bluuebunny/crossref_metadata_2025 huggingface dataset:
«Was kann ich noch tun, was darf ich noch tun?» – Das ambivalente Erleben und der Schulungsbedarf von Patienten in der Frühphase nach einer Nierentransplantation
Authors: Wiederhold Dietmar , Langer Gero , Landenberger Margarete
Published: September 2009

Mit einem Anteil von etwa 27 % an den Nierenersatzverfahren ist die Nierentransplantation (NTx) mittlerweile eine etablierte Alternative zur Dialyse geworden. Eine Literaturanalyse ergab, dass über den Zustand, wie Patienten ihre neue Situation kurz nach der NTx erleben, und über den Schulungsbedarf noch wenig bekannt ist. Das Ziel dieser deskriptiv-phänomenologischen qualitativen Studie besteht darin, das Erleben von Patienten nach einer NTx zu beschreiben, noch bevor sie aus dem stationären Bereich entlassen werden, und welche Inhalte sich daraus für eine frühzeitige Patientenschulung ergeben. Als Methode wurden zehn semistrukturierte Interviews mit Patienten nach einer allogenen Nierentransplantation durchgeführt, die zum ersten Mal eine Organspende erhielten, eine stabile Transplantatfunktion aufwiesen und noch stationär behandelt wurden. Die aufgezeichneten und transkribierten Interviews wurden nach der Methode von Colaizzi ausgewertet. Die essenzielle Struktur des Erlebens von Patienten nach einer Nierentransplantation kann als ein «Hin-und-hergerissen-Sein» beschrieben werden. Das Ergebnis zeigt, dass im subjektiven Erleben der Patienten folgende sechs Themen im Vordergrund stehen: 1) Die Abwägung zwischen der Dialyse und der Transplantation, 2) die Auseinandersetzung mit dem Organ, 3) das Erleben der positiven Veränderungen sowie 4) des daraus resultierenden Selbstvertrauens und 5) das Erleben der trotz allem bestehenden Einschränkungen und Sorgen sowie 6) des nachfolgenden Unterstützungsbedarfes. Als Schlussfolgerung für die Praxis wird es für notwendig erachtet, eine aktiv zugehende und realitätsorientierende Schulung anzubieten, um alltagspraktische Handlungskompetenz sowie ein höheres Maß an Selbstbestimmung bei den Patienten erzeugen zu können.
Umgang mit sensiblen Themen in Interviews – Einblicke in das Forschungsprojekt «Harninkontinenz im Alltag der Betroffenen»
Authors: Hayder Daniela , Cintron Alexa , Schnell Martin W. , Schnepp Wilfried
Published: September 2009

Dieser Artikel wurde innerhalb eines Forschungsprojekts zum Thema Alltagserleben von Menschen mit Harninkontinenz entwickelt. Anhand von Literaturanalyse und Beispieldarstellungen einer laufenden Studie wird beschrieben und reflektiert, wie Forscher mit schwierigen, schambesetzten Themen im Interviewprozess umgehen können. Besondere Aufmerksamkeit wird dabei den ethischen Aspekten: informierte Zustimmung als prozesshaftes Geschehen, Arten, Ort und Phasen von Interviews sowie den Teilnahmegründen von befragten Personen geschenkt. In der Diskussion wird aufgezeigt, dass die Auseinandersetzung mit dem Führen von schwierigen und schambesetzten Themen in qualitativen Untersuchungen von besonderer Bedeutung im Sinne der Teilnehmergewinnung und zentraler Elemente qualitativer Gütekriterien wie Glaubwürdigkeit und Nachvollziehbarkeit ist, aber auch, um voneinander zu lernen.
Modeling the climatology of equatorial plasma bubbles observed by DMSP
Authors: Retterer J. M. , Gentile L. C.
Published: September 2009

Space environmental sensors on polar‐orbiting Defense Meteorological Satellite Program (DMSP) spacecraft occasionally encounter plasma density depletions when they cross the geomagnetic equator in the evening sector. These equatorial plasma bubbles (EPBs) are observed around the times and locations when equatorial spread F and radio scintillation phenomena tend to occur. The solar cycle, seasonal, and longitudinal variations in the observed frequency of these depletions (determined over the past 19 years) are indeed similar to those of scintillation. To test our understanding of EPB formation, we simulated the observations using PBMOD, a suite of first‐principle models of the ambient ionosphere and EPB formation, driven by climatological models for its input parameters such as the plasma drift velocity. Maps of the model calculations of EPB frequencies at 840 km as functions of season and longitude exhibit patterns similar to the DMSP observations, including the expected peaks in EPB frequency near the equinoxes, an additional winter peak in the American sector, a summer peak in the Pacific sector, and the proper trends with solar cycle phase. Adjusting the model to reproduce the DMSP EPB occurrence frequencies in detail will allow us to fine tune PBMOD and provides a means for using the DMSP data to enhance the empirical drivers for the Communication/Navigation Outage Forecasting System (C/NOFS) mission.
Integrating Geodetic and Geologic Data in Maps of Seismic Hazard: Workshop on Geodetic and Geologic Data Sets in the Northern Walker Lane; Reno, Nevada, 21–22 April 2009
Authors: Briggs Richard , Hammond William
Published: September 2009

The northern Walker Lane (NWL) comprises a complex network of active faults in northwestern Nevada and northeastern California. It is bounded on the west by the Sierra Nevada and on the east by the extensional Basin and Range Province. Because deformation is distributed across sets of discontinuous faults, it is particularly challenging to integrate geologic and geodetic data in the NWL to assess the region's seismic hazard. Recent Global Positioning System (GPS) measurements show that roughly 1 centimeter per year of relative displacement is accumulating across a relatively narrow zone, but it is not clear where or how much of this strain might ultimately be released in damaging earthquakes.
A comparison of sensation‐seeking between dental and biological science students
Authors: Mian O. , Kay E. J.
Published: September 2009

Aim:  The aim of this study was to compare sensation‐seeking behaviour amongst dental students and age‐, sex‐matched students studying for a standard 3‐year degree in biological sciences at the Manchester University.

