bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of wild cereals during 28 years of global warming in Israel
Authors: Nevo Eviatar , Fu Yong-Bi , Pavlicek Tomas , Khalifa Souad , Tavasi Mordechai , Beiles Avigdor
Published: February 2012

Climate change is a major environmental stress threatening biodiversity and human civilization. The best hope to secure staple food for humans and animal feed by future crop improvement depends on wild progenitors. We examined 10 wild emmer wheat (
Triticum dicoccoides
Koern.) populations and 10 wild barley (
Hordeum spontaneum
K. Koch) populations in Israel, sampling them in 1980 and again in 2008, and performed phenotypic and genotypic analyses on the collected samples. We witnessed the profound adaptive changes of these wild cereals in Israel over the last 28 y in flowering time and simple sequence repeat allelic turnover. The revealed evolutionary changes imply unrealized risks present in genetic resources for crop improvement and human food production.
Estimating population diversity with CatchAll
Authors: Bunge John , Woodard Linda , Böhning Dankmar , Foster James A. , Connolly Sean , Allen Heather K.
Published: February 2012

Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments.

Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program.

Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall.

Contact:  jab18@cornell.edu
Obstructive Sleep Apnea and Incidence of Postoperative Delirium after Elective Knee Replacement in the Nondemented Elderly
Authors: Flink Benjamin J. , Rivelli Sarah K. , Cox Elizabeth A. , White William D. , Falcone Grace , Vail Thomas P. , Young Christopher C. , Bolognesi Michael P. , Krystal Andrew D. , Trzepacz Paula T. , Moon Richard E. , Kwatra Madan M.
Published: February 2012

Background

Postoperative delirium, a common complication in the elderly, can occur following any type of surgery and is associated with increased morbidity and mortality; it may also be associated with subsequent cognitive problems. Effective therapy for postoperative delirium remains elusive because the causative factors of delirium are likely multiple and varied.

Methods

Patients 65 yr or older undergoing elective knee arthroplasty were prospectively evaluated for postoperative Diagnostic and Statistical Manual of Mental Disorders-IV delirium. Exclusion criteria included dementia, mini-mental state exam score less than 24, delirium, clinically significant central nervous system/neurologic disorder, current alcoholism, or any serious psychiatric disorder. Delirium was assessed on postoperative days 2 and 3 using standardized scales. Patients' preexisting medical conditions were obtained from medical charts. The occurrence of obstructive sleep apnea was confirmed by contacting patients to check their polysomnography records. Data were analyzed using Pearson chi-square or Wilcoxon rank sum tests and multiple logistic regressions adjusted for effects of covariates.

Results

Of 106 enrolled patients, 27 (25%) developed postoperative delirium. Of the 15 patients with obstructive sleep apnea, eight (53%) experienced postoperative delirium, compared with 19 (20%) of the patients without obstructive sleep apnea (P = 0.0123, odds ratio: 4.3). Obstructive sleep apnea was the only statistically significant predictor of postoperative delirium in multivariate analyses.

Conclusions

This is the first prospective study employing validated measures of delirium to identify an association between preexisting obstructive sleep apnea and postoperative delirium.
Robotically Assisted Coronary Endarterectomy
Authors: Dawood Murtaza Y. , Lehr Eric J. , de Biasi Andreas , Haque Reyaz , Grigore Alina , Griffith Bartley P. , Bonatti Johannes O.
Published: February 2012

Robotic assistance has enabled coronary artery bypass surgery to be performed safely in a completely endoscopic fashion, but diffusely diseased target vessels may pose a technical challenge. We present a case in which coronary endarterectomy was performed on the left anterior descending coronary artery during a two-vessel totally endoscopic coronary artery bypass procedure. A 52-year-old woman presented with intermittent substernal pain. Preoperative studies showed diffuse disease in the left coronary artery system. Bilateral internal mammary arteries were harvested robotically using a skeletonized technique in a completely endoscopic fashion. Cardiopulmonary bypass was achieved via peripheral cannulation, and the heart was arrested with intermittent cold antegrade hyperkalemic blood cardioplegia delivered via an ascending aortic occlusion balloon catheter. The first obtuse marginal anastomosis was performed. The left anterior descending coronary artery was diffusely diseased and heavily calcified. An end-to-side anastomosis was attempted to the right internal mammary artery with unsatisfactory results. A localized coronary endarterectomy was performed, and an extended anastomosis was completed using the right internal mammary artery. The patient recovered uneventfully and was discharged home on postoperative day 6. Diffuse coronary artery disease was once thought to be a prohibitive challenge for minimally invasive coronary bypass procedures. This case demonstrates that local coronary endarterectomy is feasible and safe in robotic totally endoscopic coronary artery bypass surgery.
Concomitant Transapical Transcatheter Aortic Valve Implantation and Minimally Invasive Direct Coronary Artery Bypass
Authors: Baumbach Hardy , Adili Sara , Ursulescu Adrian , Franke Ulrich F. W.
Published: February 2012

