bluuebunny/crossref_metadata_2025 huggingface dataset:
Carnivore diet analysis based on next‐generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan
Authors: SHEHZAD WASIM , RIAZ TIAYYBA , NAWAZ MUHAMMAD A. , MIQUEL CHRISTIAN , POILLOT CAROLE , SHAH SAFDAR A. , POMPANON FRANÇOIS , COISSAC ERIC , TABERLET PIERRE
Published: January 2012

Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For carnivores, traditional diet analyses mostly rely upon the morphological identification of undigested remains in the faeces. Here, we developed a methodology for carnivore diet analyses based on the next‐generation sequencing. We applied this approach to the analysis of the vertebrate component of leopard cat diet in two ecologically distinct regions in northern Pakistan. Despite being a relatively common species with a wide distribution in Asia, little is known about this elusive predator. We analysed a total of 38 leopard cat faeces. After a classical DNA extraction, the DNA extracts were amplified using primers for vertebrates targeting about 100 bp of the mitochondrial 12S rRNA gene, with and without a blocking oligonucleotide specific to the predator sequence. The amplification products were then sequenced on a next‐generation sequencer. We identified a total of 18 prey taxa, including eight mammals, eight birds, one amphibian and one fish. In general, our results confirmed that the leopard cat has a very eclectic diet and feeds mainly on rodents and particularly on the Muridae family. The DNA‐based approach we propose here represents a valuable complement to current conventional methods. It can be applied to other carnivore species with only a slight adjustment relating to the design of the blocking oligonucleotide. It is robust and simple to implement and allows the possibility of very large‐scale analyses.
Evaluation of the esophagogastric junction using high resolution manometry and esophageal pressure topography
Authors: Kahrilas P. J. , Peters J. H.
Published: January 2012

Background  The assessment of the esophagogastric junction (EGJ) is the most challenging aspect of clinical esophageal manometry. Although conventional manometric systems can be optimized toward interrogating specific aspects of the EGJ, they are too limited in recording channels and/or fidelity for a comprehensive assessment. The technological advantages inherent in high resolution manometry (HRM) with esophageal pressure topography (EPT) analysis substantially change this equation providing a technology sufficiently robust to dynamically record the contractile activity within the EGJ with both good fidelity and good spatial resolution.

Purpose  This review is an update on our understanding of the application of HRM and EPT to the analysis of EGJ function. With respect to sphincter relaxation, the integrated relaxation pressure (IRP) has proven to be a robust metric in differentiating intact from impaired EGJ relaxation. In the process, it revealed that impaired EGJ relaxation could occur not only in the setting of achalasia but also with other causes of EGJ outflow obstruction including hiatus hernia. The morphological description of the EGJ by EPT has also revealed not only a spectrum of abnormality ranging from an intact sphincter to overt herniation, but also the surprise finding of spontaneous conversion among sphincter configurations, emphasizing its dynamic nature. With respect to barrier function, preliminary data have refocused on the crural diaphragm as a key‐differentiating feature between preserved and compromised function. Finally, although the accomplishments summarized above are substantial, much work remains to fully exploit the potential of EPT in the clinical characterization of the EGJ.
Mitochondrial electron transport chain deficiency, cardiomyopathy, and long‐term cardiac transplant outcome
Authors: Golden Alana S. , Law Yuk M. , Shurtleff Hillary , Warner Molly , Saneto Russell P.
Published: January 2012

Golden AS, Law YM, Shurtleff H, Warner M, Saneto RP. Mitochondrial electron transport chain deficiency, cardiomyopathy, and long‐term cardiac transplant outcome.

Abstract:  Organ transplantation in multisystemic mitochondrial cytopathies is usually not performed because of perceived untoward complications. We report three patients with demonstrated oxidative phosphorylation defects and dilated cardiomyopathy who underwent cardiac transplant. All three patients tolerated immunosuppression medications and have had an excellent long‐term outcome. Our results suggest that with proper patient selection in this population, cardiac transplantation is feasible and can have good outcomes.
Changes in cinnamyl alcohol dehydrogenase activities from sugarcane cultivars inoculated with Sporisorium scitamineum sporidia
Authors: Santiago Rocío , Alarcón Borja , de Armas Roberto , Vicente Carlos , Legaz María Estrella
Published: January 2012

This study describes a method for determining cinnamyl alcohol dehydrogenase activity in sugarcane stems using reverse phase (RP) high‐performance liquid chromatography to elucidate their possible lignin origin. Activity is assayed using the reverse mode, the oxidation of hydroxycinnamyl alcohols into hydroxycinnamyl aldehydes. Appearance of the reaction products, coniferaldehyde and sinapaldehyde is determined by measuring absorbance at 340 and 345 nm, respectively. Disappearance of substrates, coniferyl alcohol and sinapyl alcohol is measured at 263 and 273 nm, respectively. Isocratic elution with acetonitrile:acetic acid through an RP Mediterranea sea C18 column is performed. As case examples, we have examined two different cultivars of sugarcane; My 5514 is resistant to smut, whereas B 42231 is susceptible to the pathogen. Inoculation of sugarcane stems elicits lignification and produces significant increases of coniferyl alcohol dehydrogenase (CAD) and sinapyl alcohol dehydrogenase (SAD). Production of lignin increases about 29% in the resistant cultivar and only 13% in the susceptible cultivar after inoculation compared to uninoculated plants. Our results show that the resistance of My 5514 to smut is likely derived, at least in part, to a marked increase of lignin concentration by the activation of CAD and SAD.
The role of surgery in the treatment of colorectal metastases from primary skin melanoma
Authors: Szynglarewicz B. , Ekiert M. , Forgacz J. , Halon A. , Skalik R. , Matkowski R.
Published: January 2012

Aim  The study assessed the role of colorectal surgery in the treatment of metastatic melanoma and identified patients who can most benefit from surgical resection.