Methods:  A total of 268 sensation‐seeking questionnaires were distributed to second‐ and third‐year male and female dental and biological science students, studying for a degree at the University of Manchester. Each questionnaire was scored against Zuckerman's sensation‐seeking scale.

Results:  A total of 268 questionnaires were distributed, 175 were returned. The return rate was 65%. The primary findings were:

Biological Science students were more sensation‐seeking in the dimensions of disinhibition and experience‐seeking than dental students (P < 0.05).

There was a significant gender bias in sensation‐seeking. Males were significantly more sensation‐seeking than females in both courses (P < 0.05).

Males in both courses had similar sensation‐seeking tendencies (NS).

Females in the biological sciences course were less inhibited than their dental counterparts (P < 0.05).

Conclusions:  There was a clear difference in sensation‐seeking within and between groups of dental students and students studying biological sciences.
Time and cohort changes in preventive practice among Mongolian dental students
Authors: Tseveenjav Battsetseg , Vehkalahti Miira , Murtomaa Heikki
Published: September 2009

To evaluate time and cohort changes in preventive practice of dental students in Mongolia, a questionnaire was distributed to all clinical‐year students in 2000 (n = 79) and in 2002 (n = 73) of the Dental School of the Mongolian National Medical University (MNMU). The questionnaire eliciting information on students' preventive care‐related practice and knowledge, oral self‐care (OSC) behaviour, and self‐perceived competency, was administered to the students. Further, cross‐sectional (between cohorts) comparisons to study changes over time and longitudinal (within‐cohort) comparisons to reveal changes resulting from professional dental education were carried out. Statistical evaluations included chi‐square test and linear regression model. Preventive practice of the students in 2002 tended to be better than that of their counterparts in the same study‐year in 2000. Preventive practice among the fifth‐year students improved significantly compared to that in their third year, except for counselling on nutrition. Survey‐year, study‐year, and knowledge of and self‐reported competency in preventive care explained 38% of the variation in reported preventive practice. Besides the positive changes revealed, preventive practice among the students could still be improved. Regarding these tasks, professional education should provide meaningful learning experience on modern caries‐preventive methods and dental community should support practice of preventive dentistry. A special programme could help to motivate the students to improve their own OSC.
Successional changes in bacterial communities during the development of black band disease on the reef coral, Montipora hispida
Authors: Sato Yui , Willis Bette L , Bourne David G
Published: September 2009

Black band disease (BBD) consists of a mat-forming microbial consortium that migrates across coral colonies causing rapid tissue loss. Although BBD-associated microbial communities have been well characterized, little is known regarding how these complex bacterial consortia develop. This study analyzed successional changes in microbial communities leading to the development of BBD. Long-term monitoring of tagged corals throughout outbreaks of BBD in the central Great Barrier Reef documented cyanobacterium-infected lesions, herein termed cyanobacterial patch(es) (CP), which were macroscopically distinct from BBD and preceded the onset of BBD in 19% of the cases. Dominant cyanobacteria within CP lesions were morphologically distinct from ones dominating BBD lesions. Clone libraries and terminal restriction fragment length polymorphism analysis confirmed shifts within cyanobacterial assemblages, from Blennothrix sp.-affiliated sequences dominating CP lesions, to Oscillatoria sp.-affiliated sequences, similar to those retrieved from other BBD samples worldwide, dominating BBD lesions. Bacterial 16S ribosomal RNA clone libraries also showed shifts in bacterial ribotypes during transitions from CP to BBD, with Alphaproteobacteria-affiliated sequences dominant in CP libraries, whereas gammaproteobacterial and cyanobacterial ribotypes were more abundant in BBD clone libraries. Sequences affiliated with organisms identified in sulfur cycling were commonly retrieved from lesions showing characteristic field signs of BBD. As high sulfide concentrations have been implicated in BBD-mediated coral tissue degradation, proliferation of a microbial community actively involved in sulfur cycling potentially contributes to the higher progression rates found for BBD compared with CP lesions. Results show how microbial colonization of indistinct lesions may facilitate a common coral disease with proven ecological effects on coral populations.
Dairy Protein Attenuates Weight Gain in Obese Rats Better Than Whey or Casein Alone
Authors: Eller Lindsay K. , Reimer Raylene A.
Published: September 2009