We represent a successful minimally invasive combined off-pump procedure consisting of a transapical aortic valve implantation and a direct coronary artery bypass grafting in a woman with a severe aortic stenosis and a critical coronary artery disease. Due to her comorbidities, she was classified as a high-risk patient qualifying for a transcatheter procedure. We performed this combined procedure in a hybrid operation room, starting with the coronary bypass to maintain a coronary blood flow during the transapical valve implantation. The operation processed without any complications and she was discharged at the seventh postoperative day into the allocating hospital.
Transcatheter Aortic Valve Implantation and Hybrid Coronary Artery Revascularization Time to Combine Them
Authors: Unbehaun Axel , Pasic Miralem , Dreysse Stephan , Buz Semih , Kukucka Marian , Hetzer Roland , Drews Thorsten
Published: February 2012

We report on simultaneous off-pump coronary artery bypass grafting to the left anterior descending artery, modified transapical aortic valve implantation, and stenting of the circumflex and right coronary arteries in an 84-year-old patient. The poly-morbid patient with a logistic EuroSCORE of 85% experienced recent myocardial infarction; the left ventricular ejection fraction was reduced to 20%. Postoperative recovery was fast and short. The strategy described is the next logical step in broadening the indication for transcatheter aortic valve interventions.
Perceval Sutureless Aortic Valve Prosthesis Easy, Fast, and Safe
Authors: Santarpino Giuseppe , Pfeiffer Steffen , Concistrè Giovanni , Fischlein Theodor
Published: February 2012

Objective

There is an increase of old patients needing aortic valve surgery. Especially in this age group, a lot of new less-invasive strategies are proposed. Our goal was to study whether a sutureless aortic valve, which is implanted surgically after removal of the native valve, could be an alternative for a subgroup of patients.

Methods

The Sorin Perceval S is a biologic pericardial aortic valve assembled in a metal super elastic alloy stent and implanted in the aortic root without the need of suturing. As part of a premarketing multicenter study (Cavalier trial), 34 patients were screened for Perceval S implantation. All patients underwent cardiopulmonary bypass and mini-invasive approach (partial upper sternotomy).

Results

Fourteen patients were excluded due to standardized criteria. Twenty patients received a 21-mm valve (2 patients), 23-mm valve (6 patients), or 25-mm valve (12 patients). X-clamp time was 20.6 ± 7.6 minutes, and implantation time was 8.6 ± 3.1 minutes. Intra- and postoperative echocardiography showed no paravalvular leakage, low gradients (max 16.3 ± 5, mean 9.8 ± 4.2), and two patients with an intraprosthesis reflux (one patient with 1/4+, one patient with 2/4+). All patients were discharged without major in-hospital complications (intensive care unit stay 1.4 ± 0.5 days, hospital stay 7 ± 0.7 days).

Conclusions

The sutureless Perceval S aortic valve is hemodynamically excellent and a safe prosthesis in selected patients. Due to a simple and fast implantation technique, this valve could guarantee a shorter operation time in combination with a mini-invasive approach.
Surgical Treatment for Isolated Atrial Fibrillation Minimally Invasive vs Classic Cut and Sew Maze
Authors: Lee Richard , McCarthy Patrick M. , Passman Rod S. , Kruse Jane , Malaisrie S. Chris , McGee Edwin C. , Lapin Brittany , Jacobson Jason T. , Goldberger Jeffrey , Knight Bradley P.
Published: February 2012

Objective

We sought to compare outcomes after two surgical approaches for the treatment of atrial fibrillation (AF): a minimally invasive, staged hybrid approach combining surgery with catheter ablation, [Hybrid Maze (HM)] and the classic cut and sew Maze (CM).

Methods

From April 2004 to March 2010, 63 stand-alone AF procedures were performed by two surgeons at a single center and followed up for ≥6 months. CM was offered to all patients. After July 2007, patients were also prospectively offered a two-stage HM: stage 1 = a beating heart bipolar radiofrequency pulmonary vein isolation and left atrial appendage ligation; stage 2 = transvenous catheter ablation connecting the pulmonary veins to each other and the mitral annulus when AF was present after stage 1. Outcomes were compared between 25 HM and 38 CM using χ2 or Fisher exact test analysis.

Results

Postoperatively, there was no difference in 30-day mortality (0%), complications (4% HM vs 18% CM), or median length of stay (5 days). At last follow-up, 88% of HM and 95% of CM were free from AF; 80% of HM and 90% of CM were free from AF and antiarrhythmic medication (P ≥ 0.3). Twenty-nine percent of HM required a subsequent catheter ablation (stage 2) when compared with 8% of the CM patients (P = 0.04). Freedom from AF and antiarrhythmic medication at 1 year was 52% for the HM and 87.5% for the CM (P = 0.004).

