loadings were made per load application point. The magnitude of microstrain on each strain gauge was recorded in units of microstrain (μɛ). The data were analyzed statistically by two‐way ANOVA and Tukey's test (p < 0.05).

Results: The configuration factor was statistically significant (p= 0.0004), but the load factor (p= 0.2420) and the interaction between the two factors were not significant (p= 0.5494). Tukey's test revealed differences between axial offset (μɛ) (183.2 ± 93.64) and axial straight line (285.3 ± 61.04) and differences between nonaxial 1 mm offset (201.0 ± 50.24) and nonaxial 1 mm straight line (315.8 ± 59.28).

Conclusion: There was evidence that offset placement is capable of reducing the strain around an implant. In addition, the type of loading, axial force or nonaxial, did not have an influence until 2 mm.
New Advances in the Genetic Basis of Atrial Fibrillation
Authors: MAHIDA SAAGAR , ELLINOR PATRICK T.
Published: August 2012

New Genetic Loci for Atrial Fibrillation.  Over the past decade, compelling evidence has emerged from population‐based studies to suggest that AF is a heritable disease. More recently, we have begun to elucidate the genetic substrate underlying AF. Genome‐wide association studies (GWAS) have led to the identification of multiple risk loci that confer increased susceptibility to the arrhythmia. These loci harbor intriguing candidate genes including those encoding ion channels, transcription factors, and signaling molecules. Current efforts are ongoing to functionally validate the role of these genes in disease pathogenesis. In the future, novel genotyping technologies such as exome sequencing and whole‐genome sequencing promise to uncover a greater proportion of the heritability underlying AF. In this article we review recent advances in AF genetics research and discuss future developments in the field. (J Cardiovasc Electrophysiol, Vol. 23, pp. 1400‐1407, December 2012)
Impact of Chronic Obstructive Pulmonary Disease on Procedural Outcomes and Quality of Life in Patients with Atrial Fibrillation Undergoing Catheter Ablation
Authors: GU JUN , LIU XU , TAN HONGWEI , ZHOU LI , JIANG WEIFENG , WANG YUANLONG , LIU YUGANG , GU JIANING
Published: August 2012

Impact of COPD on Atrial Fibrillation Ablation. Background: Chronic obstructive pulmonary disease (COPD) is a risk factor for atrial fibrillation (AF). The aim of this study was to investigate the impact of COPD on outcomes of catheter ablation in patients with AF in terms of recurrence and quality of life (QoL).

Methods
: In this prospective study, 550 consecutive patients with symptomatic, medication‐refractory AF underwent first catheter ablation. Patients were classified into those with COPD (group 1, n = 54) and those without COPD (group 2, n = 496). Patients were followed up for atrial tachyarrhythmia (ATa) recurrence for at least 24 months. The Medical Outcomes Study SF‐36 Health Survey was used to assess QoL at baseline and 24 months after ablation.

Results
: After a single ablation, 24 patients in group 1 (44.4%) and 142 in group 2 (28.6%) had ATa recurrence during a mean follow‐up of 31.4 ± 4.8 months (P = 0.016). The second ablation was performed in 19 patients (35.2%) from group 1 and in 109 patients (22.0%) from group 2 (P = 0.029). Multivariate logistic analysis showed that nonparoxysmal AF (P = 0.013, OR = 1.767, 95% CI: 1.129–2.765) as well as the presence of COPD (P = 0.029, OR = 1.951, 95% CI: 1.070–3.557) was the independent predictor for higher ATa recurrence. Moreover, patients in group 1 had significantly lower baseline scores on all SF‐36 Health Survey subscales. At 24‐month follow‐up, both mental component summary and physical component summary scores improved markedly in group 1 and 2.