Evidence suggests that dietary calcium (Ca) and particularly dairy foods may attenuate weight gain and improve symptoms of the metabolic syndrome. The purpose of this study was to determine the effect of different Ca‐enriched dairy protein sources on the prevention of weight gain in Sprague‐Dawley diet‐induced obese (DIO) rats. Twelve week‐old DIO rats were assigned to one of eight ad libitum diets that varied in protein source (casein, whey, or complete dairy), Ca content (0.67 or 2.4%) and energy level (high fat/high sucrose (HFHS); or normal calorie density (NC)). Body composition and response to a meal tolerance test (MTT) were measured. Average daily caloric intake did not differ within normal or high energy density groups. At the end of 8 weeks, the dairy/HFHS/0.67% and 2.4% groups had significantly lower body weight than all other HFHS groups. The dairy/HFHS/0.67% and 2.4% groups also had lower body fat and greater lean mass expressed as a percent (P < 0.05). Homeostatic model assessment of insulin resistance (HOMAIR) was lowest for dairy/HFHS/0.67% and significantly different from whey/HFHS/0.67% and 2.4%. Independent of protein source, high Ca decreased plasma insulin at 30 min in the MTT more so than low Ca (P < 0.05). Hepatic sterol regulatory element–binding protein (SREBP1c) and peroxisome proliferator–activated receptor‐γ (PPARγ) mRNA was downregulated by dairy and whey compared to casein in the HFHS/0.67% diets. Overall, these data suggest that complete dairy improves body composition and insulin sensitivity to a greater extent than whey or casein alone.
Ultrasound Measurements of Visceral and Subcutaneous Abdominal Thickness to Predict Abdominal Adiposity Among Older Men and Women
Authors: Rolfe Ema De Lucia , Sleigh Alison , Finucane Francis M. , Brage Soren , Stolk Ronald P. , Cooper Cyrus , Sharp Stephen J. , Wareham Nicholas J. , Ong Ken K.
Published: September 2009

Accurate measures of visceral and abdominal subcutaneous fat are essential for investigating the pathophysiology of obesity. Classical anthropometric measures such as waist and hip circumference cannot distinguish between these two fat depots. Direct imaging methods such as computed tomography and magnetic resonance imaging (MRI) are restricted in large‐scale studies due to practical and ethical issues. We aimed to establish whether ultrasound is a valid alternative method to MRI for the quantitative assessment of abdominal fat depots in older individuals. The study population comprised 74 white individuals (41 men and 33 women, aged 67–76 years) participating in the Hertfordshire Birth Cohort Physical Activity trial. Anthropometry included height, weight, waist and hip circumferences. Abdominal fat was measured by ultrasound in two compartments: visceral fat defined as the depth from the peritoneum to the lumbar spine; and subcutaneous fat defined as the depth from the skin to the abdominal muscles and compared to reference measures by MRI (10‐mm single‐slice image). Ultrasound measures were positively correlated with MRI measures of visceral and subcutaneous fat (visceral: r = 0.82 and r = 0.80 in men and women, respectively; subcutaneous: r = 0.63 and 0.68 in men and women, respectively). In multiple regression models, the addition of ultrasound measures significantly improved the prediction of visceral fat and subcutaneous fat in both men and women over and above the contribution of standard anthropometric variables. In conclusion, ultrasound is a valid method to estimate visceral fat in epidemiological studies of older men and women when MRI and computed tomography are not feasible.
Language Features in a Mother and Daughter of a Chromosome 7;13 Translocation InvolvingFOXP2
Authors: Tomblin J. Bruce , O’Brien Marlea , Shriberg Lawrence D. , Williams Charles , Murray Jeff , Patil Shivanand , Bjork Jonathan , Anderson Steve , Ballard Kirrie
Published: September 2009

Purpose

The aims of this study were (a) to locate the breakpoints of a balanced translocation (7;13) within a mother (B) and daughter (T); (b) to describe the language and cognitive skills of B and T; and (c) to compare this profile with affected family members of the KE family who have a mutation withinFOXP2.

Method

The breakpoint locations for T and B were identified by use of fluorescent in situ hybridization analysis followed by DNA sequencing using long-range polymer chain reaction amplification methods. The cognitive and language characteristics were obtained via the use of standardized tests of intelligence, receptive and expressive vocabulary and sentence use, and a spontaneous language sample.

Results

The translocation breakpoints in T and B were found inFOXP2on chromosome 7 and inRFC3on chromosome 13. T and B’s pattern of relative strengths and weaknesses across their cognitive and language performance was found to be similar to descriptions of the affected KE family members.

Conclusions

Prior reports of individuals with chromosomal rearrangements ofFOXP2have emphasized their speech impairment. This study provides additional evidence that language—in particular, grammar—is likely to be influenced by abnormalities ofFOXP2function.
Behavior Predictors of Language Development Over 2 Years in Children With Autism Spectrum Disorders
Authors: Bopp Karen D. , Mirenda Pat , Zumbo Bruno D.
Published: September 2009

Purpose

This exploratory study examined predictive relationships between 5 types of behaviors and the trajectories of vocabulary and language development in young children with autism over 2 years.

Method

Participants were 69 children with autism assessed using standardized measures prior to the initiation of early intervention (T1) and 6 months (T2), 12 months (T3), and 24 months (T4) later. Growth curve modeling examined the extent to which behaviors at T1 and changes in behaviors between T1 and T2 predicted changes in development from T1 to T4.

Results

Regardless of T1 nonverbal IQ and autism severity, high scores for inattentive behaviors at T1 predicted lower rates of change in vocabulary production and language comprehension over 2 years. High scores for social unresponsiveness at T1 predicted lower rates of change in vocabulary comprehension and production and in language comprehension over 2 years. Scores for insistence on sameness behaviors, repetitive stereotypic motor behaviors, and acting-out behaviors at T1 did not predict the rate of change of any child measure over 2 years beyond differences accounted for by T1 autism severity and nonverbal IQ status.