Method  A retrospective analysis was made of 34 consecutive patients with skin melanoma who underwent surgical resection of large bowel metastasis.

Results  The median disease‐free interval between diagnosis of the primary and metastatic melanoma was 24 (7–98) months. Nine (27%) patients underwent emergency surgery for obstruction and 25 (73%) had an elective procedure. Resection with curative intent was performed in 14 (41%) and palliative resection in 20 (59%) patients. There was no postoperative mortality and morbidity occurred in 9%. The median survival following surgery was 11.5 (4–68) months. The 1‐, 2‐ and 5‐year survival rates were 50%, 32% and 17% respectively. Median survival was significantly increased in patients without extra‐abdominal metastases, with no evidence of non‐large‐bowel metastases, if the disease‐free interval was longer than 24 months and when curative resection was performed. In multivariate analysis, an apparently complete or palliative resection and the absence or presence of extra‐abdominal metastases were the most important prognostic factors.

Conclusion  An aggressive surgical approach to large bowel metastatic melanoma results in good palliation and effective relief of symptoms with acceptable morbidity and mortality.
Preoperative MRI sphincter morphology and anal manometry: can they be markers of functional outcome following anterior resection for rectal cancer?
Authors: How P. , Evans J. , Moran B. , Swift I. , Brown G.
Published: January 2012

Aim  Good functional outcome following anterior resection (AR) for rectal cancer is an important clinical goal, but its prediction has proven difficult. Assessments such as anal manometry have been advocated as a potential tool but functional anatomy as depicted on MRI has not been investigated. This study looked at whether sphincter complex measurements recorded from preoperative staging MRIs and preoperative anal manometry have any correlation with functional outcome.

Method  Consecutive patients with rectal adenocarcinoma underwent preoperative manometric assessment and MRI staging. MRIs were assessed with regard to anorectal angle, puborectalis thickness, canal length and external and internal anal sphincter thickness. Functional outcome was categorized into three groups according to the number of adverse postoperative symptoms (frequency, urgency, leakage, diarrhoea, use of pads, use of antidiarrhoeal medication): 0, 1 and ≥2. This was evaluated 1 year following surgery and 6 months following stoma reversal where applicable. Univariate analysis of an ordinal regression model was performed with significance at the 5% level.

Results  Thirty patients were assessed. No single preoperative manometric parameter proved significant (P > 0.05). Only puborectalis thickness showed a significant (P = 0.01) relationship with the number of adverse symptoms suffered postoperatively. On receiver operating characteristics analysis, a cut‐off value of 3.5 mm gave an optimal sensitivity of 0.5 (95% CI, 0.17–0.83) and specificity of 0.86 (95% CI, 0.64–0.96).

Conclusions  Measurements of the puborectalis thickness on preoperative staging MRIs for rectal cancer may help predict functional outcome following AR. Prospective assessment of larger numbers with a fully validated continence score are required to evaluate these findings further.
The contribution of mindfulness‐based therapies for children and families and proposed conceptual integration
Authors: Harnett Paul H. , Dawe Sharon
Published: January 2012

Background:  Mindfulness is the development of a nonjudgmental accepting awareness of moment‐by‐moment experience. Intentionally attending to one’s ongoing stream of sensations, thoughts, and emotions as they arise has a number of benefits, including the ability to react with greater flexibility to events and sustain attention. Thus the teaching of mindfulness‐based skills to children and their carers is a potential means of improving family relationships and helping children achieve more positive developmental outcomes through increased ability to sustain attention and manage emotions. We provide a review of recent studies evaluating mindfulness‐based interventions targeting children, adolescents, and families in educational and clinical settings.

Method:  Searches were conducted of several databases (including Medline, PsychINFO and Cochrane Reviews) to identify studies that have evaluated mindfulness‐based interventions targeting children, adolescents or families published since 2009.

Results:  Twenty‐four studies were identified. We conclude that mindfulness‐based interventions are an important addition to the repertoire of existing therapeutic techniques. However, large‐scale, methodologically rigorous studies are lacking. The interventions used in treatment evaluations vary in both content and dose, the outcomes targeted have varied, and no studies have employed methodology to investigate mechanisms of change.