Conclusions
: Although the presence of COPD predicted higher recurrence after single‐catheter ablation in AF patients, significant improvements in QoL were observed in the postablation COPD population. (J Cardiovasc Electrophysiol, Vol. 24, pp. 148‐154, February 2013)
Thermodynamic Assessment of P2O5
Authors: Jung In‐Ho , Hudon Pierre
Published: August 2012

All the thermodynamic property data and phase diagrams related to solid and liquid P2O5 were critically evaluated and optimized to obtain the best set of Gibbs energies for all phases. Confusion in literature data due to the very sluggish nature of the reactions involving P2O5 was resolved. The Gibbs energies of O‐ and O′‐P2O5 were evaluated for the first time based on the phase stability against gas. The Gibbs energy of liquid H‐P2O5, liquid O‐P2O5, and liquid O′‐P2O5 were also properly evaluated for the first time based on the metastable and stable vapor pressures. The calculated triple points of H‐P2O5, O‐P2O5, and O′‐P2O5 are 420°C and 4.600 bar, 575°C and 0.805 bar, and 580°C and 0.774 bar, respectively. The calculated polymorphic transition point between O‐P2O5 and O′‐P2O5 is located at 65°C and 0.001 bar.
The development of fast‐track principles in gynecological surgery
Authors: WODLIN NINNIE BORENDAL , NILSSON LENA
Published: August 2012

Fast‐track is a multimodal strategy aimed at reducing the physiological burden of surgery to achieve an enhanced postoperative recovery. The strategy combines unimodal evidence‐based interventions in the areas of preoperative preparation, anesthesia, surgical factors and postoperative care. The advantages of fast‐track most likely extend to gynecology, although so far have scarcely been reported. This review summarizes current evidence concerning use of fast‐track in general and in gynecological surgery. The main findings of this review are that there are benefits within elective gynecological surgery, but studies of quality of life, patient satisfaction and health economics in elective surgery are needed. Studies of fast‐track within the field of non‐elective gynecological surgery are lacking. Widespread education is needed to improve the rate of implementation of fast‐track. Close involvement of the entire surgical team is imperative to ensure a structured perioperative care aiming for enhanced postoperative recovery.
Vacuum extraction: development and test of a procedure‐specific rating scale
Authors: MAAGAARD MATHILDE , OESTERGAARD JEANETT , JOHANSEN MARIANNE , ANDERSEN LISE LOTTE , RINGSTED CHARLOTTE , OTTESEN BENT , SØRENSEN JETTE L.
Published: August 2012

Objectives. To develop and validate an Objective Structured Assessment of Technical Skills (OSATS) scale for vacuum extraction. Design. Two‐part study design: Primarily, development of a procedure‐specific checklist for vacuum extraction. Hereafter, validation of the developed OSATS scale for vacuum extraction in a prospective observational study. Setting. Rigshospitalet, University Hospital of Copenhagen. Population. For development, an obstetric expert from each labor ward in Denmark (28 departments) was invited to participate. For validation, nine first‐year residents and 10 chief physicians with daily work in the obstetric field were tested. Methods. The Delphi method was used for development of the scale. In a simulated vacuum extraction scenario, first‐year residents and obstetric chief physicians were rated using the developed OSATS scale for vacuum extraction to test construct validity of the scale. Main outcome measures. Consensus for the content of the scale. To test the scale of Cronbach's alpha, interclass correlation and differential item function was calculated in the prospective study. Results. 89% completed the first and 61% completed the second Delphi round. Hereafter, consensus was obtained. There was a significant difference between residents’ and experts’ performance for total score and for the score of the separate parts of the scale. Cronbach's alpha for total score and for the separate parts of the scale was 0.91–0.95 and interclass correlation 0.84–0.9. Conclusions. The OSATS scale for vacuum extraction is a reliable test for differentiating between competence levels in a simulated setting.
MRI in the diagnosis and surgical management of abnormal placentation
Authors: PALACIOS‐JARAQUEMADA JOSÉ MIGUEL , BRUNO CLAUDIO HERNÁN , MARTÍN EDUARDO
Published: August 2012