Conclusions

The results are discussed with regard to their implications for early intervention and understanding the complex factors that affect developmental outcomes.
The Visual Search of an Illusory Figure: A Comparison between 6-Month-Old Infants and Adults
Authors: Bulf Hermann , Valenza Eloisa , Simion Francesca
Published: September 2009

The aim of the present study was to investigate how perceptual binding and selective attention operate during infants' and adults' visual search of an illusory figure. An eye-tracker system was used to test adults and infants in two conditions: illusory and non-illusory (real). In the illusory condition, a Kanizsa triangle was embedded among distractor pacmen which did not generate illusory contours. In the non-illusory condition, a real triangle was included in the same pacmen's display. The results showed that adults detected both the Kanizsa and the real figure automatically and without focal attention (experiment 1). In contrast, 6-month-old infants showed a pop-out effect only for the real figure (experiment 2). The failure of the illusory figure to trigger infants' attention was not due to infants' inability to perceive the illusory figure per se, as infants preferred the illusory figure over a non-illusory control stimulus in a classical preferential-looking task (experiment 3). Overall, these findings indicate that the illusory Kanizsa triangle triggers visual attention in adults, but not in infants, supporting evidence that at 6 months of age the binding processes involved in the perception of a Kanizsa figure do not operate in an adult-like manner.
What are the Uncurved Lines in Our Visual Field? A Fresh Look at Helmholtz's Checkerboard
Authors: Oomes Augustinus H J , Koenderink Jan J , van Doorn Andrea J , de Ridder Huib
Published: September 2009

What are the uncurved lines in our visual field? To answer this question, Helmholtz developed a geometrical model of line-curvature perception, and demonstrated it with his famous checkerboard pattern with pin-cushion distortion. He claimed it looked perfectly regular when viewed monocularly at close range while fixating the centre. Recently, doubts have been expressed whether this demonstration actually works. We tested twenty monocular, stationary observers who could adjust the distortion of a checkerboard pattern over a large range, from barrel-shaped to pin-cushion-shaped. Their task was to adjust the curvature of the edges of the checks such that the checkerboard looked straight and regular. In one condition they had to fixate the centre of the pattern, in another condition they were instructed to let their gaze wander. We found that most observers indeed perceived a pattern with pin-cushion distortion as undeformed, thereby seeing hyperbolic curves in the figure as uncurved lines in the visual field. They set a more strongly curved pattern in the fixation condition than in the free-viewing condition, as also described by Helmholtz. Interestingly, the effect is about half as strong as Helmholtz claimed. Furthermore, we found considerable inter-individual differences.
Global Shape Mediates the Perception of the Parts of a Picture, Not Vice Versa: Comments on “Ellipses on the Surface of a Picture” by Hammad et al (2008)
Authors: Maniatis Lydia M
Published: September 2009

Hammad et al (2008, Perception37 504–510) argue that the apparent shape of a drawn ellipse in the context of a drawn cylinder is mediated by the presence of local ‘depth cues’. I attempt to show that such features are incapable of constraining the shape of the whole pattern—and thus of its parts—in the manner claimed by the authors, and offer alternative explanations for their experimental outcome.
Evolution and Nucleosynthesis in Extremely Metal-Poor, Asymptotic Giant Branch Stars
Authors: Iwamoto Nobuyuki
Published: September 2009

We evolve extremely metal-poor ([Fe/H]≃–3), thermally pulsing Asymptotic Giant Branch (AGB) models with the mass range of 1–8 M⊙. The chemical yields ejected from the models are obtained by considering mass loss. We find that the 1- and 2-M⊙ AGB models are not affected by hot bottom burning (HBB). Nevertheless, they produce large amount of 7Li in an H-flash event. The occurrence of this event is associated with the ingestion of protons from the overlying H-rich envelope into the He convective shell driven by thermal pulse. The resulting 7Li abundances in the ejecta are higher than the primordial one predicted in Big-Bang nucleosynthesis. The efficient production of 7Li by the operation of HBB is also confirmed in the models of 4–8 M⊙. If these AGB stars have a low-mass companion, it is probable that mass loss from the primary AGB star brings the materials enriched in 7Li into the secondary star. This makes the surface composition of the secondary Li-rich. The formation of Li-rich stars, however, is strongly dependent on the mass loss history and binary separation. The nucleosynthesis for the other light nuclei is also calculated up to the end of the AGB phase. We find that the abundance patterns of the metal-poor stars CS 29528–041 and CS 29497–030 are well reproduced by yields from our AGB models.
Why Do Low-Mass Stars Become Red Giants?
Authors: Stancliffe Richard J. , Chieffi Alessandro , Lattanzio John C. , Church Ross P.
Published: September 2009

We revisit the problem of why stars become red giants. We modify the physics of a standard stellar evolution code in order to determine what does and what does not contribute to a star becoming a red giant. In particular, we have run tests to try to separate the effects of changes in the mean molecular weight and in the energy generation. The implications for why stars become red giants are discussed. We find that while a change in the mean molecular weight is necessary (but not sufficient) for a 1-M⊙ star to become a red giant, this is not the case in a star of 5 M⊙. It therefore seems that there may be more than one way to make a giant.
Co-Production of Light p-, s- and r-Process Isotopes in the High-Entropy Wind of Type II Supernovae
Authors: Farouqi K. , Kratz K.-L. , Pfeiffer B.
Published: September 2009

