bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre‐Bötzinger complex receives glutamatergic innervation from galaninergic and other retrotrapezoid nucleus neurons
Authors: Bochorishvili Genrieta , Stornetta Ruth L. , Coates Melissa B. , Guyenet Patrice G.
Published: September 2011

The retrotrapezoid nucleus (RTN) contains CO2‐responsive neurons that regulate breathing frequency and amplitude. These neurons (RTN‐Phox2b neurons) contain the transcription factor Phox2b, vesicular glutamate transporter 2 (VGLUT2) mRNA, and a subset contains preprogalanin mRNA. We wished to determine whether the terminals of RTN‐Phox2b neurons contain galanin and VGLUT2 proteins, to identify the specific projections of the galaninergic subset, to test whether RTN‐Phox2b neurons contact neurons in the pre‐Bötzinger complex, and to identify the ultrastructure of these synapses. The axonal projections of RTN‐Phox2b neurons were traced by using biotinylated dextran amine (BDA), and many BDA‐ir boutons were found to contain galanin immunoreactivity. RTN galaninergic neurons had ipsilateral projections that were identical with those of this nucleus at large: the ventral respiratory column, the caudolateral nucleus of the solitary tract, and the pontine Kölliker‐Fuse, intertrigeminal region, and lateral parabrachial nucleus. For ultrastructural studies, RTN‐Phox2b neurons (galaninergic and others) were transfected with a lentiviral vector that expresses mCherry almost exclusively in Phox2b‐ir neurons. After spinal cord injections of a catecholamine neuron‐selective toxin, there was a depletion of C1 neurons in the RTN area; thus it was determined that the mCherry‐positive terminals located in the pre‐Bötzinger complex originated almost exclusively from the RTN‐Phox2b (non‐C1) neurons. These terminals were generally VGLUT2‐immunoreactive and formed numerous close appositions with neurokinin‐1 receptor‐ir pre‐Bötzinger complex neurons. Their boutons (n = 48) formed asymmetric synapses filled with small clear vesicles. In summary, RTN‐Phox2b neurons, including the galaninergic subset, selectively innervate the respiratory pattern generator plus a portion of the dorsolateral pons. RTN‐Phox2b neurons establish classic excitatory glutamatergic synapses with pre‐Bötzinger complex neurons presumed to generate the respiratory rhythm. J. Comp. Neurol. 520:1047–1061, 2012. © 2011 Wiley Periodicals, Inc.
Neuropsychiatric symptoms in geriatric patients admitted to skilled nursing facilities in nursing homes for rehabilitation after stroke: a longitudinal multicenter study
Authors: Buijck Bianca I , Zuidema Sytse U , Spruit‐van Eijk Monica , Geurts Alexander CH , Koopmans Raymond TCM
Published: September 2011

Objective

To investigate the prevalence and course of neuropsychiatric symptoms (NPS) in geriatric patients admitted to skilled nursing facilities (SNFs) for rehabilitation after stroke.

Methods

This was a longitudinal multicenter study within 15 SNFs in the Netherlands. NPS were assessed in 145 patients with stroke through the Neuropsychiatric Inventory–Nursing Home version (NPI‐NH) with measurements on admission and at discharge. The prevalence and course of NPS were described in terms of cumulative prevalence (symptoms either on admission or at discharge), conversion (only symptoms at discharge), remission (only symptoms on admission), and persistence (symptoms both on admission and at discharge) for patients who were discharged to an independent living situation within one year after admission and patients who had to stay in the SNF for long term care.

Results

Eighty percent had a first‐ever stroke and 74% could be successfully discharged. Overall, the most common NPS were depression (33%), eating changes (18%), night‐time disturbances (19%), anxiety (15%), irritability (12%), and disinhibition (12%). One year after admission, the patients who were still in the SNF showed significantly more hallucinations (p = 0.016), delusions (p = 0.016), agitation (p = 0.004), depression (p = 0.000), disinhibition (p = 0.004), irritability (p = 0.018), and night‐time disturbances (p = 0.001) than those who had been discharged.

Discussion

The overall prevalence of NPS in this study was lower than reported by other studies in different settings. There was a high prevalence of NPS in patients that could not be successfully discharged.

Conclusions

The findings suggest that NPS should be optimally treated to improve outcome of rehabilitation. Copyright © 2011 John Wiley & Sons, Ltd.
Functionally distinct regions for spatial processing and sensory motor integration in the planum temporale
Authors: Isenberg A. Lisette , Vaden Kenneth I. , Saberi Kourosh , Muftuler L. Tugan , Hickok Gregory
Published: September 2011