Objective. To determine the usefulness of placental magnetic resonance imaging (MRI) in the diagnosis and surgical management of abnormal placentation. Design. Retrospective follow‐up. Setting. Buenos Aires, Argentina. Population. 547 pregnant women. Methods. In all cases, a direct and reliable description of abnormal placentation features was obtained by the operating surgeon. Placental MRI was analyzed according to: (1) primary description, (2) invasion topography, (3) modification required to the surgical tactics or techniques and (4) by positive and negative predictive values. Main outcome measures. Ultrasound and MRI findings were compared with surgical results, which were considered a final diagnosis in relation to primary diagnostic indications. Results. Placental MRI was obtained because of diagnostic doubt in 78 cases, for deep invasion diagnosis in 148 cases and to define the invasion area in 346 cases. Placental MRI allowed accurate demarcation and assessment of the degree of placental invasion, parametrial involvement and cervico‐trigonal vascular hyperplasia, permitting changes in the surgical tactical approach. Ultrasound and MRI differences were associated with placenta previa, uterine scar thinning and use of different criteria for placental invasion through definitions or terminology. Six cases of false‐negative and 11 of false‐positive findings were reported. Conclusion. Placental MRI provides excellent characterization of the degree and extension of placental invasion. Its usefulness in cases of adherent placentation is directly associated to the therapeutic measures, especially where dissection maneuvers are needed. Diagnostic differences between ultrasound and MRI related to the presence or not of placenta previa and uterine scar thinning.
Effects of Ovariectomy and Dehydroepiandrosterone (DHEA) on Vaginal Wall Thickness and Innervation
Authors: Pelletier Georges , Ouellet Johanne , Martel Céline , Labrie Fernand
Published: August 2012

Introduction

One mechanism by which low sexual steroid activity observed after menopause could cause sexual dysfunction is by deficient vaginal innervation. Recently, it has been shown that intravaginal administration of dehydroepiandrosterone (DHEA) could produce beneficial effects on sexual dysfunction in postmenopausal women.

Aim

The goal of this study was to determine if DHEA could modify innervation in the rat vagina.

Main Outcome Measures

The area occupied by the nerve fibers immunoreactive for protein gene product 9.5 (PGP 9.5), a panneuronal marker or tyrosine hydroxylase (TH), a sympathetic nerve fiber marker, in the lamina propria and muscular layers, respectively, as well as the total area of each of these 2 layers were measured by stereological analysis.

Methods

The innervation of the rat vagina was examined 9 months after ovariectomy (OVX) compared to intact animals and treatment of OVX animals with DHEA (80 mg/kg). Four sections from each vagina (5 animals/groups) were immunostained.

Results

In OVX animals, the lamina propria area was decreased to 44%, an effect which was reversed by DHEA to 69% of the intact value. OVX also caused a 59% decrease in the area of PGP 9.5 fibers, an effect which was prevented by DHEA, thus showing a 68% stimulatory effect of DHEA on the density of PGP 9.5 fibers in the lamina propria compared to OVX animals. Following OVX, the muscular layer area was decreased by 61%. DHEA treatment induced 118% and 71% increases in TH fiber area compared to OVX and intact animals, respectively. The density of TH fibers was 182% increased over intact controls by DHEA treatment of OVX animals.

Conclusions

The relatively potent stimulatory effect of DHEA on intravaginal nerve fiber density provides a possible explanation for the beneficial effects of intravaginal DHEA on sexual dysfunction observed in postmenopausal women.
Erectile Function Significant Enough for Penetration During Sexual Intercourse After Removal of Inflatable Penile Prosthesis
Authors: Martinez Daniel R. , Mennie Peter A. , Carrion Rafael
Published: August 2012

Introduction

Fifty-two-year-old male with history of multiple insults to his erectile tissue, including insertion and removal of penile implant, presents with significant partial erectile function, substantial enough for anal penetration during sexual intercourse.