We have performed large-scale nucleosynthesis calculations within the high-entropy-wind (HEW) scenario of Type II supernovae. The primary aim was to constrain the conditions for the production of the classical ‘p-only’ isotopes of the light trans-Fe elements. We find, however, that for electron fractions in the range 0.458 ≤ Ye ≤ 0.478, sizeable abundances of p-, s- and r-process nuclei between 64Zn and 98Ru are coproduced in the HEW at low entropies (S ≤ 100) by a primary charged-particle process after an α-rich freezeout. With the above Ye–S correlation, most of the predicted isotopic abundance ratios within a given element, e.g. 64Zn(p)/70Zn(r) or 92Mo(p)/94Mo(p), as well as of neighboring elements, e.g. 70Ge(s + p)/74Se(p) or 74Se(p)/78Kr(p) agree with the observed Solar-System ratios. Taking the Mo isotopic chain as a particularly challenging example, we show that our HEW model can account for the production of all 7 stable isotopes, from ‘p-only’ 92Mo, via ‘s-only’ 96Mo up to ‘r-only’ 100Mo. Furthermore, our model is able to reproduce the isotopic composition of Mo in presolar SiC X-grains.
Sufficient symmetry conditions for Topological Quantum Order
Authors: Nussinov Zohar , Ortiz Gerardo
Published: September 2009

We prove sufficient conditions for Topological Quantum Order at zero and finite temperatures. The crux of the proof hinges on the existence of low-dimensional Gauge-Like Symmetries, thus providing a unifying framework based on a symmetry principle. These symmetries may be actual invariances of the system, or may emerge in the low-energy sector. Prominent examples of Topological Quantum Order display Gauge-Like Symmetries. New systems exhibiting such symmetries include Hamiltonians depicting orbital-dependent spin exchange and Jahn–Teller effects in transition metal orbital compounds, short-range frustrated Klein spin models, and p+ip superconducting arrays. We analyze the physical consequences of Gauge-Like Symmetries (including topological terms and charges) and show the insufficiency of the energy spectrum, topological entanglement entropy, maximal string correlators, and fractionalization in establishing Topological Quantum Order. General symmetry considerations illustrate that not withstanding spectral gaps, thermal fluctuations may impose restrictions on suggested quantum computing schemes. Our results allow us to go beyond standard topological field theories and engineer systems with Topological Quantum Order.
Niches and distributional areas: Concepts, methods, and assumptions
Authors: Soberón Jorge , Nakamura Miguel
Published: September 2009

Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue that conceptual clarity is enhanced by adopting restricted definitions of “niche” that enable operational definitions of basic concepts like fundamental, potential, and realized niches and potential and actual distributional areas. We apply these definitions to the question of niche conservatism, addressing what it is that is conserved and showing with a quantitative example how niche change can be measured. In this example, we display the extremely irregular structure of niche space, arguing that it is an important factor in understanding niche evolution. Many cases of apparently successful models of distributions ignore biotic factors: we suggest explanations to account for this paradox. Finally, relating the probability of observing a species to ecological factors, we address the issue of what objects are actually calculated by different niche modeling algorithms and stress the fact that methods that use only presence data calculate very different quantities than methods that use absence data. We conclude that the results of niche modeling exercises can be interpreted much better if the ecological and mathematical assumptions of the modeling process are made explicit.
A strategy for blood biomarker amplification and localization using ultrasound
Authors: D'Souza Aloma L. , Tseng Jeffrey R. , Pauly Kim Butts , Guccione Samira , Rosenberg Jarrett , Gambhir Sanjiv S. , Glazer Gary M.
Published: September 2009

Blood biomarkers have significant potential applications in early detection and management of various diseases, including cancer. Most biomarkers are present in low concentrations in blood and are difficult to discriminate from noise. Furthermore, blood measurements of a biomarker do not provide information about the location(s) where it is produced. We hypothesize a previously undescribed strategy to increase the concentration of biomarkers in blood as well as localize the source of biomarker signal using ultrasound energy directly applied to tumor cells. We test and validate our hypothesis in cell culture experiments and mouse tumor xenograft models using the human colon cancer cell line LS174T, while measuring the biomarker carcinoembryonic antigen (CEA) before and after the use of ultrasound to liberate the biomarker from the tumor cells. The results demonstrate that the application of low-frequency ultrasound to tumor cells causes a significant release of tumor biomarker, which can be measured in the blood. Furthermore, we establish that this release is specific to the direct application of the ultrasound to the tumor, enabling a method for localization of biomarker production. This work shows that it is possible to use ultrasound to amplify and localize the source of CEA levels in blood of tumor-bearing mice and will allow for a previously undescribed way to determine the presence and localization of disease more accurately using a relatively simple and noninvasive strategy.
Optimizing rotary processes in synthetic molecular motors
Authors: Geertsema Edzard M. , van der Molen Sense Jan , Martens Marco , Feringa Ben L.
Published: September 2009