There has been much debate recently over the functional role played by the planum temporale (PT) within the context of the dorsal auditory processing stream. Some studies indicate that regions in the PT support spatial hearing and other auditory functions, whereas others demonstrate sensory‐motor response properties. This multifunctionality has led to the claim that the PT is performing a common computational pattern matching operation, then routing the signals (spatial, object, sensory‐motor) into an appropriate processing stream. An alternative possibility is that the PT is functionally subdivided with separate regions supporting various functions. We assess this possibility using a within subject fMRI block design. DTI data were also collected to examine connectivity. There were four auditory conditions: stationary noise, moving noise, listening to pseudowords, and shadowing pseudowords (covert repetition). Contrasting the shadow and listen conditions should activate regions specific to sensory‐motor processes, while contrasting the stationary and moving noise conditions should activate regions involved in spatial hearing. Subjects (N= 16) showed greater activation for shadowing in left posterior PT, area Spt, when the shadow and listen conditions were contrasted. The motion vs. stationary noise contrast revealed greater activation in a more medial and anterior portion of left PT. Seeds from these two contrasts were then used to guide the DTI analysis in an examination of connectivity via streamline tractography, which revealed different patterns of connectivity. Findings support a heterogeneous model of the PT, with functionally distinct regions for sensory‐motor integration and processes involved in auditory spatial perception. Hum Brain Mapp 33:2453–2463, 2012. © 2011 Wiley Periodicals, Inc.
Tissue engineering of annulus fibrosus using electrospun fibrous scaffolds with aligned polycaprolactone fibers
Authors: Koepsell Laura , Remund Tyler , Bao Jing , Neufeld Daniel , Fong Hao , Deng Ying
Published: September 2011

In tissue engineering, it is important to fabricate a three‐dimensional scaffold that resemble the extracellular matrix (ECM) and topographical appearance of native tissue. The aim of this study is to test the hypothesis that varying microstructures of electrospun fibrous scaffolds by manipulating the relative degree of fiber alignment would influence the behaviors of porcine annulus fibrosus cells. Five types of electrospun fibrous scaffolds with polycaprolactone fibers having random or partially aligned arrangements have been prepared and investigated. The scaffold microstructures have been examined, and in vitro experiments have been carried out to assess cell‐material interaction, cell proliferation, and ECM production. The results indicate that the scaffold with oriented fibers provides strong guidance to the cell orientation and ECM distribution. In addition, albeit the tensile moduli of electrospun fibrous scaffolds are lower than that of native tissue, they are comparable to those reported in literature; hence, the constructs cultured with optimized conditions including the scaffold material selection and dynamic mechanical conditioning would have the potential to possess the moduli closer to that of native tissue. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2011.
Aberrant supplementary motor complex and limbic activity during motor preparation in motor conversion disorder
Authors: Voon Valerie , Brezing Christina , Gallea Cecile , Hallett Mark
Published: September 2011

Conversion disorder (CD) is characterized by unexplained neurological symptoms presumed related to psychological issues. The main hypotheses to explain conversion paralysis, characterized by a lack of movement, include impairments in either motor intention or disruption of motor execution, and further, that hyperactive self‐monitoring, limbic processing or top‐down regulation from higher order frontal regions may interfere with motor execution. We have recently shown that CD with positive abnormal or excessive motor symptoms was associated with greater amygdala activity to arousing stimuli along with greater functional connectivity between the amygdala and supplementary motor area. Here we studied patients with such symptoms focusing on motor initiation. Subjects performed either an internally or externally generated 2‐button action selection task in a functional MRI study. Eleven CD patients without major depression and 11 age‐ and gender‐matched normal volunteers were assessed. During both internally and externally generated movement, conversion disorder patients relative to normal volunteers had lower left supplementary motor area (SMA) (implicated in motor initiation) and higher right amygdala, left anterior insula, and bilateral posterior cingulate activity (implicated in assigning emotional salience). These findings were confirmed in a subgroup analysis of patients with tremor symptoms. During internally versus externally generated action in CD patients, the left SMA had lower functional connectivity with bilateral dorsolateral prefrontal cortices. We propose a theory in which previously mapped conversion motor representations may in an arousing context hijack the voluntary action selection system, which is both hypoactive and functionally disconnected from prefrontal top‐down regulation. © 2011 Movement Disorder Society
Aerosol characterization at the sub‐Arctic site Andenes (69°N, 16°E), by the analysis of columnar optical properties
Authors: Rodríguez E. , Toledano C. , Cachorro V. E. , Ortiz P. , Stebel K. , Berjón A. , Blindheim S. , Gausa M. , de Frutos A. M.
Published: September 2011