Conclusions:  There is increasing evidence that mindfulness‐based therapeutic techniques can have a positive impact on a range of outcome variables. A greater understanding of the mechanisms of change is an important future direction of research. We argue that locating mindfulness‐based therapies targeting children and families within the broader child and family field has greater promise in improving child and family functioning than viewing mindful parenting as an independent endeavor.
Is the Problem of European Citizenship a Problem of Social Citizenship? Social Policy, Federalism, and Democracy in the EU and United States*
Authors: Schall Carly Elizabeth
Published: January 2012

The development of supranational (European) social rights, and therefore social citizenship, is undermined by strong, direct relationships between citizens and national welfare states. Social policies contribute to national identities because they entail direct relationships between states and citizens. In well‐developed European welfare states strong relationships between citizens and their member‐states are expected. This may prevent the development of a similar relationship at the European level. The U.S. provides a comparison case, wherein a successful transference of citizenship identity from a lower to higher level has occurred, partly as a result of the building of national‐level social citizenship, at least for certain classes of people. Revolutionary War Pensions provide an example of how social policy influences national identity. The lack of EU‐level social policy precludes the possibility of this type of identity formation. Finally, the interplay of social citizenship and democracy in both cases is explored. T.H. Marshall’s work regarding citizenship as the basis for democracy is used to understand how the inability to create a common social policy in the EU is harmful to democracy.
Inhibition of P‐glycoprotein enhances transport of imipramine across the blood–brain barrier: microdialysis studies in conscious freely moving rats
Authors: O'Brien FE , Clarke G , Fitzgerald P , Dinan TG , Griffin BT , Cryan JF
Published: January 2012

BACKGROUND AND PURPOSE

Recent studies indicate that efflux of antidepressants by the multidrug resistance transporter P‐glycoprotein (P‐gp) at the blood–brain barrier (BBB) may contribute to treatment‐resistant depression (TRD) by limiting intracerebral antidepressant concentrations. In addition, clinical experience shows that adjunctive treatment with the P‐gp inhibitor verapamil may improve the clinical outcome in TRD. Therefore, the present study aimed to investigate the effect of P‐gp inhibition on the transport of the tricyclic antidepressant imipramine and its active metabolite desipramine across the BBB.

EXPERIMENTAL APPROACH

Intracerebral microdialysis in rats was used to monitor brain levels of imipramine and desipramine following i.v. imipramine administration, with or without pretreatment with one of the P‐gp inhibitors verapamil or cyclosporin A (CsA). Plasma drug levels were also determined at regular intervals.

KEY RESULTS

Pretreatment with either verapamil or CsA resulted in significant increases in imipramine concentrations in the microdialysis samples, without altering imipramine plasma pharmacokinetics. Furthermore, pretreatment with verapamil, but not CsA, led to a significant elevation in plasma and brain levels of desipramine.

CONCLUSIONS AND IMPLICATIONS

The present study demonstrated that P‐gp inhibition enhanced the intracerebral concentration of imipramine , thus supporting the hypothesis that P‐gp activity restricts brain levels of certain antidepressants, including imipramine. These findings may help to explain reports of a beneficial response to adjunctive therapy with verapamil in TRD.
Hospitalized Patients’ Acceptability of Nurse‐Delivered Screening, Brief Intervention, and Referral to Treatment
Authors: Broyles Lauren M. , Rosenberger Emily , Hanusa Barbara H. , Kraemer Kevin L. , Gordon Adam J.
Published: January 2012

Background:  Inpatient healthcare providers in the United States may soon be required to offer alcohol screening, brief intervention, and referral to treatment (SBIRT) for hospital accreditation, but little is known about inpatient acceptability for SBIRT, particularly when performed by nonphysician providers such as nurses. The purpose of this study was to assess patient acceptability for and comfort with nurse‐delivered SBIRT care among hospitalized patients and to identify factors associated with SBIRT acceptability.

Methods:  We conducted a cross‐sectional survey of 370 hospitalized medical–surgical patients at a large university‐affiliated medical center, which is part of the U.S. Department of Veterans Affairs.

Results:  Patient acceptability for 8 of 10 individual nurse‐delivered SBIRT tasks was >84%. Patients were more accepting of SBIRT tasks if they felt able to determine their alcohol risk, able to reduce alcohol‐related health risks, and expressed some degree of concern about their own use of alcohol. Approximately 20% of patients reported some degree of personal discomfort with alcohol‐related discussions. Patients who were less comfortable with these discussions had lower perceived ability to reduce alcohol‐related health risk, were >60 years old, had a positive AUDIT‐C screening, and were of nonblack race.

Conclusions:  Among hospitalized patients, patient acceptability for nurse‐delivered SBIRT is high, and alcohol‐related risk perceptions appear to be important factors associated with acceptability for SBIRT tasks. Providers can proceed with greater confidence in SBIRT‐related discussions with most hospitalized patients but may need particular sensitivity and skill addressing alcohol with patient subgroups such as older patients and those with positive alcohol screenings.
Information Disclosure and Corporate Governance
Authors: HERMALIN BENJAMIN E. , WEISBACH MICHAEL S.
Published: January 2012

Public policy discussions typically favor greater corporate disclosure as a way to reduce firms' agency problems. This argument is incomplete because it overlooks that better disclosure regimes can also aggravate agency problems and related costs, including executive compensation. Consequently, a point can exist beyond which additional disclosure decreases firm value. Holding all else equal, we further show that larger firms will adopt stricter disclosure rules than smaller firms and firms with better disclosure will employ more able management. We show that mandated increases in disclosure could, in part, explain recent increases in both CEO compensation and CEO turnover rates.
When It Pays to Pay Your Investment Banker: New Evidence on the Role of Financial Advisors in M&As
Authors: GOLUBOV ANDREY , PETMEZAS DIMITRIS , TRAVLOS NICKOLAOS G.
Published: January 2012