Conclusions

In AF patients reluctant to undergo a CM but willing to undergo subsequent catheter ablation, a minimally invasive approach is a reasonable strategy. Because pulmonary vein isolation alone may be sufficient in two-thirds of patients and delayed reconnection is common, an interval two-stage hybrid approach may prove preferable over a one-stage combined hybrid approach; however, successful sinus restoration may take longer with this approach.
Pilot Study of Sternal Plating for Primary Closure of the Sternum in Cardiac Surgical Patients
Authors: Bennett-Guerrero Elliott , Phillips-Bute Barbara , Waweru Peter M. , Gaca Jeffrey G , Spann James C. , Milano Carmelo A.
Published: February 2012

Objective

Postoperative sternal wound complications are a significant problem in high-risk patients. In addition to closure with conventional wires, several systems involving rigid fixation with metal plates are currently available. The Rapid Sternal Closure System (Talon) is approved for stabilization and fixation of the anterior chest wall. Anecdotal evidence suggests that use of the Talon may result in improved postoperative recovery.

Methods

Fifty-one cardiac surgical patients at higher risk for sternal wound complications were enrolled at two sites. Subjects were randomized to insertion of Talons (n = 28) or wires only (control, n = 23) for sternal closure. The primary endpoint was a comparison between study groups of the percent of baseline incentive spirometry volume through postoperative day 7. Secondary endpoints included other measures of quality of recovery, sternal wound infection, and nonunion.

Results

The percentage of preoperative incentive spirometry volume achieved was higher in the Talon arm (67% ± 32%) versus control (58% ± 24%); however, this was not statistically significant (P = 0.41). Use of the Talon was associated with decreased use of opiates (21.3 ± 11.8 vs 25.4 ± 21.6 mg, P = 0.44), increased ability to ambulate 1000 ft on postoperative day 5 (25% vs 13%, P = 0.28), and decreased duration of mechanical ventilation (median 0.5 vs 1.0 days, P = 0.24) and hospital length of stay (4.5 ± 3.2 vs 5.3 ± 4.0 days, P = 0.40). One superficial sternal wound infection was observed in each study arm. There were no cases of nonunion.

Conclusions

In this pilot study, the primary endpoint was not statistically different between the treatment groups. Use of the Talon was associated with trends toward benefit in endpoints consistent with enhanced postoperative recovery, highlighting a need for additional data from larger randomized trials.
Nutrition Education for Pediatric Gastroenterology, Hepatology, and Nutrition Fellows
Authors: Martinez J. Andres , Koyama Tatsuki , Acra Sari , Mascarenhas Maria R. , Shulman Robert J.
Published: February 2012

Objectives:

The aim of the study was to assess the methodology and content of nutrition education during gastroenterology fellowship training and the variability among the different programs.

Methods:

A survey questionnaire was completed by 43 fellowship training directors of 62 active programs affiliated to the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition, including sites in the United States, Canada, and Mexico. The data were examined for patterns in teaching methodology and coverage of specific nutrition topics based on level 1 training in nutrition, which is the minimum requirement according to the published North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition fellowship training guidelines.

Results:

The majority of the teaching was conducted by MD‐degree faculty (61%), and most of the education was provided through clinical care experiences. Only 31% of the level 1 nutrition topics were consistently covered by >80% of programs, and coverage did not correlate with the size of the programs. Competency in nutrition training was primarily assessed through questions to individuals or groups of fellows (77% and 65%, respectively). Program directors cited a lack of faculty interested in nutrition and a high workload as common obstacles for teaching.

Conclusions:

The methodology of nutrition education during gastroenterology fellowship training is, for the most part, unstructured and inconsistent among the different programs. The minimum level 1 requirements are not consistently covered. The development of core curriculums and learning modules may be beneficial in improving nutrition education.
Divergent host-plant use promotes reproductive isolation among cynipid gall wasp populations
Authors: Egan Scott P. , Hood Glen R. , Feder Jeff L. , Ott James R.
Published: February 2012

Ecological speciation occurs when reproductive isolation evolves as a consequence of divergent natural selection among environments. A direct prediction of this process is that ecologically divergent pairs of populations will exhibit greater reproductive isolation than ecologically similar pairs of populations. By comparing allopatric populations of the cynipid gall wasp
Belonocnema treatae
infesting
Quercus virginiana
and
Quercus geminata
, we tested the role that divergent host use plays in generating ecological divergence and sexual isolation. We found differences in body size and gall structure associated with divergent host use, but no difference in neutral genetic divergence between populations on the same or different host plant. We observed significant assortative mating between populations from alternative host plants but not between allopatric populations on the same host plant. Thus, we provide evidence that divergent host use promotes speciation among gall wasp populations.
Cross-hemisphere migration of a 25 g songbird
Authors: Bairlein Franz , Norris D. Ryan , Nagel Rolf , Bulte Marc , Voigt Christian C. , Fox James W. , Hussell David J. T. , Schmaljohann Heiko
Published: February 2012