Aim

Erectile function rigid enough for anal penetration, let alone any erectile function after removal of an inflatable penile prosthesis (IPP), is rare. This article, to our knowledge, is the first case of a patient who has undergone multiple insults to his erectile tissue, including an episode of ischemic priapism followed by implantation and removal of an IPP, who presents with erectile function sufficient enough for coitus.

Main Outcome Measures

Outcome measured via standardized patient questionnaires and penile Doppler following injection of Trimix.

Method

An objective measure of the patient’s erectile function was performed via penile Doppler.

Results

Penile Doppler after 10-mcg injection of Trimix revealed numerous perforating vessels from the corpora spongiosum providing blood flow to the corpora cavernosa. The patient obtained approximately 60–70% rigid erection.

Conclusions

To our knowledge, and after thorough review of the literature, we could not find any reports of erectile function significant enough to take part in sexual intercourse and penetration after removal of a three-piece IPP. The implant usually disrupts the normal anatomy which allows for cavernosal arterial vasodilation and increased blood flow into the corpora. Following dilation of the corpora the cylinders are inserted and inflated, and the smooth muscle that makes up the corpora cavernosum is compressed against the wall of the tunica albuginea. Theoretically, the remaining smooth muscle tissue may retain some of its physiologic function, adding some additional girth to the penis with an already activated IPP during sexual intercourse.
The sudden appearance of CO emission in LHA 115-S 65
Authors: Oksala M. E. , Kraus M. , Arias M. L. , Borges Fernandes M. , Cidale L. , Muratore M. F. , Curé M.
Published: August 2012

Molecular emission has been detected in several Magellanic Cloud B[e] supergiants. In this Letter, we report on the detection of CO band head emission in the B[e] supergiant LHA 115-S 65, and present a K-band near-infrared spectrum obtained with the Spectrograph for INtegral Field Observation in the Near-Infrared (SINFONI; R= 4500) on the ESO VLT UT4 telescope. The observed molecular band head emission in S65 is quite surprising in the light of a previous non-detection by McGregor, Hyland & McGinn, as well as a high-resolution (R= 50 000) Gemini/Phoenix spectrum of this star taken nine months earlier showing no emission. Based on analysis of the optical spectrum by Kraus, Borges Fernandes & de Araújo, we suspect that the sudden appearance of molecular emission could be due to density build-up in an outflowing viscous disc, as seen for Be stars. This new discovery, combined with variability in two other similar evolved massive stars, indicates an evolutionary link between B[e] supergiants and luminous blue variables.
Trends in Food Attitudes and Behaviors Among Adults with 6–11‐Year‐Old Children
Authors: HOY MARIEA G. , CHILDERS COURTNEY C.
Published: August 2012

This study presents an analysis of survey data measuring food attitudes and behaviors among a nationally representative sample of adults with 6–11‐year‐old children for 2002–2010 from Experian Simmons Market Research. Results show numerous significantly positive improvements in attitudes and behaviors regarding healthier diets. In general, parents report increasing fiber intake, thinking about calories, and reducing sweets consumption as well as a generic effort to eat healthier. However, some areas still needing improvement include relatively neutral views that their diet is “very healthy” and that they only snack on healthy foods. While there are a number of improvements in parents' attitudes and behaviors regarding a healthy diet, the majority of the ground gained was early, from 2002 to between 2003 and 2006. This study's results suggest that a better understanding of the parental “snacking mindset” and indulgence‐healthy diet paradox might further assist in addressing childhood obesity.
Increased gingival crevicular fluid levels of soluble triggering receptor expressed on myeloid cells (sTREM) ‐1 in severe periodontitis
Authors: Bisson Catherine , Massin Frédéric , Lefevre Pierre Arthur , Thilly Nathalie , Miller Neal , Gibot Sébastien
Published: August 2012

Aim

This study was designed to evaluate the presence of a new regulator of innate immunity in periodontitis: the soluble form of triggering receptor on myeloid cells‐1 (sTREM‐1) in gingival crevicular fluid (GCF).