We provide new evidence on the role of financial advisors in M&As. Contrary to prior studies, top‐tier advisors deliver higher bidder returns than their non‐top‐tier counterparts but in public acquisitions only, where the advisor reputational exposure and required skills set are relatively larger. This translates into a $65.83 million shareholder gain for an average bidder. The improvement comes from top‐tier advisors' ability to identify more synergistic combinations and to get a larger share of synergies to accrue to bidders. Consistent with the premium price–premium quality equilibrium, top‐tier advisors charge premium fees in these transactions.
Aging Effect on the Tribological Behavior of a Novel 3Y‐TZP/Nb Biocomposite Against Ultra High Molecular Weight Polyethylene
Authors: Gutiérrez‐González Carlos F. , Smirnov Anton , Bartolomé Jose F.
Published: January 2012

The aim of this study was to evaluate the friction and wear behavior of ultra high molecular weight polyethylene (UHMWPE) against 3Y‐TZP and a novel 3Y‐TZP/niobium (Nb) biocomposite. The ceramic and the biocomposite materials were subjected to an accelerated aging process to evaluate the changes in the tribological behavior after this treatment. To carry out the tribological tests, a reciprocating pin‐on‐flat contact configuration was used. The results show a lower friction coefficient and wear rate for biocomposite/UHMWPE couples than those for 3Y‐TZP/UHMWPE couples. The present study demonstrates that the excellent wear properties of this new biocomposite should never be influenced by aging. Based on these data, the potential of zirconia‐Nb as an alternative bearing biomaterial is discussed.
Reoxidation Effects of Ba‐Excessive Barium Titanate Ceramics for Laminated Positive Temperature Coefficient Thermistors
Authors: Liu Jianqiao , Gong Shuping , Quan Lin , Chen Binbin , Zhou Dongxiang
Published: January 2012

Using tape casting technique Ba‐excessive BaTiO3 ceramics were prepared, and their reoxidation effects for laminated positive temperature coefficient thermistors are investigated. These ceramics exhibit fine grains of size ~1.15 μm. A resistivity of 727 Ω·cm and a PTCR jump about 3.3 orders of magnitude can be observed when the sample was sintered in reducing atmosphere at 1150°C and successively reoxidized at 850°C for 15 min. The influences of reoxidation on ceramic characteristics are discussed. The correlation of room temperature resistivity against reoxidation temperature showed an anomalous trend. This anomaly can be explained by the enhancement of ferroelectricity led by annihilation of oxygen vacancies. The influences of reoxidation time on ceramic characteristics were found to be limited. The impedance analysis revealed that the resistance of grain boundary is more likely to be influenced during reoxidation compared to that of grain bulk. The low acceptor‐state densities of 2 × 1012–6 × 1012 cm−2 at grain boundaries were also estimated.
Intranasal Fentanyl and High‐concentration Inhaled Nitrous Oxide for Procedural Sedation: A Prospective Observational Pilot Study of Adverse Events and Depth of Sedation
Authors: Seith Robert W. , Theophilos Theane , Babl Franz E.
Published: January 2012

ACADEMIC EMERGENCY MEDICINE 2012; 19:31–36 © 2012 by the Society for Academic Emergency Medicine

Objectives: Nitrous oxide (N2O) is an attractive agent for pediatric procedural sedation and analgesia (PSA) with rapid onset and offset of sedation. However, it has limited analgesic efficacy. Intranasal fentanyl (INF) provides nonparenteral analgesia. There are currently no data on the combined use of N2O and INF for PSA in children. The authors set out to prospectively assess the depth of sedation and incidence of adverse events when N2O and INF are used in combination in pediatric patients.

Methods: This was a prospective observational pilot study of combined N2O and INF for PSA at a tertiary children’s hospital emergency department (ED). INF was administered at a precalculated dose of 1.5 μg/kg for preascertained weight ranges. N2O concentration, dose, timing of INF, adverse events, and sedation depth were recorded. Sedation depth was recorded using the University of Michigan Sedation Scale (UMSS).

Results: A total of 41 patients, aged 1 to 14 years, received INF within 2 hours prior to N2O. N2O was administered at a maximal concentration of 70% in 40 patients, and at 50% in one patient. Most patients (80%) were minimally to moderately sedated (sedation score 1 or 2). Deep sedation (sedation score 3) was recorded in 14.6% of patients (95% confidence interval [CI] = 3.4% to 24.6%). No patients had serious adverse events; vomiting was recorded in 19.5% (95% CI = 7.4% to 31.6%). There were two patients (4.9%) who were deeply sedated and vomited during the procedure.

Conclusions: There were no serious adverse events identified in this pilot study of combined N2O and INF. However, there was an increased incidence of vomiting and deeper levels of sedation when compared to published data of single‐agent use of N2O, which could lead to more serious adverse events. Further investigation is needed to establish the analgesic efficacy of combining N2O and INF and to clarify the safety profile before this combination can be recommended for PSA in children.
Computer-assisted cognitive remediation in adolescents with psychosis or at risk for psychosis: a 6-month follow-up
Authors: Urben Sébastien , Pihet Sandrine , Jaugey Laure , Halfon Olivier , Holzer Laurent
Published: January 2012

Urben S, Pihet S, Jaugey L, Halfon O, Holzer L. Computer-assisted cognitive remediation in adolescents with psychosis or at risk for psychosis: a 6-month follow-up.