The northern wheatear (
Oenanthe oenanthe
) is a small (approx. 25 g), insectivorous migrant with one of the largest ranges of any songbird in the world, breeding from the eastern Canadian Arctic across Greenland, Eurasia and into Alaska (AK). However, there is no evidence that breeding populations in the New World have established overwintering sites in the Western Hemisphere. Using light-level geolocators, we demonstrate that individuals from these New World regions overwinter in northern sub-Sahara Africa, with Alaskan birds travelling approximately 14 500 km each way and an eastern Canadian Arctic bird crossing a wide stretch of the North Atlantic (approx. 3500 km). These remarkable journeys, particularly for a bird of this size, last between one to three months depending on breeding location and season (autumn/spring) and result in mean overall migration speeds of up to 290 km d
−1
. Stable-hydrogen isotope analysis of winter-grown feathers sampled from breeding birds generally support the notion that Alaskan birds overwinter primarily in eastern Africa and eastern Canadian Arctic birds overwinter mainly in western Africa. Our results provide the first evidence of a migratory songbird capable of linking African ecosystems of the Old World with Arctic regions of the New World.
Using digital photography to implement the McFarland method
Authors: Lahuerta Zamora L. , Pérez-Gracia M. T.
Published: February 2012

The McFarland method allows the concentration of bacterial cells in a liquid medium to be determined by either of two instrumental techniques: turbidimetry or nephelometry. The microbes act by absorbing and scattering incident light, so the absorbance (turbidimetry) or light intensity (nephelometry) measured is directly proportional to their concentration in the medium. In this work, we developed a new analytical imaging method for determining the concentration of bacterial cells in liquid media. Digital images of a series of McFarland standards are used to assign turbidity-based colour values with the aid of dedicated software. Such values are proportional to bacterial concentrations, which allow a calibration curve to be readily constructed. This paper assesses the calibration reproducibility of an intra-laboratory study and compares the turbidimetric and nephelometric results with those provided by the proposed method, which is relatively simple and affordable; in fact, it can be implemented with a digital camera and the public domain software I
mage
J.
A nonlinear programming approach for estimation of transmission parameters in childhood infectious disease using a continuous time model
Authors: Word Daniel P. , Cummings Derek A. T. , Burke Donald S. , Iamsirithaworn Sopon , Laird Carl D.
Published: February 2012

Mathematical models can enhance our understanding of childhood infectious disease dynamics, but these models depend on appropriate parameter values that are often unknown and must be estimated from disease case data. In this paper, we develop a framework for efficient estimation of childhood infectious disease models with seasonal transmission parameters using continuous differential equations containing model and measurement noise. The problem is formulated using the simultaneous approach where all state variables are discretized, and the discretized differential equations are included as constraints, giving a large-scale algebraic nonlinear programming problem that is solved using a nonlinear primal–dual interior-point solver. The technique is demonstrated using measles case data from three different locations having different school holiday schedules, and our estimates of the seasonality of the transmission parameter show strong correlation to school term holidays. Our approach gives dramatic efficiency gains, showing a 40–400-fold reduction in solution time over other published methods. While our approach has an increased susceptibility to bias over techniques that integrate over the entire unknown state-space, a detailed simulation study shows no evidence of bias. Furthermore, the computational efficiency of our approach allows for investigation of a large model space compared with more computationally intensive approaches.
Thermal-aware DC IR-drop co-analysis using non-conformal domain decomposition methods
Authors: Shao Yang , Peng Zhen , Lee Jin-Fa
Published: February 2012

Almost all practical engineering applications are multi-physics in nature, and various physical phenomena usually interact and couple with each other. For instance, the resistivity of most conducting metals increases linearly with increases in the surrounding temperature resulting from Joule heating by electrical currents flowing through conductors. Therefore, in order to accurately characterize the performance of high-power integrated circuits (ICs), packages and printed circuit boards (PCBs), it is essential to account for both electrical and thermal effects and the intimate couplings between them. In this paper, we present non-conformal, non-overlapping domain decomposition methods (DDMs) for thermal-aware direct current (DC) IR drop co-analysis of high-power chip-package-PCBs. Here, IR stands for the finite resistivity (R) of metals and current (I) drawn off from the power/ground planes. The proposed DDM starts by partitioning the composite device into inhomogeneous sub-regions with temperature-dependent material properties. Subsequently, each sub-domain is meshed independently according to its own characteristic features. As a consequence, the troublesome mesh-generation task for complex ICs can be greatly subdued. The proposed thermal-aware DC IR drop co-analysis applies the non-conformal DDM for both conduction and steady-state heat-transfer analyses with a two-way coupling between them. Numerical examples, including an IC package and a chip-package-PCB, demonstrate the flexibility and potential of the proposed thermal-aware DC IR-drop co-analysis using non-conformal DDMs.
Stable isotope series from elephant ivory reveal lifetime histories of a true dietary generalist
Authors: Codron Jacqueline , Codron Daryl , Sponheimer Matt , Kirkman Kevin , Duffy Kevin J. , Raubenheimer Erich J. , Mélice Jean-Luc , Grant Rina , Clauss Marcus , Lee-Thorp Julia A.
Published: February 2012