We deal with the issue of quantifying and optimizing the rotation dynamics of synthetic molecular motors. For this purpose, the continuous four-stage rotation behavior of a typical light-activated molecular motor was measured in detail. All reaction constants were determined empirically. Next, we developed a Markov model that describes the full motor dynamics mathematically. We derived expressions for a set of characteristic quantities, i.e., the average rate of quarter rotations or “velocity,”
V
, the spread in the average number of quarter rotations,
D
, and the dimensionless Péclet number,
Pe
=
V/D
. Furthermore, we determined the rate of full, four-step rotations (Ω
eff
), from which we derived another dimensionless quantity, the “rotational excess,”
r.e
. This quantity, defined as the relative difference between total forward (Ω
+
) and backward (Ω
−
) full rotations, is a good measure of the unidirectionality of the rotation process. Our model provides a pragmatic tool to optimize motor performance. We demonstrate this by calculating
V
,
D
,
Pe
, Ω
eff
, and
r.e.
for different rates of thermal versus photochemical energy input. We find that for a given light intensity, an optimal temperature range exists in which the motor exhibits excellent efficiency and unidirectional behavior, above or below which motor performance decreases.
Universal architecture of bacterial chemoreceptor arrays
Authors: Briegel Ariane , Ortega Davi R. , Tocheva Elitza I. , Wuichet Kristin , Li Zhuo , Chen Songye , Müller Axel , Iancu Cristina V. , Murphy Gavin E. , Dobro Megan J. , Zhulin Igor B. , Jensen Grant J.
Published: September 2009

Chemoreceptors are key components of the high-performance signal transduction system that controls bacterial chemotaxis. Chemoreceptors are typically localized in a cluster at the cell pole, where interactions among the receptors in the cluster are thought to contribute to the high sensitivity, wide dynamic range, and precise adaptation of the signaling system. Previous structural and genomic studies have produced conflicting models, however, for the arrangement of the chemoreceptors in the clusters. Using whole-cell electron cryo-tomography, here we show that chemoreceptors of different classes and in many different species representing several major bacterial phyla are all arranged into a highly conserved, 12-nm hexagonal array consistent with the proposed “trimer of dimers” organization. The various observed lengths of the receptors confirm current models for the methylation, flexible bundle, signaling, and linker sub-domains in vivo. Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution.
Suppression of retinal degeneration in
Drosophila
by stimulation of ER-associated degradation
Authors: Kang Min-Ji , Ryoo Hyung Don
Published: September 2009

Mutations in the rhodopsin gene that disrupt the encoded protein's folding properties are a major cause of autosomal dominant retinitis pigmentosa (ADRP). This disease is faithfully modeled in
Drosophila
where similar mutations in the
ninaE
gene, encoding rhodopsin-1 (Rh-1), cause ER stress and dominantly trigger age-related retinal degeneration. In addition, mutant flies bearing certain
ninaE
alleles have dramatically reduced Rh-1 protein levels, but the underlying mechanism for this reduction and significance of its contribution to the ADRP phenotype remains unclear. To address this question, we specifically analyzed the role of
Drosophila
genes homologous to the known yeast and animal regulators of the ER-associated degradation (ERAD) pathway, a process that reduces levels of misfolded proteins in the ER through proteasomal degradation. We found that loss-of-function of these putative ERAD factors resulted in increased levels of Rh-1 in
ninaE
mutant flies. Conversely, in an ER stress assay where mutant or wild-type Rh-1 were overexpressed in developing imaginal discs beyond the ER protein folding capacity of those cells, co-expression of certain ERAD factors was sufficient to reduce Rh-1 protein levels and to completely suppress ER stress reporter activation. Significantly, those ERAD factors that specifically reduced misfolded Rh-1 in the imaginal disc assay also delayed age-related retinal degeneration caused by an endogenous
ninaE
allele, indicating that ERAD acts as a protective mechanism against retinal degeneration in the
Drosophila
model for ADRP. These results suggest that manipulation of ERAD may serve as a powerful therapeutic strategy against a number of diseases associated with ER stress.
Orthogonal analytical approaches to detect potential contaminants in heparin
Authors: Guerrini Marco , Zhang Zhenqing , Shriver Zachary , Naggi Annamaria , Masuko Sayaka , Langer Robert , Casu Benito , Linhardt Robert J. , Torri Giangiacomo , Sasisekharan Ram
Published: September 2009

Heparin is a widely used anticoagulant and antithrombotic agent. Recently, a contaminant, oversulfated chondroitin sulfate (OSCS), was discovered within heparin preparations. The presence of OSCS within heparin likely led to clinical manifestations, most prevalently, hypotension and abdominal pain leading to the deaths of several dozens of patients. Given the biological effects of OSCS, one continuing item of concern is the ability for existing methods to identify other persulfonated polysaccharide compounds that would also have anticoagulant activity and would likely elicit a similar activation of the contact system. To complete a more extensive analysis of the ability for NMR and capillary electrophoresis (CE) to capture a broader array of potential contaminants within heparin, we completed a systematic study of NMR, both mono- and bidimensional, and CE to detect both various components of sidestream heparin and their persulfonated derivatives. We show that given the complexity of heparin samples, and the requirement to ensure their purity and safety, use of orthogonal analytical techniques is effective at detecting an array of potential contaminants that could be present.
CCR7-mediated migration of developing thymocytes to the medulla is essential for negative selection to tissue-restricted antigens
Authors: Nitta Takeshi , Nitta Sachiko , Lei Yu , Lipp Martin , Takahama Yousuke
Published: September 2009