Since 2002 sun photometer measurements were carried out at Andenes (Norway), in the ALOMAR observatory, to investigate the aerosol optical properties in the European sub‐Arctic region. From 2002 to 2005 measurements were performed during summer campaigns. Since 2006 a Cimel sun photometer has been permanently deployed at the site. The instrument is part of the Red Ibérica de medida de Aerosoles Atmosféricos aerosol robotic network (RIMA–AERONET). The aerosol optical depth (AOD) and the Ångström exponent (AE) were analysed to investigate the aerosol content, type and seasonality in this sub‐Arctic location. Back trajectories were used to provide information about the air‐mass origin, especially for cases of moderate turbidity produced by long‐range transported aerosols from mid‐latitudes. The AOD was in general very low, with mean AOD units of 0.10 ± 0.05 and characteristics of clean continental or marine type aerosols (AE = 1.2 ± 0.4). The lower mean monthly values were obtained in February (0.04) and November (0.06), and the maximum was found in May (0.12). Episodes of long‐range transported aerosol occurred at any time when observations were made, with the highest frequency in May, and originated in central and eastern Europe. The associated air masses transported anthropogenic pollution, biomass burning aerosols and in some cases also Saharan dust. A characterization of microphysical properties was performed, showing that the fine mode dominated the particle size distribution, with an average fine mode volume fraction of 0.69. In Arctic regions, enhanced levels of aerosol concentrations occur frequently in late winter and spring due Arctic haze. In our study such hazy periods were not observed at Andenes. Copyright © 2011 Royal Meteorological Society
GROUNDWATER INFLUENCES ON THE DISTRIBUTION AND ABUNDANCE OF RIVERINE SMALLMOUTH BASS, MICROPTERUS DOLOMIEU, IN PASTURE LANDSCAPES OF THE MIDWESTERN USA
Authors: Brewer Shannon K.
Published: September 2011

This study examined how spring‐flow (SF) contributions to streams related to the distribution and abundance of smallmouth bass Micropterus dolomieu in a predominately pasture landscape in Missouri, USA. Stream segments (N = 13) with similar landscape characters were classified by SF volume into high SF (HSF) or low SF (LSF) groups. The densities of smallmouth bass, channel unit (CU) use and temperature‐selection patterns were assessed for several life stages and frequency distributions for age 0 fish. More smallmouth bass were present in stream segments with HSF influence. Age 0 fish were twice as likely to be present in HSF stream segments. Older age classes were present in stream reaches independent of SF contribution. For all age classes, the use of particular CUs did not depend on SF influence. All age classes were more likely to be present in pools than other CUs. Microhabitat temperature selection differed among age classes. Age 0 fish selected warmer temperatures with a gradual shift towards cooler temperatures for older age classes. The length frequency of age 0 fish was skewed towards larger individuals in streams with limited SF influence, whereas the length frequency in HSF stream segments was skewed towards smaller individuals. The benefits of significant groundwater via SF influence seem to be related to increased hatch or survival of age 0 fish and the availability of optimal temperatures for adult smallmouth bass growth. Thermal refugia and stable flows provided by springs should be recognised for their biological potential to provide suitable habitat as climate change and other land‐use alterations increase temperature regimes and alter flow patterns. Published in 2011 by John Wiley & Sons, Ltd.
Measuring knowledge integration: Validation of four‐year assessments
Authors: Liu Ou Lydia , Lee Hee‐Sun , Linn Marcia C.
Published: September 2011

Science education needs valid, authentic, and efficient assessments. Many typical science assessments primarily measure recall of isolated information. This paper reports on the validation of assessments that measure knowledge integration ability among middle school and high school students. The assessments were administered to 18,729 students in five states. Rasch analyses of the assessments demonstrated satisfactory item fit, item difficulty, test reliability, and person reliability. The study showed that, when appropriately designed, knowledge integration assessments can be balanced between validity and reliability, authenticity and generalizability, and instructional sensitivity and technical quality. Results also showed that, when paired with multiple‐choice items and scored with an effective scoring rubric, constructed‐response items can achieve high reliabilities. Analyses showed that English language learner status and computer use significantly impacted students' science knowledge integration abilities. Students who took the assessment online, which matched the format of content delivery, performed significantly better than students who took the paper‐and‐pencil version. Implications and future directions of research are noted, including refining curriculum materials to meet the needs of diverse students and expanding the range of topics measured by knowledge integration assessments. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 48: 1079–1107, 2011
Science motivation questionnaire II: Validation with science majors and nonscience majors
Authors: Glynn Shawn M. , Brickman Peggy , Armstrong Norris , Taasoobshirazi Gita
Published: September 2011

From the perspective of social cognitive theory, the motivation of students to learn science in college courses was examined. The students—367 science majors and 313 nonscience majors—responded to the Science Motivation Questionnaire II, which assessed five motivation components: intrinsic motivation, self‐determination, self‐efficacy, career motivation, and grade motivation. Exploratory and confirmatory factor analyses provided evidence of questionnaire construct validity. The motivation components, especially self‐efficacy, were related to the students' college science grade point averages. The science majors scored higher than the nonscience majors on all of the motivation components. Among both science majors and nonscience majors, men had higher self‐efficacy than women, and women had higher self‐determination than men. The findings suggest that the questionnaire is a valid and efficient tool for assessing components of students' motivation to learn science in college courses, and that the components play a role in students' science achievement. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 48: 1159–1176, 2011
Right hepatectomy using Glissonean pedicle transection method with anterior approach (with video)
Authors: Katagiri Satoshi , Ariizumi Shun‐ichi , Kotera Yoshihito , Takahashi Yutaka , Yamamoto Masakazu
Published: September 2011