Material and Methods

GCF was collected at four sites, three pathological and one healthy from 17 patients with periodontitis, and at one healthy site from 23 control patients. An enzyme‐linked immunosorbent assay (ELISA) kit was used to quantify sTREM‐1 levels in collected crevicular fluid. Recorded clinical parameters were probing pocket depth (PPD), bleeding upon probing, tooth mobility, plaque index (PlI), and gingival index (GI).

Results

The mean sTREM‐1 level in collected fluid was significantly higher in pathological sites than in healthy sites from either periodontal or control patients: 353.9 pg/ml, 50.2 pg/ml and 25.4 pg/ml respectively. Soluble TREM‐1 concentration was significantly correlated with PPD. The sTREM‐1 levels increased with the augmentation of the PlI and GI scores and levelled off at score 2 for both indexes. In multivariate analysis, periodontal pocket depth and smoking status were statistically associated with highest sTREM‐1 concentrations.

Conclusion

sTREM‐1 was detected in crevicular fluid and its concentration was higher in pathological sites. It could be a marker of periodontal tissue destruction.
Novel Podoviridae Family Bacteriophage Infecting Weissella cibaria Isolated from Kimchi
Authors: Kleppen Hans Petter , Holo Helge , Jeon Sang-Rok , Nes Ingolf F. , Yoon Sung-Sik
Published: August 2012

The first complete genome sequence of a phage infecting
Weissella cibaria
(
Weissella kimchii
) is presented. The bacteriophage ϕYS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, ϕYS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that ϕYS61 resembles
Podoviridae
of the subfamily
Picovirinae
. Within the subfamily
Picovirinae
, the ϕ29-like phages have been extensively studied, and their terminal protein-primed DNA replication is well characterized. Our data strongly suggest that ϕYS61 also replicates by a protein-primed mechanism.
Weissella
phage ϕYS61 is, however, markedly different from members of the
Picovirinae
with respect to genome size and morphology.
Picovirinae
are characterized by small (approximately 20-kb) genomes which contrasts with the 33,594-bp genome of ϕYS61. Based on electron microscopy analysis, ϕYS61 was classified as a member of the
Podoviridae
of morphotype C2, similar to the ϕ29-like phages, but its capsid dimensions are significantly larger than those reported for these phages. The novelty of ϕYS61 was also emphasized by the low number of open reading frames (ORFs) showing significant similarity to database sequences. We propose that the bacteriophage ϕYS61 should represent a new subfamily within the family
Podoviridae
.
Thermodynamics of Formate-Oxidizing Metabolism and Implications for H
2
Production
Authors: Lim Jae Kyu , Bae Seung Seob , Kim Tae Wan , Lee Jung-Hyun , Lee Hyun Sook , Kang Sung Gyun
Published: August 2012

Formate-dependent proton reduction to H
2
(HCOO
−
+ H
2
O → HCO
3
−
+ H
2
) has been reported for hyperthermophilic
Thermococcus
strains. In this study, a hyperthermophilic archaeon,
Thermococcus onnurineus
strain NA1, yielded H
2
accumulation to a partial pressure of 1 × 10
5
to 7 × 10
5
Pa until the values of Gibbs free energy change (Δ
G
) reached near thermodynamic equilibrium (−1 to −3 kJ mol
−1
). The bioenergetic requirement for the metabolism to conserve energy was demonstrated by Δ
G
values as small as −5 kJ mol
−1
, which are less than the biological minimum energy quantum, −20 kJ mol
−1
, as calculated by Schink (B. Schink, Microbiol. Mol. Biol. Rev. 61:262-280, 1997). Considering formate as a possible H
2
storage material, the H
2
production potential of the strain was assessed. The volumetric H
2
production rate increased linearly with increasing cell density, leading to 2,820 mmol liter
−1
h
−1
at an optical density at 600 nm (OD
600
) of 18.6, and resulted in the high specific H
2
production rates of 404 ± 6 mmol g
−1
h
−1
. The H
2
productivity indicates the great potential of
T. onnurineus
strain NA1 for practical application in comparison with H
2
-producing microbes. Our result demonstrates that
T. onnurineus
strain NA1 has a highly efficient metabolic system to thrive on formate in hydrothermal systems.
Ectoine Biosynthesis in Mycobacterium smegmatis
Authors: Ofer Naomi , Wishkautzan Marina , Meijler Michael , Wang Ying , Speer Alexander , Niederweis Michael , Gur Eyal
Published: August 2012