Immature double-positive thymocytes are generated in the thymic cortex, and on positive selection, are induced to differentiate into mature single-positive thymocytes and relocate to the medulla. CCR7 is pivotal for cortex-to-medulla migration of positively selected thymocytes, and CCR7-mediated migration to the medulla is essential for establishing central tolerance, thereby, preventing tissue-specific autoimmunity. However, it was unclear how CCR7-mediated migration to the medulla affects the establishment of self-tolerance. Here, we show that the deletion of thymocytes specific for insulin-promoter-driven tissue-restricted antigens (TRAs) is significantly impaired in CCR7- or CCR7-ligand-deficient mice. These results indicate that CCR7-mediated migration to the medulla contributes to the negative selection of TRA-reactive thymocytes.
Structural basis for Ca
2+
-independence and activation by homodimerization of tomato subtilase 3
Authors: Ottmann Christian , Rose Rolf , Huttenlocher Franziska , Cedzich Anna , Hauske Patrick , Kaiser Markus , Huber Robert , Schaller Andreas
Published: September 2009

Subtilases are serine proteases found in Archae, Bacteria, yeasts, and higher eukaryotes. Plants possess many more of these subtilisin-like endopeptidases than animals, e.g., 56 identified genes in
Arabidopsis
compared with only 9 in humans, indicating important roles for subtilases in plant biology. We report the first structure of a plant subtilase, SBT3 from tomato, in the active apo form and complexed with a chloromethylketone (cmk) inhibitor. The domain architecture comprises an N-terminal protease domain displaying a 132 aa protease-associated (PA) domain insertion and a C-terminal seven-stranded jelly-roll fibronectin (Fn) III-like domain. We present the first structural evidence for an explicit function of PA domains in proteases revealing a vital role in the homo-dimerization of SBT3 and in enzyme activation. Although Ca
2+
-binding sites are conserved and critical for stability in other subtilases, SBT3 was found to be Ca
2+
-free and its thermo stability is Ca
2+
-independent.
Discovery and validation of colonic tumor-associated proteins via metabolic labeling and stable isotopic dilution
Authors: Huttlin Edward L. , Chen Xiaodi , Barrett-Wilt Gregory A. , Hegeman Adrian D. , Halberg Richard B. , Harms Amy C. , Newton Michael A. , Dove William F. , Sussman Michael R.
Published: September 2009

The unique biology of a neoplasm is reflected by its distinct molecular profile compared with normal tissue. To understand tumor development better, we have undertaken a quantitative proteomic search for abnormally expressed proteins in colonic tumors fromApcMin/+(Min) mice. By raising pairs of Min and wild-type mice on diets derived from natural-abundance or15N-labeled algae, we used metabolic labeling to compare protein levels in colonic tumor versus normal tissue. Because metabolic labeling allows internal control throughout sample preparation and analysis, technical error is minimized as compared with in vitro labeling. Several proteins displayed altered expression, and a subset was validated via stable isotopic dilution using synthetic peptide standards. We also compared gene and protein expression among tumor and nontumor tissue, revealing limited correlation. This divergence was especially pronounced for species showing biological change, highlighting the complementary perspectives provided by transcriptomics and proteomics. Our work demonstrates the power of metabolic labeling combined with stable isotopic dilution as an integrated strategy for the identification and validation of differentially expressed proteins using rodent models of human disease.
Somatic evolutionary genomics: Mutations during development cause highly variable genetic mosaicism with risk of cancer and neurodegeneration
Authors: Frank Steven A.
Published: September 2009

Somatic mutations must happen often during development because of the large number of cell divisions to expand from a single-cell zygote to a full organism. A mutation in development carries forward to all descendant cells, causing genetic mosaicism. Widespread genetic mosaicism may influence diseases that derive from a few genetically altered cells, such as cancer. I show how to predict the expected amount of mosaicism and the variation in mosaicism between individuals. I then calculate the predicted risk of cancer derived from developmental mutations. The calculations show that a significant fraction of cancer in later life likely arises from developmental mutations in early life. In addition, much of the variation in the risk of cancer between individuals may arise from variation in the degree of genetic mosaicism set in early life. I also suggest that certain types of neurodegeneration, such as amyotrophic lateral sclerosis (ALS), may derive from a small focus of genetically altered cells. If so, then the risk of ALS would be influenced by developmental mutations and the consequent variation in genetic mosaicism. New technologies promise the ability to measure genetic mosaicism by sampling a large number of cellular genomes within an individual. The sampling of many genomes within an individual will eventually allow one to reconstruct the cell lineage history of genetic change in a single body. Somatic evolutionary genomics will follow from this technology, providing new insight into the origin and progression of disease with increasing age.
Hec1 Contributes to Mitotic Centrosomal Microtubule Growth for Proper Spindle Assembly through Interaction with Hice1
Authors: Wu Guikai , Wei Randy , Cheng Eric , Ngo Bryan , Lee Wen-Hwa
Published: September 2009

Previous studies have stipulated Hec1 as a conserved kinetochore component critical for mitotic control in part by directly binding to kinetochore fibers of the mitotic spindle and by recruiting spindle assembly checkpoint proteins Mad1 and Mad2. Hec1 has also been reported to localize to centrosomes, but its function there has yet to be elucidated. Here, we show that Hec1 specifically colocalizes with Hice1, a previously characterized centrosomal microtubule-binding protein, at the spindle pole region during mitosis. In addition, the C-terminal region of Hec1 directly binds to the coiled-coil domain 1 of Hice1. Depletion of Hice1 by small interfering RNA (siRNA) reduced levels of Hec1 in the cell, preferentially at centrosomes and spindle pole vicinity. Reduction of de novo microtubule nucleation from mitotic centrosomes can be observed in cells treated with Hec1 or Hice1 siRNA. Consistently, neutralization of Hec1 or Hice1 by specific antibodies impaired microtubule aster formation from purified mitotic centrosomes in vitro. Last, disruption of the Hec1/Hice1 interaction by overexpressing Hice1ΔCoil1, a mutant defective in Hec1 interaction, elicited abnormal spindle morphology often detected in Hec1 and Hice1 deficient cells. Together, the results suggest that Hec1, through cooperation with Hice1, contributes to centrosome-directed microtubule growth to facilitate establishing a proper mitotic spindle.
Density-dependent distribution of Atlantic cod (Gadus morhua) into deep waters on the Faroe Plateau
Authors: Steingrund Petur , Ofstad Lise H.
Published: September 2009