Right hepatectomy for hepatocellular carcinoma is the most common major operation in liver surgery; therefore, liver surgeons should know the fundamental surgical concept and techniques of the Glissonean pedicle approach. A J‐shaped or reversed T laparotomy is performed in the right subcostal area. The Glissonean pedicle approach is performed at the hepatic hilus. In this approach, the right anterior and posterior Glissonean pedicles are encircled and ligated without liver dissection. The right hepatic artery, right portal vein and right hepatic duct in the hepatoduodenal ligament should be divided if the Glissonean pedicles cannot be approached easily. After confirming the border between the right and left liver, the liver parenchyma is dissected from the anterior surface of the liver to the anterior surface of the inferior vena cava (IVC). The V5 and V8 middle hepatic veins are divided and liver dissection is performed along the main middle hepatic vein. Finally, the anterior surface of the IVC and the trunk of the right hepatic vein are identified in the liver. This approach is widely known as the anterior approach described by Lai and Fan (World J Surg 20:314–8, 1996). However, this procedure had already been reported by Takasaki et al. (Shoukakigeka 7:1545–51, 1984) but since they did not report this procedure in English, their pioneering work on the anterior approach has not been recognized. The liver hanging maneuver described by Belghiti et al. (J Am Coll Surg 193:109–111, 2001) is also useful in right hepatectomy. Among the techniques used in right hepatectomy, the Glissonean pedicle approach, the anterior approach and the liver hanging maneuver are considered to be the most important.
Early versus delayed laparoscopic cholecystectomy after percutaneous transhepatic gallbladder drainage
Authors: Han In Woong , Jang Jin‐Young , Kang Mee Joo , Lee Kyoung Bun , Lee Seung Eun , Kim Sun‐Whe
Published: September 2011

Background

Percutaneous transhepatic gallbladder drainage (PTGBD) is a procedure to resolve acute cholecystitis (AC). It may decrease the technical difficulty of laparoscopic cholecystectomy (LC) and thus may facilitate successful surgery when a patients’ condition improves. However, the timing of LC after PTGBD remains controversial.

Methods

From 2004 to 2010, cholecystectomy after PTGBD was performed in 67 patients with AC. Group I members underwent LC within 72 h of PTGBD (n = 21), whereas group II members underwent LC at more than 72 h after PTGBD (n = 46).

Results

The open conversion rate was similar in the two groups. The perioperative complication rate was higher in group I than in group II, but with marginal significance (19.0 vs. 4.3%;p = 0.07). Mean operative time was longer in group I than in group II (79.3 ± 25.3 vs. 53.7 ± 45.3 min;p = 0.02). However, overall hospital stay was shorter in group I than in group II, but with marginal significance (10.8 ± 4.5 vs. 14.7 ± 9.3 days;p = 0.08).

Conclusions

Pros and cons were well balanced between the two groups. Decisions on the timing of cholecystectomy after PTGBD should be made based on considerations of patient condition, hospital facilities, and surgical experience.
An Emerging Action Science of Social Settings
Authors: Seidman Edward
Published: September 2011

Seymour B. Sarason's innovative ideas have influenced much of my work. These same ideas—in particular, his concepts of social settings, behavioral and programmatic regularities, and the universe of alternatives—also serve as the foundation for an action science of social settings. Questions regarding theory, measurement, intervention, and research design and data analysis are central to the development of this action science, and there have been recent innovations in each of these areas. However, future challenges remain for the field. We must continue to move forward to advance an action science of social settings and make a real difference in people's lives.
Bromodomains as therapeutic targets
Authors: Muller Susanne , Filippakopoulos Panagis , Knapp Stefan
Published: September 2011

Acetylation of lysine residues is a post-translational modification with broad relevance to cellular signalling and disease biology. Enzymes that ‘write’ (histone acetyltransferases, HATs) and ‘erase’ (histone deacetylases, HDACs) acetylation sites are an area of extensive research in current drug development, but very few potent inhibitors that modulate the ‘reading process’ mediated by acetyl lysines have been described. The principal readers of ɛ-N-acetyl lysine (Kac) marks are bromodomains (BRDs), which are a diverse family of evolutionary conserved protein-interaction modules. The conserved BRD fold contains a deep, largely hydrophobic acetyl lysine binding site, which represents an attractive pocket for the development of small, pharmaceutically active molecules. Proteins that contain BRDs have been implicated in the development of a large variety of diseases. Recently, two highly potent and selective inhibitors that target BRDs of the BET (bromodomains and extra-terminal) family provided compelling data supporting targeting of these BRDs in inflammation and in an aggressive type of squamous cell carcinoma. It is likely that BRDs will emerge alongside HATs and HDACs as interesting targets for drug development for the large number of diseases that are caused by aberrant acetylation of lysine residues.
The Danish Cartoon Controversy and the Challenges of Multicultural Politics
Authors: Downs Donald
Published: September 2011

Jytte Klausen's The Cartoons That Shook the World offers an interesting political science account of the Danish cartoon controversy and of a broader set of tensions between multiculturalism, civility, and freedom of expression. The book is also a fascinating case study of how political science can itself become the object of dispute, due to Yale University Press' decision to publish the book without any reproductions of the controversial cartoons.