Longitudinal studies have revealed how variation in resource use within consumer populations can impact their dynamics and functional significance in communities. Here, we investigate multi-decadal diet variations within individuals of a keystone megaherbivore species, the African elephant (
Loxodonta africana
), using serial stable isotope analysis of tusks from the Kruger National Park, South Africa. These records, representing the longest continuous diet histories documented for any extant species, reveal extensive seasonal and annual variations in isotopic—and hence dietary—niches of individuals, but little variation between them. Lack of niche distinction across individuals contrasts several recent studies, which found relatively high levels of individual niche specialization in various taxa. Our result is consistent with theory that individual mammal herbivores are nutritionally constrained to maintain broad diet niches. Individual diet specialization would also be a costly strategy for large-bodied taxa foraging over wide areas in spatio-temporally heterogeneous environments. High levels of within-individual diet variability occurred within and across seasons, and persisted despite an overall increase in inferred C
4
grass consumption through the twentieth century. We suggest that switching between C
3
browsing and C
4
grazing over extended time scales facilitates elephant survival through environmental change, and could even allow recovery of overused resources.
Clinical Manifestations Vary with Different Age Spectrums in Infants with Kawasaki Disease
Authors: Liu Hao-Chuan , Lo Chiao-Wei , Hwang Betau , Lee Pi-Chang
Published: February 2012

Background. Kawasaki disease (KD) is an acute systemic vasculitis with unknown etiology. The diagnosis of KD depends on clinical manifestations. The prevalence of coronary artery abnormality (CAA) is 11.0% and results in cardiac sequelae, such as myocardial infarction or coronary aneurysm, which are the most serious complications in KD.Methods. We divided KD's children into different age groups: ≤6 months old, 7 months to 1 year old, and >1 year old, respectively. Different parameters were compared in each group.Results. Infants ≤6 months old are less likely to fulfill KD's major diagnostic criteria within 10 days, are prone to develop incomplete KD with the lowest cholesterol level, and have the greatest chance to have CAA and the laboratory features associated with CAA, such as the longest time needed to confirm CA diagnosis, lower hemoglobin level, lower albumin level, and higher platelet count. Infants <1 year old develop higher percentage of leukocytosis and sterile pyuria. But this group has fewer patients with neck lymphadenopathy.
The Use of Clay-Polymer Nanocomposites in Wastewater Pretreatment
Authors: Rytwo Giora
Published: February 2012

Some agricultural effluents are unsuitable for discharge into standard sewage-treatment plants: their pretreatment is necessary to avoid clogging of the filtering devices by colloidal matter. The colloidal stability of the effluents is mainly due to mutual repulsive forces that keep charged particles in suspension. Pretreatment processes are based on two separate stages: (a) neutralization of the charges (“coagulation”) and (b) bridging between several small particles to form larger aggregates that sink, leaving clarified effluent (“flocculation”). The consequent destabilization of the colloidal suspension lowers total suspended solids (TSSs), turbidity, and other environmental quality parameters, making the treatments that follow more efficient. Clay-based materials have been widely used for effluent pretreatment and pollutant removal. This study presents the use of nanocomposites, comprised of an anchoring particle and a polymer, as “coagoflocculants” for the efficient and rapid reduction of TSS and turbidity in wastewater with a high organic load. The use of such particles combines the advantages of coagulant and flocculant by neutralizing the charge of the suspended particles while bridging between them and anchoring them to a denser particle (the clay mineral), enhancing their precipitation. Very rapid and efficient pretreatment is achieved in one single treatment step.
Identification of a target cell permissive factor required for contact-dependent growth inhibition (CDI)
Authors: Diner Elie J. , Beck Christina M. , Webb Julia S. , Low David A. , Hayes Christopher S.
Published: February 2012

Bacterial contact-dependent growth inhibition (CDI) is mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effector proteins are exported onto the surface of CDI+ inhibitor cells, where they interact with susceptible bacteria and deliver effectors/toxins derived from their C-terminal regions (CdiA-CT). CDI+ cells also produce an immunity protein that binds the CdiA-CT and blocks its activity to prevent autoinhibition. Here, we show that the CdiA-CT from uropathogenic Escherichia coli strain 536 (UPEC536) is a latent tRNase that requires activation by the biosynthetic enzyme CysK (O-acetylserine sulfhydrylase A). UPEC536 CdiA-CT exhibits no nuclease activity in vitro, but cleaves within transfer RNA (tRNA) anti-codon loops when purified CysK is added. CysK and CdiA-CT form a stable complex, and their binding interaction appears to mimic that of the CysK/CysE cysteine synthase complex. CdiA-CT activation is also required for growth inhibition. Synthesis of CdiA-CT in E. coli cysK+ cells arrests cell growth, whereas the growth of ΔcysK mutants is unaffected by the toxin. Moreover, E. coli ΔcysK cells are completely resistant to inhibitor cells expressing UPEC536 CdiA, indicating that CysK is required to activate the tRNase during CDI. Thus, CysK acts as a permissive factor for CDI, providing a potential mechanism to modulate growth inhibition in target cells.
Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes
Authors: Bodner Martin , Perego Ugo A. , Huber Gabriela , Fendt Liane , Röck Alexander W. , Zimmermann Bettina , Olivieri Anna , Gómez-Carballa Alberto , Lancioni Hovirag , Angerhofer Norman , Bobillo Maria Cecilia , Corach Daniel , Woodward Scott R. , Salas Antonio , Achilli Alessandro , Torroni Antonio , Bandelt Hans-Jürgen , Parson Walther
Published: February 2012