Mycobacterium smegmatis
is a commonly used mycobacterial model system. Here, we show that
M. smegmatis
protects itself against elevated salinity by synthesizing ectoine and hydroxyectoine and characterize the phenotype of a nonproducing mutant. This is the first analysis of
M. smegmatis
halotolerance and of the molecular mechanism that supports it.
Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils
Authors: Naether Astrid , Foesel Bärbel U. , Naegele Verena , Wüst Pia K. , Weinert Jan , Bonkowski Michael , Alt Fabian , Oelmann Yvonne , Polle Andrea , Lohaus Gertrud , Gockel Sonja , Hemp Andreas , Kalko Elisabeth K. V. , Linsenmair Karl Eduard , Pfeiffer Simone , Renner Swen , Schöning Ingo , Weisser Wolfgang W. , Wells Konstans , Fischer Markus , Overmann Jörg , Friedrich Michael W.
Published: August 2012

In soil,Acidobacteriaconstitute on average 20% of all bacteria, are highly diverse, and are physiologically activein situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1Acidobacteria. The analysis of a large number of sites (n= 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed thatAcidobacteriadiversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations ofAcidobacteriasubpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters withAcidobacteria, individual populations within subgroups have to be considered.
Proteogenomic Elucidation of the Initial Steps in the Benzene Degradation Pathway of a Novel Halophile, Arhodomonas sp. Strain Rozel, Isolated from a Hypersaline Environment
Authors: Dalvi Sonal , Azetsu Sei , Patrauchan Marianna A. , Aktas Deniz F. , Fathepure Babu Z.
Published: August 2012

Lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. The focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. The extremely halophilic bacteria
Arhodomonas
sp. strain Seminole and
Arhodomonas
sp. strain Rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 M NaCl), were isolated from enrichments developed from contaminated hypersaline environments. To obtain insights into the physiology of this novel group of organisms, a draft genome sequence of the Seminole strain was obtained. A cluster of 13 genes predicted to be functional in the hydrocarbon degradation pathway was identified from the sequence. Two-dimensional (2D) gel electrophoresis and liquid chromatography-mass spectrometry were used to corroborate the role of the predicted open reading frames (ORFs). ORFs 1080 and 1082 were identified as components of a multicomponent phenol hydroxylase complex, and ORF 1086 was identified as catechol 2,3-dioxygenase (2,3-CAT). Based on this analysis, it was hypothesized that benzene is converted to phenol and then to catechol by phenol hydroxylase components. The resulting catechol undergoes ring cleavage via the meta pathway by 2,3-CAT to form 2-hydroxymuconic semialdehyde, which enters the tricarboxylic acid cycle. To substantiate these findings, the Rozel strain was grown on deuterated benzene, and gas chromatography-mass spectrometry detected deuterated phenol as the initial intermediate of benzene degradation. These studies establish the initial steps of the benzene degradation pathway in halophiles.
Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting
Authors: Verbruggen Erik , Kuramae Eiko E. , Hillekens Remy , de Hollander Mattias , Kiers E. Toby , Röling Wilfred F. M. , Kowalchuk George A. , van der Heijden Marcel G. A.
Published: August 2012

The cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing theBacillus thuringiensisCry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA- and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA- and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as within-field temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.
Discovery of a Novel (+)-γ-Lactamase from Bradyrhizobium japonicum USDA 6 by Rational Genome Mining
Authors: Zhu Shaozhou , Gong Cuiyu , Song Dawei , Gao Shuaihua , Zheng Guojun
Published: August 2012

A novel (+)-γ-lactamase used for the resolution of racemic γ-lactam from
Bradyrhizobium japonicum
USDA 6 was found as a result of sequence-structure guided genome mining. It consists of 409 amino acids, only 49% of which are identical to the amino acid sequences of the known (+)-γ-lactamase from
Sulfolobus solfataricus
. This is only the third (+)-γ-lactamase gene to be reported.
Epidemiology of a Salmonella enterica subsp. enterica Serovar Typhimurium Strain Associated with a Songbird Outbreak
Authors: Hernandez Sonia M. , Keel Kevin , Sanchez Susan , Trees Eija , Gerner-Smidt Peter , Adams Jennifer K. , Cheng Ying , Ray Al , Martin Gordon , Presotto Andrea , Ruder Mark G. , Brown Justin , Blehert David S. , Cottrell Walter , Maurer John J.
Published: August 2012

Salmonella enterica
subsp.
enterica
serovar Typhimurium is responsible for the majority of salmonellosis cases worldwide. This
Salmonella
serovar is also responsible for die-offs in songbird populations. In 2009, there was an
S
. Typhimurium epizootic reported in pine siskins in the eastern United States. At the time, there was also a human outbreak with this serovar that was associated with contaminated peanuts. As peanuts are also used in wild-bird food, it was hypothesized that the pine siskin epizootic was related to this human outbreak. A comparison of songbird and human
S
. Typhimurium pulsed-field gel electrophoresis (PFGE) patterns revealed that the epizootic was attributed not to the peanut-associated strain but, rather, to a songbird strain first characterized from an American goldfinch in 1998. This same
S
. Typhimurium strain (PFGE type A3) was also identified in the PulseNet USA database, accounting for 137 of 77,941 total
S
. Typhimurium PFGE entries. A second molecular typing method, multiple-locus variable-number tandem-repeat analysis (MLVA), confirmed that the same strain was responsible for the pine siskin epizootic in the eastern United States but was distinct from a genetically related strain isolated from pine siskins in Minnesota. The pine siskin A3 strain was first encountered in May 2008 in an American goldfinch and later in a northern cardinal at the start of the pine siskin epizootic. MLVA also confirmed the clonal nature of
S
. Typhimurium in songbirds and established that the pine siskin epizootic strain was unique to the finch family. For 2009, the distribution of PFGE type A3 in passerines and humans mirrored the highest population density of pine siskins for the East Coast.
Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters
Authors: Staley Christopher , Gordon Katrina V. , Schoen Mary E. , Harwood Valerie J.
Published: August 2012

Before new, rapid quantitative PCR (qPCR) methods for assessment of recreational water quality and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant source has been diluted in environmental waters is needed. This study determined the limits of detection and quantification of the human-associated
Bacteroides
sp. (HF183) and human polyomavirus (HPyV) qPCR methods for sewage diluted in buffer and in five ambient, Florida water types (estuarine, marine, tannic, lake, and river). HF183 was quantifiable in sewage diluted up to 10
−6
in 500-ml ambient-water samples, but HPyVs were not quantifiable in dilutions of >10
−4
. Specificity, which was assessed using fecal composites from dogs, birds, and cattle, was 100% for HPyVs and 81% for HF183. Quantitative microbial risk assessment (QMRA) estimated the possible norovirus levels in sewage and the human health risk at various sewage dilutions. When juxtaposed with the MST marker detection limits, the QMRA analysis revealed that HF183 was detectable when the modeled risk of gastrointestinal (GI) illness was at or below the benchmark of 10 illnesses per 1,000 exposures, but the HPyV method was generally not sensitive enough to detect potential health risks at the 0.01 threshold for frequency of illness. The tradeoff between sensitivity and specificity in the MST methods indicates that HF183 data should be interpreted judiciously, preferably in conjunction with a more host-specific marker, and that better methods of concentrating HPyVs from environmental waters are needed if this method is to be useful in a watershed management or monitoring context.
Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils
Authors: Andrew David R. , Fitak Robert R. , Munguia-Vega Adrian , Racolta Adriana , Martinson Vincent G. , Dontsova Katerina
Published: August 2012