Objective: To investigate short-term outcomes of a computer-assisted cognitive remediation (CACR) for adolescents with psychotic disorders or at high risk for psychosis.

Method: Cognitive abilities and clinical status were assessed at baseline (N = 32) and at 6-month follow-up (N = 22) after enrolment in either a CACR (treatment group) or a computer games (control group) program (8 weeks).

Results: With regard to the cognitive abilities, no amelioration was found in the control group while, in the CACR group, significant improvements in inhibition (p = 0.040) and reasoning (p = 0.005) were observed. Furthermore, symptom severity decreased significantly in the control group (p = 0.046) and marginally in the CACR group (p = 0.088). Improvements in cognitive abilities were not associated with symptoms' amelioration. Finally, increase in reasoning abilities was related to the median effective work time in sessions of CACR (R = 0.64, p = 0.024).

Conclusion: At follow-up, enhanced cognitive abilities (reasoning and inhibition), which are necessary for executing higher-order goals or adapting behaviour to the ever-changing environment, were reported in adolescents participants of the CACR. Thus, further studies are needed to confirm and extend these interesting results.
Insights into the structure and assembly of Escherichia coli outer membrane protein A
Authors: Reusch Rosetta N.
Published: January 2012

Outer membrane protein A (OmpA) of Escherichia coli is a paradigm for the biogenesis of outer membrane proteins; however, the structure and assembly of OmpA have remained controversial. A review of studies to date supports the hypothesis that native OmpA is a single‐domain large pore, while a two‐domain narrow‐pore structure is a folding intermediate or minor conformer. The in vitro refolding of OmpA to the large‐pore conformation requires isolation of the protein from outer membranes with retention of an intact disulfide bond followed by sufficient incubation in lipids at temperatures of ≥ 26 °C to overcome the high energy of activation for refolding. The in vivo maturation of the protein involves covalent modification of serines in the eighth β‐barrel of the N‐terminal domain by oligo‐(R)‐3‐hydroxybutyrates as the protein is escorted across the cytoplasm by SecB for post‐translational secretion across the secretory translocase in the inner membrane. After cleavage of the signal sequence, protein chaperones, such as Skp, DegP and SurA, guide OmpA across the periplasm to the β‐barrel assembly machinery (BAM) complex in the outer membrane. During this passage, a disulfide bond is formed between C290 and C302 by DsbA, and the hydrophobicity of segments of the C‐terminal domain, which are destined for incorporation as β‐barrels in the outer membrane bilayer, is increased by covalent attachment of oligo‐(R)‐3‐hydroxybutyrates. With the aid of the BAM complex, OmpA is then assembled into the outer membrane as a single‐domain large pore.
Polyphenol Compounds in Artichoke Plant Tissues and Varieties
Authors: Negro Donatella , Montesano Vincenzo , Grieco Sabrina , Crupi Pasquale , Sarli Giulio , De Lisi Antonino , Sonnante Gabriella
Published: January 2012

Abstract:  Polyphenol compounds, particularly caffeoylquinic acids and flavonoids, were measured in different tissues and developmental stages of  6 artichoke varietal types diffused in the Mediterranean region. Flower heads were subdivided into external, intermediate, internal bracts, and receptacle, while leaves were collected at the vegetative and productive stages. The main polyphenols detected were chlorogenic acid, cynarin, luteolin 7‐O‐rutinoside, and luteolin 7‐O‐glucoside. “Violet de Provence” artichoke proved to retain the highest content of total phenols. Single polyphenols accumulated preferentially in specific parts of capitula. In leaves, most polyphenols were detected in the productive stage of the plant. Altogether, results provide useful indications for the promotion of artichoke as nutraceutical food and for the extraction of health‐promoting substances in particular tissues/stages of the artichoke plant.

Practical Application:  We describe the content of phenolic compounds in various artichoke tissues, developmental stages, and varieties. Results indicate that artichoke leaves represent an important source of these health‐promoting compounds, also useful for phytopharmaceutical applications. A wider utilization of specific artichoke types should be strongly encouraged not only as a food for the fresh market, as they are now used, but also for the pharmaceutical industry, since the content of phenolic compounds is abundant both in the heads and in the leaves.
Multiplex Reverse Transcription Polymerase Chain Reaction to Study the Expression of Virulence and Stress Response Genes in Staphylococcus aureus
Authors: Shrihari Rohinishree Yadahalli , Singh Negi Pradeep
Published: January 2012

Abstract:  Staphylococcus aureus survives well in different stress conditions. The ability of this organism to adapt to various stresses is the result of a complex regulatory response, which is attributed to regulation of multiple genes. The aims of the present study were (1) to develop a multiplex PCR for the detection of genes which are involved in stress adaptation (asp23, dnaK, and groEL); alternative sigma factor (sigB) and virulence determination (entB and spa) and (2) to study the expression of these genes during stress conditions for S. aureus culture collection strains (FRI 722 and ATCC 6538) and S. aureus food isolates at mRNA level using multiplex reverse transcription polymerase chain reaction (RT‐PCR). During heat shock treatment groEL, dnaK, asp23, sodA, entB, spa, and sigB genes were up regulated up to 2.58, 2.07, 2.76, 2.55, 3.55, 2.71, and 2.62‐ folds, respectively, whereas in acid shock treatment, sodA and groEL were up regulated; dnaK was downregulated; and entB and sigB genes were not expressed in food isolates. Multiplex PCR assay standardized in this study offers an inexpensive alternative to uniplex PCR for detection of various virulence and stress response genes. This study is relevant to rapid and accurate detection of potential pathogenic S. aureus in foods.
Autolytic Degradation of Skipjack Tuna during Heating As Affected by Initial Quality and Processing Conditions
Authors: Stagg Nicola J. , Amato Penny M. , Giesbrecht Francis , Lanier Tyre C.
Published: January 2012