Steingrund, P., and Ofstad, L. H. 2010. Density-dependent distribution of Atlantic cod (Gadus morhua) into deep waters on the Faroe Plateau. – ICES Journal of Marine Science, 67: 102–110. The natural production of cod on the Faroe Plateau depends on the spatial overlap between cod and their prey. However, cod tend to be distributed shallower than the bulk of their prey fish, such as Norway pout and blue whiting. We used commercial and survey catch per unit effort (cpue) data to investigate the distribution of cod in the deep water (150–400 m) on the Faroe Plateau. Cod often move to deep water when they are 4 or 5 years old. The extent of this habitat shift was positively correlated with the total biomass of 3- or 4-year-old cod on the Faroe Plateau, whereas prey densities in the shallow and deep areas, respectively, seemed to have much less influence. Hence, year classes that were a year older than strong year classes were distributed deeper than normal, and vice versa. The cpue in deep water for all ages pooled was strongly correlated with the age 3–6 biomass of cod on the entire Faroe Plateau. These findings are discussed in relation to food utilization and management.
Elevations of lobster fishery groundlines in relation to their potential to entangle endangered North Atlantic right whales in the Bay of Fundy, Canada
Authors: Brillant Sean W. , Trippel Edward A.
Published: September 2009

Brillant, S. W., and Trippel, E. A. 2010. Elevations of lobster fishery groundlines in relation to their potential to entangle endangered North Atlantic right whales in the Bay of Fundy, Canada. – ICES Journal of Marine Science, 67: 355–364. Fishing gear is known to be a threat to North Atlantic right whales (Eubalaena glacialis), and groundlines used in the American lobster (Homarus americanus) trap fishery are hypothesized to be an integral component of entanglements that may, in some incidents, lead to mortality. This research measured the elevations above the seabed of 17 regular groundlines on commercially active lobster gear in the Bay of Fundy and evaluated several factors governing rope elevation profiles. Mean elevation was 1.6 m (s.d. = 0.9, n = 5968, range = 0.0–7.0 m). The hypothesis that groundline elevations were ≤1.0 m (predicted height of taut groundlines) was rejected (Fisher's C = 66.9, p < 0.01), as was the hypothesis that elevations were >3.0 m (approximate body height of a right whale; Fisher's C = 129.5, p < 0.01). The proportion of groundline elevations ≤1.0 m was 0.32, and that <3.0 m was 0.92. Groundline elevations were negatively related to tidal current velocity at the time of setting (p < 0.001, r2 = 0.33) and were closer to the seabed in deep than in shallow water (p < 0.05, r2 = 0.07). It is suggested that groundlines in the Bay of Fundy may not constitute a large part of the risk associated with the entanglement of right whales, because most lines remained below the elevation hypothesized to be a threat (3 m). We also identified factors within the control of fishers setting trawls that minimize groundline elevations.
Evicting cuckoo nestlings from the nest: a new anti-parasitism behaviour
Authors: Sato Nozomu J. , Tokue Kihoko , Noske Richard A. , Mikami Osamu K. , Ueda Keisuke
Published: September 2009

As avian brood parasitism usually reduces hosts' reproductive success, hosts often exhibit strong defence mechanisms. While such host defences at the egg stage (especially egg rejection) have been extensively studied, defence mechanisms at the nestling stage have been reported only recently. We found a previously unknown anti-parasitism behaviour in the large-billed Gerygone, which is a host species of the little bronze-cuckoo, a host-evicting brood parasite. The hosts forcibly pulled resisting nestlings out of their nests and dumped them. Although it has been suggested that defence mechanisms at the nestling stage may evolve when host defence at the egg stage is evaded by the parasite, the studied host seems to lack an anti-parasitism strategy at the egg stage. This suggests that the evolutionary pathway may be quite different from those of previously studied cuckoo–host systems. Future research on this unique system may give us new insights into the evolution of avian brood parasitism.
Life history, sexual dimorphism and ‘ornamental’ feathers in the mesozoic bird
Confuciusornis sanctus
Authors: Peters Winfried S. , Peters Dieter Stefan
Published: September 2009

The life history of
Confuciusornis sanctus
is controversial. Recently, the species’ body size spectrum was claimed to contradict osteohistological evidence for a rapid, bird-like development. Moreover, sexual size dimorphism was rejected as an explanation for the observed bimodal size distribution since the presence of elongated rectrices, an assumed ‘male’ trait, was uncorrelated with size. However, this interpretation (i) fails to explain the size spectrum of
C. sanctus
which is trimodal rather than bimodal, (ii) requires implausible neonate masses and (iii) is not supported by analogy with sexual dimorphisms in modern birds, in which elongated central rectrices are mostly sex-independent. Available information on
C. sanctus
is readily reconciled if we assume a bird-like life history, as well as a pronounced sexual size dimorphism and sexually isomorphic extravagant feathers as frequently observed in extant species.