We have thus asked a range of political scientists to comment on the Danish cartoon imbroglio, the book's analysis of it, and the controversy over the book itself.—Jeffrey C. Isaac, Editor
The false promise of the better argument
Authors: Hanrieder Tine
Published: September 2011

Effective argumentation in international politics is widely conceived as a matter of persuasion. In particular, the ‘logic of arguing’ ascribes explanatory power to the ‘better argument’ and promises to illuminate the conditions of legitimate normative change. This article exposes the self-defeating implications of the Habermasian symbiosis between the normative and the empirical force of arguments. Since genuine persuasion is neither observable nor knowable, its analysis critically depends on what scholars consider to be the better argument. Seemingly, objective criteria such as universality only camouflage such moral reification. The paradoxical consequence of an explanatory concept of arguing is that moral discourse is no longer conceptualized as an open-ended process of contestation and normative change, but has recently been recast as a governance mechanism ensuring the compliance of international actors with pre-defined norms. This dilemma can be avoided through a positivist reification of valid norms, as in socialization research, or by adopting a critical and emancipatory focus on the obstacles to true persuasion. Still, both solutions remain dependent on the ‘persuasion vs. coercion’ problem that forestalls an insight into successful justificatory practices other than rational communication. The conclusion therefore pleas for a pragmatic abstention from better arguments and points to the insights to be gained from pragmatist norms research in sociology.
Attentional Capture by Change in Direct Gaze
Authors: Yokoyama Takemasa , Ishibashi Kazuya , Hongoh Yuki , Kita Shinichi
Published: September 2011

In three experiments, we examined whether change in direct gaze was better at capturing visuospatial attention than non-direct gaze change. Also, change in direct gaze can be categorised into two types: ‘look toward’, which means gaze changing to look toward observers, and ‘look away’, which means gaze changing to look away from observers. Thus, we also investigated which type of change in direct gaze was more effective in capturing visuospatial attention. Each experiment employed a change-detection task, and we compared detection accuracy between ‘look away’, ‘look toward’, and non-direct gaze-change conditions. In experiment 1, we found detection advantage for change in direct gaze relative to non-direct gaze change, and for ‘look toward’ compared with ‘look away’. In experiment 2, we conducted control experiments to exclude possibilities of simple motion detection and geometrical factors of eyes, and confirm detection advantage in experiment 1 only occurred when the stimuli were processed as faces and gazes. In experiment 3, we manipulated the head deviation, but the results in experiment 1 persisted despite changes in head orientation. The findings establish that individuals are sensitive to change in direct relative to non-direct gaze change, and ‘look toward’ compared with ‘look away’.
Inhibitor of apoptosis-stimulating protein of p53 (iASPP) prevents senescence and is required for epithelial stratification
Authors: Notari Mario , Hu Ying , Koch Sofia , Lu Min , Ratnayaka Indrika , Zhong Shan , Baer Caroline , Pagotto Anna , Goldin Robert , Salter Victoria , Candi Eleonora , Melino Gerry , Lu Xin
Published: September 2011

Inhibitor of apoptosis-stimulating protein of p53 (iASPP) is the most ancient member of the ASPP family of proteins and an evolutionarily conserved inhibitor of p53. iASPP is also a binding partner and negative regulator of p65RelA. Because p65RelA and the p53 family members often have opposite effects in controlling cell fate, it is important to understand the cellular context in which iASPP can regulate their activities. To address this question and to study the biological importance of iASPP in vivo, we generated a transgenic mouse in which iASPP expression is controlled by the Cre/loxP recombination system. We observed that iASPP is able to prevent premature cellular senescence in mouse embryonic fibroblasts. iASPP loss resulted in increased differentiation of primary keratinocytes both in vitro and in vivo. In stratified epithelia, nuclear iASPP often colocalized with p63 in the nuclei of basal keratinocytes. Consistent with this, iASPP bound p63 and inhibited the transcriptional activity of both TAp63α and ΔNp63α in vitro and influenced the expression level of p63-regulated genes such as
loricrin
and
involucrin
in vivo. In contrast, under the same conditions, p65RelA was frequently expressed as a cytoplasmic protein in the suprabasal layers of stratified epithelia and rarely colocalized with nuclear iASPP. Thus, iASPP is likely to control epithelial stratification by regulating p63's transcriptional activity, rather than p65RelA's. This study identifies iASPP as an inhibitor of senescence and a key player in controlling epithelial stratification.
Reconciling molecular phylogenies with the fossil record
Authors: Morlon Hélène , Parsons Todd L. , Plotkin Joshua B.
Published: September 2011