Abstract:  Several factors were studied as affecting protein degradation and texture of skipjack tuna muscle following ambient pressure thermal processing (precooking). These included degree of mushy tuna syndrome (MTS) evidenced in the raw meat, raw meat pH, abusive thawing/holding, and precooking temperature/time. Slurries and intact pieces from frozen skipjack tuna, either tempered for 2 h or thawed and held at 25 °C for 22 h (abusive treatment) were heated at temperatures ranging from 40 to 80 °C for up to 2 h, and also at 90 °C for 1 h, with or without prior adjustment of pH to 5 or 7 to favor cathepsin or calpain activity, respectively. Proteolysis of precooked samples was monitored by Lowry assay and SDS–PAGE; cooked texture of intact meat was measured using a Kramer shear press and by sensory profile analysis. Proteolysis maximally occurred in slurries of skipjack tuna muscle that had been abusively stored (22 h at 25 °C) and adjusted to pH 5 prior to heating at 55 °C. Intact pieces of tuna abusively thawed/held for 22 h with subsequent heating at 55 °C also evidenced the most proteolysis and were the least firm in texture. Raw fish that evidenced higher severity of MTS when raw displayed higher levels of proteolysis prior to cooking, which were further increased after cooking at 55 °C.

Practical Application:  The kinetic data presented here can be used to optimize processing conditions for skipjack tuna canning to minimize textural degradation and optimize quality.
Development and Validation of a Real‐Time TaqMan Assay for the Detection and Enumeration of Pseudomonas fluorescens ATCC 13525 Used as a Challenge Organism in Testing of Food Equipments
Authors: Saha Ratul , Bestervelt Lorelle L. , Donofrio Robert S.
Published: January 2012

Abstract:  Pseudomonas fluorescens ATCC 13525 is used as the challenge organism to evaluate the efficacy of the clean‐in‐place (CIP) process of food equipment (automatic ice‐maker) as per NSF/ANSI Standard 12. Traditional culturing methodology is presently used to determine the concentration of the challenge organism, which takes 48 h to confirm the cell density. Storage of the challenge preparation in the refrigerator might alter the cell density as P. fluorescens is capable of growing at 4 °C. Also, background organism can grow on the Pseudomonas F agar (PFA) used for the recovery of P. fluorescens thus affecting the results of the test. Real‐time TaqMan assay targeting the cpn60 gene was developed for the enumeration and the identification of P. fluorescens because of its specificity, accuracy, and shorter turnaround time. The TaqMan primer‐probe pair developed using the Allele ID® 7.0 probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10 colony forming units (CFU)/mL. The assay was also successful in determining the concentration of the challenge preparation within 2 h. Based on these observations, TaqMan assay targeting the cpn60 gene can be efficiently used for strain level identification and enumeration of bacteria.

Practical Application:  Pseudomonas fluorescens ATCC 13525 is used as a challenge organism in the efficacy testing of clean‐in‐place process of food equipments. Currently, culturing technique is used for its identification and estimation, which is not only time‐consuming but also prone to error. Real‐time TaqMan assay is more specific, sensitive, and accurate along with a shorter turnaround time compared to culturing techniques, thereby increasing the overall quality of the testing methodology to evaluate the clean‐in‐place process critical for the food industry to protect public health and safety.
Pragmatic Choice in Conversation
Authors: Gibbs Raymond W. , Van Orden Guy
Published: January 2012

How do people decide what to say in context? Many theories of pragmatics assume that people have specialized knowledge that drives them to utter certain words in different situations. But these theories are mostly unable to explain both the regularity and variability in people’s speech behaviors. Our purpose in this article is to advance a view of pragmatics based on complexity theory, which specifically explains the pragmatic choices speakers make in conversations. The concept of self‐organized criticality sheds light on how a history of utterances and subtle details of a situation surrounding a conversation may directly specify language behavior. Under this view, pragmatic choice in discourse does not reflect the output of any dedicated pragmatic module but arises from a complex coordination or coupling between speakers and their varying communicative tasks.
Self‐Organization Takes Time Too
Authors: van Rooij Iris
Published: January 2012

Four articles in this issue of topiCS (volume 4, issue 1) argue against a computational approach in cognitive science in favor of a dynamical approach. I concur that the computational approach faces some considerable explanatory challenges. Yet the dynamicists’ proposal that cognition is self‐organized seems to only go so far in addressing these challenges. Take, for instance, the hypothesis that cognitive behavior emerges when brain and body (re‐)configure to satisfy task and environmental constraints. It is known that for certain systems of constraints, no procedure can exist (whether modular, local, centralized, or self‐organized) that reliably finds the right configuration in a realistic amount of time. Hence, the dynamical approach still faces the challenge of explaining how self‐organized constraint satisfaction can be achieved by human brains and bodies in real time. In this commentary, I propose a methodology that dynamicists can use to try to address this challenge.
Precise temporal association between cortical potentials evoked by motor imagination and afference induces cortical plasticity
Authors: Mrachacz‐Kersting Natalie , Kristensen Signe Rom , Niazi Imran Khan , Farina Dario
Published: January 2012

Key points 

Here we use the naturally generated brain activation when a person imagines a simple movement and combine this with the afferent inflow that would be generated had the movement been performed rather than imagined.