High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (
Carnegiea gigantea
) and cardón (
Pachycereus pringlei
) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant
Crenarchaeota
class
Thermoprotei
, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla
Proteobacteria
,
Actinobacteria
,
Planctomycetes
,
Firmicutes
,
Bacteroidetes
,
Chloroflexi
, and
Acidobacteria
. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.
Counterselection System for Geobacillus kaustophilus HTA426 through Disruption of
pyrF
and
pyrR
Authors: Suzuki Hirokazu , Murakami Ayano , Yoshida Ken-ichi
Published: August 2012

Counterselection systems facilitate marker-free genetic modifications in microbes by enabling positive selections for both the introduction of a marker gene into the microbe and elimination of the marker from the microbe. Here we report a counterselection system for
Geobacillus kaustophilus
HTA426, established through simultaneous disruption of the
pyrF
and
pyrR
genes. The
pyrF
gene, essential for pyrimidine biosynthesis and metabolization of 5-fluoroorotic acid (5-FOA) to toxic metabolites, was disrupted by homologous recombination. The resultant MK54 strain (Δ
pyrF
) was auxotrophic for uracil and resistant to 5-FOA. MK54 complemented with
pyrF
was prototrophic for uracil but insensitive to 5-FOA in the presence of uracil. To confer 5-FOA sensitivity, the
pyrR
gene encoding an attenuator to repress pyrimidine biosynthesis by sensing uracil derivatives was disrupted. The resultant MK72 strain (Δ
pyrF
Δ
pyrR
) was auxotrophic for uracil and resistant to 5-FOA. MK72 complemented with
pyrF
was prototrophic for uracil and 5-FOA sensitive even in the presence of uracil. The results suggested that
pyrF
could serve as a counterselection marker in MK72, which was demonstrated by efficient marker-free integrations of heterologous β-galactosidase and α-amylase genes. The integrated genes were functionally expressed in
G. kaustophilus
and conferred new functions on the thermophile. This report describes the first establishment of a
pyrF
-based counterselection system in a
Bacillus
-related bacterium, along with the first demonstration of homologous recombination and heterologous gene expression in
G. kaustophilus
. Our results also suggest a new strategy for establishment of counterselection systems.
Detection of Salmonella enterica Isolates Producing CTX-M Cephalosporinase in U.S. Livestock Populations
Authors: Wittum Thomas E. , Mollenkopf Dixie F. , Erdman Matthew M.
Published: August 2012

We report the detection of
Salmonella
carrying
bla
CTX-M
in U.S. livestock populations. We identified 12 of 2,034 (0.6%)
Salmonella
isolates originating from turkeys, horses, and pigs from at least 6 U.S. states, all carrying
bla
CTX-M-1
, many on a pandemic sequence type 1 IncN plasmid.
Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes
Authors: Yue Min , Schmieder Robert , Edwards Robert A. , Rankin Shelley C. , Schifferli Dieter M.
Published: August 2012

A novel targeted massive parallel sequencing approach identified genetic variation in eight known or predicted fimbrial adhesins for 46
Salmonella
strains. The results highlight associations between specific adhesin alleles, host species, and antimicrobial resistance. The differentiation of allelic variants has potential applications for diagnostic microbiology and epidemiological investigations.