It is now widely agreed that the Native American founders originated from a Beringian source population ∼15–18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina). We selected and completely sequenced 43 D1g and D1j mtDNA genomes applying highest quality standards. Molecular and phylogeographic analyses revealed extensive variation within each of the two clades and possibly distinct dispersal patterns. Their age estimates agree with the dating of the earliest archaeological sites in South America and indicate that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr. This study confirms that major sampling and sequencing efforts are mandatory for uncovering all of the most basal variation in the Native American mtDNA haplogroups and for clarification of Paleo-Indian migrations, by targeting, if possible, both the general mixed population of national states and autochthonous Native American groups, especially in South America.
Role of cis-12-Oxo-Phytodienoic Acid in Tomato Embryo Development
Authors: Goetz Stephan , Hellwege Anja , Stenzel Irene , Kutter Claudia , Hauptmann Valeska , Forner Susanne , McCaig Bonnie , Hause Gerd , Miersch Otto , Wasternack Claus , Hause Bettina
Published: February 2012

Oxylipins including jasmonates are signaling compounds in plant growth, development, and responses to biotic and abiotic stresses. In Arabidopsis (Arabidopsis thaliana) most mutants affected in jasmonic acid (JA) biosynthesis and signaling are male sterile, whereas the JA-insensitive tomato (Solanum lycopersicum) mutant jai1 is female sterile. The diminished seed formation in jai1 together with the ovule-specific accumulation of the JA biosynthesis enzyme allene oxide cyclase (AOC), which correlates with elevated levels of JAs, suggest a role of oxylipins in tomato flower/seed development. Here, we show that 35S::SlAOC-RNAi lines with strongly reduced AOC in ovules exhibited reduced seed set similarly to the jai1 plants. Investigation of embryo development of wild-type tomato plants showed preferential occurrence of AOC promoter activity and AOC protein accumulation in the developing seed coat and the embryo, whereas 12-oxo-phytodienoic acid (OPDA) was the dominant oxylipin occurring nearly exclusively in the seed coat tissues. The OPDA- and JA-deficient mutant spr2 was delayed in embryo development and showed an increased programmed cell death in the developing seed coat and endosperm. In contrast, the mutant acx1a, which accumulates preferentially OPDA and residual amount of JA, developed embryos similar to the wild type, suggesting a role of OPDA in embryo development. Activity of the residual amount of JA in the acx1a mutant is highly improbable since the known reproductive phenotype of the JA-insensitive mutant jai1 could be rescued by wound-induced formation of OPDA. These data suggest a role of OPDA or an OPDA-related compound for proper embryo development possibly by regulating carbohydrate supply and detoxification.
Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems
Authors: Chan Cheong Xin , Zäuner Simone , Wheeler Glen , Grossman Arthur R. , Prochnik Simon E. , Blouin Nicolas A. , Zhuang Yunyun , Benning Christoph , Berg Gry Mine , Yarish Charles , Eriksen Renée L. , Klein Anita S. , Lin Senjie , Levine Ira , Brawley Susan H. , Bhattacharya Debashish
Published: February 2012

Membrane transporters play a central role in many cellular processes that rely on the movement of ions and organic molecules between the environment and the cell, and between cellular compartments. Transporters have been well characterized in plants and green algae, but little is known about transporters or their evolutionary histories in the red algae. Here we examined 482 expressed sequence tag contigs that encode putative membrane transporters in the economically important red seaweed Porphyra (Bangiophyceae, Rhodophyta). These contigs are part of a comprehensive transcriptome dataset from Porphyra umbilicalis and Porphyra purpurea. Using phylogenomics, we identified 30 trees that support the expected monophyly of red and green algae/plants (i.e. the Plantae hypothesis) and 19 expressed sequence tag contigs that show evidence of endosymbiotic/horizontal gene transfer involving stramenopiles. The majority (77%) of analyzed contigs encode transporters with unresolved phylogenies, demonstrating the difficulty in resolving the evolutionary history of genes. We observed molecular features of many sodium-coupled transport systems in marine algae, and the potential for coregulation of Porphyra transporter genes that are associated with fatty acid biosynthesis and intracellular lipid trafficking. Although both the tissue-specific and subcellular locations of the encoded proteins require further investigation, our study provides red algal gene candidates associated with transport functions and novel insights into the biology and evolution of these transporters.
Phenotypic compromises in a long‐distance migrant during the transition from migration to reproduction in the High Arctic
Authors: Vézina François , Williams Tony D. , Piersma Theunis , Guy Morrison R. I.
Published: February 2012

1. Seasonal carry‐over effects may be important structuring components of avian life‐history cycles. However, little is known on physiological transitions between stages and on phenotypic compromises that may be made at such time to improve fitness.