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.
Neuronal circuits underlying acute morphine action on dopamine neurons
Authors: Jalabert Marion , Bourdy Romain , Courtin Julien , Veinante Pierre , Manzoni Olivier J. , Barrot Michel , Georges François
Published: September 2011

Morphine is a highly potent analgesic with high addictive potential in specific contexts. Although dopamine neurons of the ventral tegmental area (VTA) are widely believed to play an essential role in the development of drug addiction, neuronal circuits underlying morphine action on dopamine neurons have not been fully elucidated. Here we combined in vivo electrophysiology, tract-tracing experiments, and targeted neuronal inactivation to dissect a neural circuit for acute morphine action on dopamine neurons in rats. We found that in vivo, morphine targets the GABAergic tail of the VTA, also called the rostromedial tegmental nucleus, to increase the firing of dopamine neurons through the activation of VTA μ opioid receptors expressed on tail of the VTA/rostromedial tegmental nucleus efferents. Our data also reveal that in the absence of VTA glutamatergic tone, there is no morphine-induced activation of dopamine neurons. These results define the anatomical organization and functional role of a neural circuit for acute morphine action on dopamine neurons.
Thaumarchaeotes abundant in refinery nitrifying sludges express
amoA
but are not obligate autotrophic ammonia oxidizers
Authors: Mußmann Marc , Brito Ivana , Pitcher Angela , Sinninghe Damsté Jaap S. , Hatzenpichler Roland , Richter Andreas , Nielsen Jeppe L. , Nielsen Per Halkjær , Müller Anneliese , Daims Holger , Wagner Michael , Head Ian M.
Published: September 2011

Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all
amoA
-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying
amoA
were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently,
14
CO
2
fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal
amoA
, and very weak in situ labeling of crenarchaeol after addition of
13
CO
2
, was independent of the addition of ammonium. These data demonstrate that some
amoA
-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs.
E339…R416 salt bridge of nucleoprotein as a feasible target for influenza virus inhibitors
Authors: Shen Yu-Fang , Chen Yu-Hou , Chu Shao-Ying , Lin Meng-I , Hsu Hua-Ting , Wu Pei-Yu , Wu Chao-Jung , Liu Hui-Wen , Lin Fu-Yang , Lin Gialih , Hsu Pang-Hung , Yang An-Suei , Cheng Yih-Shyun E. , Wu Ying-Ta , Wong Chi-Huey , Tsai Ming-Daw
Published: September 2011

The nucleoprotein (NP) of the influenza virus exists as trimers, and its tail-loop binding pocket has been suggested as a potential target for antiinfluenza therapeutics. The possibility of NP as a drug target was validated by the recent reports that nucleozin and its analogs can inhibit viral replication by inducing aggregation of NP trimers. However, these inhibitors were identified by random screening, and the binding site and inhibition mechanism are unclear. We report a rational approach to target influenza virus with a new mechanism—disruption of NP–NP interaction. Consistent with recent work, E339A, R416A, and deletion mutant Δ402–428 were unable to support viral replication in the absence of WT NP. However, only E339A and R416A could form hetero complex with WT NP, but the complex was unable to bind the RNA polymerase, leading to inhibition of viral replication. These results demonstrate the importance of the E339…R416 salt bridge in viral survival and establish the salt bridge as a sensitive antiinfluenza target. To provide further support, we showed that peptides encompassing R416 can disrupt NP–NP interaction and inhibit viral replication. Finally we performed virtual screening to target E339…R416, and some small molecules identified were shown to disrupt the formation of NP trimers and inhibit replication of WT and nucleozin-resistant strains. This work provides a new approach to design antiinfluenza drugs.
Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines
Authors: Somwar Romel , Erdjument-Bromage Hediye , Larsson Erik , Shum David , Lockwood William W. , Yang Guangli , Sander Chris , Ouerfelli Ouathek , Tempst Paul J. , Djaballah Hakim , Varmus Harold E.
Published: September 2011

We previously described four small molecules that reduced the growth of lung adenocarcinoma cell lines with either epidermal growth factor receptor (EGFR) or KRAS mutations in a high-throughout chemical screen. By combining affinity proteomics and gene expression analysis, we now propose superoxide dismutase 1 (SOD1) as the most likely target of one of these small molecules, referred to as lung cancer screen 1 (LCS-1). siRNAs againstSOD1slowed the growth of LCS-1 sensitive cell lines; conversely, expression of aSOD1cDNA increased proliferation of H358 cells and reduced sensitivity of these cells to LCS-1. In addition, SOD1 enzymatic activity was inhibited in vitro by LCS-1 and two closely related analogs. These results suggest that SOD1 is an LCS-1–binding protein that may act in concert with mutant proteins, such as EGFR and KRAS, to promote cell growth, providing a therapeutic target for compounds like LCS-1.
Parkin, a p53 target gene, mediates the role of p53 in glucose metabolism and the Warburg effect
Authors: Zhang Cen , Lin Meihua , Wu Rui , Wang Xiaowen , Yang Bo , Levine Arnold J. , Hu Wenwei , Feng Zhaohui
Published: September 2011