We show that the excitability of the neural projections connecting the relevant brain areas to the target muscle is increased only when the afferent inflow arrives during the highest activation phase.

Furthermore, the changes are specific to the task and the neural connections between the brain and muscle involved in the task.

This novel intervention will open up the possibilities to alter afferent‐generated feedback depending on the demands of the movement to be performed.
Efficient synthesis of tension modulation in strings and membranes based on energy estimation
Authors: Avanzini Federico , Marogna Riccardo , Bank Balázs
Published: January 2012

String and membrane vibrations cannot be considered as linear above a certain amplitude due to the variation in string or membrane tension. A relevant special case is when the tension is spatially constant and varies in time only in dependence of the overall string length or membrane surface. The most apparent perceptual effect of this tension modulation phenomenon is the exponential decay of pitch in time. Pitch glides due to tension modulation are an important timbral characteristic of several musical instruments, including the electric guitar and tom-tom drum, and many ethnic instruments. This paper presents a unified formulation to the tension modulation problem for one-dimensional (1-D) (string) and two-dimensional (2-D) (membrane) cases. In addition, it shows that the short-time average of the tension variation, which is responsible for pitch glides, is approximately proportional to the system energy. This proportionality allows the efficient physics-based sound synthesis of pitch glides. The proposed models require only slightly more computational resources than linear models as opposed to earlier tension-modulated models of higher complexity.
Aeroacoustics of the swinging corrugated tube: Voice of the Dragon
Authors: Nakiboğlu Güneş , Rudenko Oleksii , Hirschberg Avraham
Published: January 2012

When one swings a short corrugated pipe segment around one’s head, it produces a musically interesting whistling sound. As a musical toy it is called a “Hummer” and as a musical instrument, the “Voice of the Dragon.” The fluid dynamics aspects of the instrument are addressed, corresponding to the sound generation mechanism. Velocity profile measurements reveal that the turbulent velocity profile developed in a corrugated pipe differs notably from the one of a smooth pipe. This velocity profile appears to have a crucial effect both on the non-dimensional whistling frequency (Strouhal number) and on the amplitude of the pressure fluctuations. Using a numerical model based on incompressible flow simulations and vortex sound theory, excellent predictions of the whistling Strouhal numbers are achieved. The model does not provide an accurate prediction of the amplitude. In the second part of the paper the sound radiation from a Hummer is discussed. The acoustic measurements obtained in a semi-anechoic chamber are compared with a theoretical radiation model. Globally the instrument behaves as a rotating (Leslie) horn. The effects of Doppler shift, wall reflections, bending of the tube, non-constant rotational speed on the observed frequency, and amplitude are discussed.
Cross-linguistic studies of children’s and adults’ vowel spaces
Authors: Chung Hyunju , Kong Eun Jong , Edwards Jan , Weismer Gary , Fourakis Marios , Hwang Youngdeok
Published: January 2012

This study examines cross-linguistic variation in the location of shared vowels in the vowel space across five languages (Cantonese, American English, Greek, Japanese, and Korean) and three age groups (2-year-olds, 5-year-olds, and adults). The vowels /a/, /i/, and /u/ were elicited in familiar words using a word repetition task. The productions of target words were recorded and transcribed by native speakers of each language. For correctly produced vowels, first and second formant frequencies were measured. In order to remove the effect of vocal tract size on these measurements, a normalization approach that calculates distance and angular displacement from the speaker centroid was adopted. Language-specific differences in the location of shared vowels in the formant values as well as the shape of the vowel spaces were observed for both adults and children.
Sea-ice thickness measurement based on the dispersion of ice swell
Authors: Marsan David , Weiss Jérôme , Larose Eric , Métaxian Jean-Philippe
Published: January 2012

The dispersion of flexural waves propagating in the Arctic sea ice cover is exploited in order to locally measure the ice thickness. The observed dispersion, for waves filtered in the 4–20 s period interval, at up to 4 broad-band seismometers deployed in Spring 2007 near the North Pole, is compared to a parameterized model that accounts for a complex wavefield made of a superposition of independent plane waves with different amplitudes and back-azimuth angles. The parameterization, that includes finding the best modeled ice thickness, is performed by using the cross-correlation functions between the seismometers. The ice thickness is estimated to 2.5±0.2 m for the ~1 km-large floe the seismic stations were deployed on, which is coherent with other, independent measurements at this site. This study thus demonstrates the feasibility of using broad-band seismometers deployed on the sea-ice in order to passively measure the ice thickness, without requiring active sources nor human intervention.
The biosonar field around an Atlantic bottlenose dolphin (Tursiops truncatus)
Authors: Au Whitlow W. L. , Branstetter Brian , Moore Patrick W. , Finneran James J.
Published: January 2012