2. We studied postmigratory body remodelling in red knots (Calidris canutus islandica) arriving on the Arctic breeding grounds. Our objectives were to determine the effects of body reconstruction and preparation for breeding on maintenance energy costs and to determine whether weather conditions can force compromises between functions required for postmigration recovery of body composition, thermoregulation and breeding.

3. During two consecutive springs at the northernmost land on Earth (Alert, Ellesmere Island, Canada, 82°30′N), we monitored changes in knots post‐arrival body stores. Using ultrasonography, we also tracked changes in gizzard size, an indicator of gut size, and pectoral muscle thickness, not only an endogenous protein source but also a thermogenic organ. We measured basal metabolic rate (BMR) throughout reconstruction and compared it with BMR of nonbreeding red knots wintering in the Dutch Wadden Sea.

4. Arriving knots faced temperatures up to 13 °C lower than during midwinter. Birds arrived with large body stores and pectoral muscles, which declined in size while they grew their gizzard and prepared for breeding. BMR at arrival was indistinguishable from winter BMR and increased linearly throughout reconstruction. BMR increased up to 69% faster in females than males, likely due to the development of their reproductive organs.

5. Birds had lower body stores but larger muscles in the colder year, and muscle loss was correlated with the warming of spring temperatures. Therefore, muscles would not only serve as a nutrient source, but their thermogenic function could also provide the flexibility to cope with high thermostatic costs in the spring. However, retaining muscles for shivering may limit protein recirculation and delay the onset of breeding.

6. Postmigratory recovery therefore involves significant energy costs and arriving birds likely have to make physiological compromises, depending on spring conditions, which may impact on fitness. Although this period is clearly critical in the life cycle of red knots, it is one of the least understood life‐history stages in Arctic‐breeding shorebirds.
Prognostic value of Ki67 index in anaplastic oligodendroglial tumours – a translational study of the European Organization for Research and Treatment of Cancer Brain Tumor Group
Authors: Preusser Matthias , Hoeftberger Romana , Woehrer Adelheid , Gelpi Ellen , Kouwenhoven Mathilde , Kros Johan M , Sanson Marc , Idbaih Ahmed , Brandes Alba A , Heinzl Harald , Gorlia Thierry , Hainfellner Johannes A , van den Bent Martin
Published: February 2012

Preusser M, Hoeftberger R, Woehrer A, Gelpi E, Kouwenhoven M, Kros J M, Sanson M, Idbaih A, Brandes A A, Heinzl H, Gorlia T, Hainfellner J A & van den Bent M  (2012) Histopathology 60, 885–894  Prognostic value of Ki67 index in anaplastic oligodendroglial tumours – a translational study of the European Organization for Research and Treatment of Cancer Brain Tumor Group

Aims:  To evaluate the prognostic value and clinical utility of Ki67 tumour cell proliferation index in anaplastic oligodendroglial tumours (AOT).

Methods and results:  We performed anti‐Ki67 immunostaining (MIB‐1 antibody) of formalin‐fixed and paraffin‐embedded tumour tissue specimens of 128 patients with newly diagnosed AOT that were treated in a randomized Phase III trial. Ki67 index was assessed by three independent observers and was correlated to clinical, histopathological and molecular features (including 1p/19q co‐deletion, epithelial growth factor receptor gene (EGFR) amplification, isocitrate dehydrogenase (IDH1) mutations, O6‐methylguanine‐DNA methyltransferase gene (MGMT) promoter methylation, and patient survival times. Intra‐ and inter‐observer agreement of Ki67 index assessment was excellent. Univariable analysis (n = 79) showed that patients with a low Ki67 index had significantly more favourable progression‐free survival (PFS) (P‐value = 0.004, log‐rank test) and overall survival (OS) (P‐value = 0.003, log‐rank test) than patients with a high Ki67 index, respectively. On multivariable analysis (n = 43), Ki67 index showed no independent association with PFS or OS.

Conclusions:  In AOT the Ki67 index has a strong prognostic impact on univariable analysis, but no independent influence on multivariable analysis. However, further prospective studies including larger numbers of cases and standardized evaluation of Ki67 index in conjunction with other relevant prognostic parameters are needed to draw definitive conclusions.
Optimisation of cross‐linking β‐cyclodextrin and its recycling efficiency for cholesterol removal in milk and cream
Authors: Lee Yun‐Kyung , Ganesan Palanivel , Kwak Hae‐Soo
Published: February 2012