Regulation of energy metabolism is a novel function of p53 in tumor suppression.
Parkin (PARK2)
, a Parkinson disease-associated gene, is a potential tumor suppressor whose expression is frequently diminished in tumors. Here Parkin was identified as a p53 target gene that is an important mediator of p53's function in regulating energy metabolism. The human and mouse
Parkin
genes contain functional p53 responsive elements, and p53 increases the transcription of Parkin in both humans and mice. Parkin contributes to the function of p53 in glucose metabolism; Parkin deficiency activates glycolysis and reduces mitochondrial respiration, leading to the Warburg effect. Restoration of Parkin expression reverses the Warburg effect in cells. Thus, Parkin deficiency is a novel mechanism for the Warburg effect in tumors. Parkin also contributes to the function of p53 in antioxidant defense. Furthermore, Parkin deficiency sensitizes mice to γ-irradiation-induced tumorigenesis, which provides further direct evidence to support a role of Parkin in tumor suppression. Our results suggest that as a novel component in the p53 pathway, Parkin contributes to the functions of p53 in regulating energy metabolism, especially the Warburg effect, and antioxidant defense, and thus the function of p53 in tumor suppression.
Efficacy of Single‐Suture Incision Closures in Tagged Juvenile Chinook Salmon Exposed to Simulated Turbine Passage
Authors: Boyd James W. , Deters Katherine A. , Brown Richard S. , Eppard M. Brad
Published: September 2011

Reductions in the size of acoustic transmitters implanted in migrating juvenile salmonids have resulted in the use of a shorter incision—one that may warrant only a single suture for closure. However, it is not known whether a single suture will sufficiently hold the incision closed when fish are decompressed and when outward pressure is placed on the surgical site during turbine passage through hydroelectric dams. The objective of this study was to evaluate the effectiveness of single‐suture incision closures on five response variables in juvenile Chinook salmon Oncorhynchus tshawytscha that were subjected to simulated turbine passage. An acoustic transmitter (0.43 g in air) and a passive integrated transponder tag (0.10 g in air) were implanted in each fish; the 6‐mm incisions were closed with either one suture or two sutures. After exposure to simulated turbine passage, none of the fish exhibited expulsion of transmitters. In addition, the percentage of fish with suture tearing, incision tearing, or mortal injury did not differ between treatments. Expulsion of viscera through the incision was higher among fish that received one suture (12%) than among fish that received two sutures (1%). The higher incidence of visceral expulsion through single‐suture incisions warrants concern. Consequently, for cases in which tagged juvenile salmonids may be exposed to turbine passage, we do not recommend the use of one suture to close 6‐mm incisions associated with acoustic transmitter implantation.
The Dreams of Shaykh Safi al-Din and Safavid Historical Writing
Authors: Quinn Sholeh A.
Published: September 2011

In their narratives of the rise of the Safavid dynasty, many Safavid chroniclers include accounts of either one or two dreams of Shaykh Safi al-Din (1253-1334), founder of the Safavid order. A historiographical reading of the various renditions of the dreams serves several important purposes: it gives insight into the historical methodology of the Safavid chroniclers, it indicates changing religious perspectives in Safavid Iran, and it demonstrates the patterns of political legitimacy that evolved from the reign of Shah Isma'il (1501-1524) to the reign of Shah ‘Abbas I (1587-1629). This paper will thus examine six versions of Shaykh Safi's dreams and show how interpretations of the dreams changed over time, based on evolving religious and political attitudes.

Scholars have long been aware of the importance of dreams in Islamic history, and have outlined the many religious and political functions of dream episodes in historical and philosophical texts.
An Exile's Sense of Place: Three Poems by Nader Naderpur
Authors: Naderpur Nader
Published: September 2011

Crucial to an exile's perception of his or her identity is a sense of place and the exile's relationship with it. This has been one of the most productive sources of imagery that has shaped by Nader Naderpur's poetry since he left Iran in 1981. In much of his poetry of exile, strong emotions stand out: rage at the powers in Iran that caused him to go into exile, grief at what happened to his country as well as to himself, half-acknowledged acceptance of exile, tinged with nostalgia. The feelings aroused by increasing age and the pain of seemingly endless separation from Iran combine to make him contemplate an obscure future in a land without sun. Running through all these poems is the poet's sense of place. As exile, Naderpur inhabits two places at once: an inner, remembered place, now evoked in ever-more nostalgic images, and an outer, physical place where he dwells and passes his days.
Doing more with less: the Justice and Development Party (AKP), Turkish elections, and the uncertain future of Turkish politics
Authors: Fabbe Kristin
Published: September 2011