The use of remote autonomous passive acoustic recorders (PAR) to determine the distribution of dolphins at a given locations has become very popular. Some investigators are using echolocation clicks to gather information on the presence of dolphins and to identify species. However, in all of these cases, the PAR probably recorded mainly off-axis clicks, even some from behind the animals. Yet there is a very poor understanding of the beam pattern and the click waveform and spectrum from different azimuths around the animal’s body. The beam pattern completely around an echo locating dolphin was measured at 16 different but equally spaced angles in the horizontal plane using an 8-hydrophone array in sequence. Eight channels of data were digitized simultaneously at a sampling rate of 500 kHz. The resulting beam patterns in both planes showed a continuous drop off in sound pressure with azimuth around the animal and reached levels below −50 dB relative to the signal recorded on the beam axis. The signals began to break up into two components at angles greater than ± 45° in the horizontal plane. The center frequency dropped off from its maximum at 0° in a non-uniform matter.
Single-receiver geoacoustic inversion using modal reversal
Authors: Bonnel J. , Gervaise C. , Nicolas B. , Mars J. I.
Published: January 2012

This paper introduces a single-receiver geoacoustic-inversion method based on dispersion analysis and adapted to low-frequency impulsive sources in shallow-water environments. In this context, most existing methods take advantage of the modal dispersion curves in the time-frequency domain. Inversion is usually performed by matching estimated dispersion curves with simulated replicas. The method proposed here is different. It considers the received modes in the frequency domain. The modes are transformed using an operator called modal reversal, which is parameterized using environmental parameters. When modal reversal is applied using parameters that match the real environment, dispersion is compensated for in all of the modes. In this case, the reversed modes are in phase and add up constructively, which is not the case when modal reversal is ill-parameterized. To use this phenomenon, a criterion that adds up the reversed modes has been defined. The geoacoustic inversion is finally performed by maximizing this criterion. The proposed method is benchmarked against simulated data, and it is applied to experimental data recorded during the Shallow Water 2006 experiment.
Subcritical penetration of acoustic waves into inhomogenous seafloors
Authors: Peng Linhui , Yu Gaokun
Published: January 2012

A generalized model is applied to estimate the incoherent penetration ratio caused by volume scattering at grazing angles below the critical grazing angle. The factors that affect volume scattering have been discussed using experimental data in literature. A two-layered model that refers to sound scattering in two-layered media is used to evaluate the incoherent penetration ratio for most typical sediments. But for special cases, such as the experiment, SAX04, a three-layered model is necessary to describe scattering features especially for grazing angles θ<30∘. It is shown that subcritical penetration is enhanced when the scale of volume fluctuations is comparable with the acoustic wavelength, and the scattered waves into the seafloor dominate over evanescent waves at depths larger than a few wavelengths.
Sensitivity kernel for surface scattering in a waveguide
Authors: Sarkar Jit , Marandet Christian , Roux Philippe , Walker Shane , Cornuelle Bruce D. , Kuperman W. A.
Published: January 2012

Using the Born approximation, a linearized sensitivity kernel is derived to describe the relationship between a local change at the free surface and its effect on the acoustic propagation in the water column. The structure of the surface scattering kernel is investigated numerically and experimentally for the case of a waveguide at the ultrasonic scale. To better demonstrate the sensitivity of the multipath propagation to the introduction of a localized perturbation at the air-water interface, the kernel is formulated both in terms of point-to-point and beam-to-beam representations. Agreement between theory and experiment suggests applications to sensitivity analysis of the wavefield for sea surface perturbations.
Interleukin-11 Links Oxidative Stress and Compensatory Proliferation
Authors: Nishina Takashi , Komazawa-Sakon Sachiko , Yanaka Saeko , Piao Xuehua , Zheng Dong-Mei , Piao Jiang-Hu , Kojima Yuko , Yamashina Shunhei , Sano Emiko , Putoczki Tracy , Doi Takahiro , Ueno Takashi , Ezaki Junji , Ushio Hiroko , Ernst Matthias , Tsumoto Kouhei , Okumura Ko , Nakano Hiroyasu
Published: January 2012

In dying cells, reactive oxygen species stimulate the production of a cytokine that triggers the healthy neighboring cells to proliferate.
TACE Trafficking
Authors: Mueller Kristen L.
Published: January 2012

A pseudoprotease is required for the proteolytic cleavage of the proinflammatory cytokine tumor necrosis factor.
Fluoride Riboswitch
Authors: Riddihough Guy
Published: January 2012

A fluoride-sensing riboswitch regulates the expression of putative fluoride channels in prokaryotes.
Long-Lasting Pain Killer
Authors: Stern Peter R.
Published: January 2012

Opioid administration turns down a pain amplifier by reversing synaptic long-term potentiation in spinal nociceptive pathways.
Nuclear PTEN Promotes Neuronal Survival
Authors: Gough Nancy R.
Published: January 2012

The Nedd4 ubiquitin ligase adaptor Ndfip1 is needed for nuclear translocation of the lipid phosphatase Pten after cerebral ischemia.
Wnt Signaling and Cilia Intertwined
Authors: VanHook Annalisa M.
Published: January 2012

Wnt signaling is required for proper formation of motile cilia in zebrafish.