This study was carried out to investigate the optimum conditions of cross‐linking β‐cyclodextrin (β‐CD) and recycling for cholesterol removal in milk and cream. The cross‐linked β‐CD was prepared with a 15% adipic acid solution, and the water solubility of the β‐CD was measured for the optimum conditions based on mixing temperature, mixing time, cross‐linking temperature, cross‐linking reaction time and cooling time. In the results of this study, optimum conditions were 80 °C mixing temperature, 2 h mixing time, 60 °C cross‐linking temperature, 24 h cross‐linking reaction time and 48 h cooling time. After determining the optimum conditions, the recyclable yields of the cross‐linked β‐CD ranged from 90.01% to 55.17% in six recyclings and the percentage of cholesterol removal by 15% cross‐linked β‐CD was over 90% until eighth recycling. On the basis of the results, this study suggests that 15% adipic acid‐added cross‐linked β‐CD maximised recyclable yield and that cholesterol removal was improved during recycling.
Student centredness in clinical learning: the influence of the clinical teacher
Authors: Newton Jennifer M. , Jolly Brian C. , Ockerby Cherene M. , Cross Wendy M.
Published: February 2012

newton j.m., jolly b.c., ockerby c.m. & cross w.m. (2012) Student centredness in clinical learning: the influence of the clinical teacher. Journal of Advanced Nursing68(10), 2331–2340.

Aim.  This article reports a longitudinal study examining how nursing students learn on clinical placements in three cohorts of undergraduates at a large Australian university.

Background.  Preceptorship models of clinical learning are increasing in popularity as a strategy to maximize collaboration between university and healthcare organizations. A clinical education model, underpinned by preceptorship, was offered by an Australian university in partnership with a tertiary healthcare organization to some students.

Design.  The study utilized a mixed method approach of surveys and interviews.

Method.  It was hypothesized that students participating in the preceptorship partnership model would have more positive perceptions of the clinical learning environment than students participating in other models of clinical education. Data were collected over 3 years, from 2006–2008, using a modified Clinical Learning Environment Inventory from second (n = 396) and third (n = 263) year nursing students. Students were classified into three groups based on which educational model they received.

Results.  On the inventory factor, ‘Student centredness’, a Welch test indicated an important difference between the responses of students in the three groups. Games‐Howell post hoc test indicated that students in the clinical preceptorship partnership model responded more positively than students who had both a clinical teacher and a preceptor in a non‐preceptorship partnership model.

Conclusion.  Developing sustainable approaches to enhance the clinical learning environment experience for student nurses is an international concern. The significance of continuity of clinical teachers to the contribution of student centredness is an important aspect to be considered.
Evidence databases application: comparison of university faculties versus clinical residents in a developing country
Authors: Sadeghi‐Ghyassi Fatemeh , Nosraty Lily , Ghojazadeh Morteza , Mostafaie Ali
Published: February 2012

Rationale, aims and objectives  One of the main barriers against the implementation of evidence‐based medicine (EBM) is the lack of search skills, an element that affects the finding of the best available evidence. Faculty staff should be capable of using the best evidence in practice and of teaching students to implement EBM elements. They should be familiar with search strategies and evidence databases. The aim of this study is to compare the application of evidence databases by faculties and by residents with no training in this field.

Methods  Two hundred fifty‐seven faculties and first‐year residents of the Tabriz University of Medical Sciences filled out a valid self‐administered questionnaire on information‐seeking behaviour from August 2008 to June 2010. A chi‐square test was used to compare the variables.

Results  There were 52.1% of the respondents who were faculty members and 47.9% were residents. Only 8.7% used the Internet for their practice mostly. While Google was the most used resource, TRIP and Cochrane were less used. Significantly, the faculties used these resources more than the residents in both cases. Furthermore, two‐thirds of the participants were unfamiliar with medical subject headings (MeSH), and only 14.5% consulted a clinical librarian for help.

Conclusion  Significantly, clinicians used evidence databases and online resources minimally for their practice. Additionally, as the faculties used EBM resources more than the residents, this programme should be considered for inclusion in the curricula of medical schools.
Sustained use of a tool for lifestyle intervention implemented in primary health care: a 2‐year follow‐up
Authors: Carlfjord Siw , Lindberg Malou , Andersson Agneta
Published: February 2012

Rational, aims and objectives  Sustainability of new methods implemented in health care is one of the most central issues in addressing the gap between research and practice, but is seldom assessed in implementation studies. The aim of this study was to evaluate the implementation of a new tool for lifestyle intervention in primary health care (PHC) 2 years after the introduction, and assess if the implementation strategy used influenced sustainability.

Method  A computer‐based lifestyle intervention tool (CLT) was introduced at six PHC units in Sweden in 2008, using two implementation strategies: explicit and implicit. The main difference between the strategies was a 4‐week test period followed by a decision session, included in the explicit strategy. Evaluations were performed after 6, 9 and 24 months. After 24 months, the RE‐AIM framework was applied to assess and compare outcome according to strategy.

Results  A more positive outcome regarding reach, effectiveness, adoption and implementation in the explicit group could be almost completely attributed to one of the units. Maintenance was low and after 24 months, differences according to strategy were negligible.

Conclusion  After 24 months, the most positive outcomes regarding all RE‐AIM dimensions were found in one of the units where the explicit strategy was used. The explicit strategy per se had some effect on the dimension effectiveness, but was not associated with sustainability overall. Staff at the most successful unit earlier had positive expectations regarding the CLT and found it compatible with existing routines.