The outcome of Turkey's June 2011 elections temporarily quelled – though by no means entirely put to rest – growing concern over the creeping autocratic tendencies of the ruling Justice and Development Party (AKP). To ensure that democracy remains durable, the AKP must now clearly demonstrate that it is willing to shun heavy-handed tactics and instead engage the opposition in a genuine dialog regarding important matters of constitutional change, especially those related to individual rights and identity issues. A slide toward autocracy has been an all-too-common pitfall in Turkish politics over the years. Should it so choose, the AKP is well poised to break the cycle at this critical juncture in Turkish politics.
Effects of Visual Similarity on Serial Report and Item Recognition
Authors: Avons S.E. , Mason Andrea
Published: September 2011

Four experiments examined the sensitivity of visual short-term memory to visual pattern similarity. Experiment 1 showed that immediate serial memory for novel visual patterns was sensitive to similarity. Using an item reocgnition task, Experiment 2 showed that subjects learned the descriptions of sets of similar and dissimilar patterns at the same rate. But repeated presentations of patterns in a serial memory task again showed a marked and persistent similarity effect (Experiment 3). The final experiment showed the visual similarity effect in serial memory for patterns that had been previously learned. The results show that (a) serial memory for patterns is sensitive to visual similarity, (b) the visual similarity effect is not due to perceptual confusions but originates in memory, (c) there is a clear dissociation between item and order errors, and (d) the visual similarity effect survives articulatory suppression. Visual serial order memory and verbal serial recall appear to share several of these properties, suggesting that the same constraints govern serial memory in each modality. Implications for the understanding of short-term memory are discussed.
Type I interferon is selectively required by dendritic cells for immune rejection of tumors
Authors: Diamond Mark S. , Kinder Michelle , Matsushita Hirokazu , Mashayekhi Mona , Dunn Gavin P. , Archambault Jessica M. , Lee Hsiaoju , Arthur Cora D. , White J. Michael , Kalinke Ulrich , Murphy Kenneth M. , Schreiber Robert D.
Published: September 2011

Cancer immunoediting is the process whereby the immune system suppresses neoplastic growth and shapes tumor immunogenicity. We previously reported that type I interferon (IFN-α/β) plays a central role in this process and that hematopoietic cells represent critical targets of type I IFN’s actions. However, the specific cells affected by IFN-α/β and the functional processes that type I IFN induces remain undefined. Herein, we show that type I IFN is required to initiate the antitumor response and that its actions are temporally distinct from IFN-γ during cancer immunoediting. Using mixed bone marrow chimeric mice, we demonstrate that type I IFN sensitivity selectively within the innate immune compartment is essential for tumor-specific T cell priming and tumor elimination. We further show that mice lacking IFNAR1 (IFN-α/β receptor 1) in dendritic cells (DCs; Itgax-Cre+Ifnar1f/f mice) cannot reject highly immunogenic tumor cells and that CD8α+ DCs from these mice display defects in antigen cross-presentation to CD8+ T cells. In contrast, mice depleted of NK cells or mice that lack IFNAR1 in granulocytes and macrophage populations reject these tumors normally. Thus, DCs and specifically CD8α+ DCs are functionally relevant targets of endogenous type I IFN during lymphocyte-mediated tumor rejection.
Development of membrane stress measurement equipment for membrane structures: proposal of measuring method and its experimental verification
Authors: Jin Sang-Wook , Ohmori Hiroshi
Published: September 2011

One of the most important issues in keeping membrane structures in good condition is to maintain the proper tension distribution over the membrane. However, it is not easy to determine the real stress level in the membrane quantitatively after completion of the structures. Fluttering by strong wind or ponding caused by rain water may cause severe damage to the membrane structure itself. Therefore, it is very important to know the magnitude of existing stress in membrane structures for their maintenance and management. In this paper, the authors propose a new method that can measure membrane stress using sound waves, and hold experimental tests of membrane stress measurement that use the sound external excitation with sine wave and white noise.
Triviality of fibers for Misiurewicz parameters in the exponential family
Authors: Benini Anna
Published: September 2011

We consider the family of holomorphic maps

e
z

+
c

e^z+c

and show that fibers of postsingularly finite parameters are trivial. This can be considered as the first and simplest class of non-escaping parameters for which we can obtain results about triviality of fibers in the exponential family.
A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans
Authors: Linhart Chaim , Halperin Yonit , Darom Amir , Kidron Shahar , Broday Limor , Shamir Ron
Published: September 2011

In this study we report on a novel pair of cis-regulatory motifs in promoter sequences of the nematode Caenorhabditis elegans. The motif pair exhibits extraordinary genomic traits: The order and the orientation of the two motifs are highly specific, and the distance between them is almost always one of two frequent distances. In contrast, the sequence between the motifs is variable across occurrences. Thus, the motif pair constitutes a nearly combinatorial sequence configuration. We further show that this module is conserved among, and unique to, the entire Caenorhabditis genus. By analyzing several gene expression data sets, our data suggest that this motif pair may function in germline development, oogenesis, and early embryogenesis. Finally, we verify that the motifs are indeed functional cis-regulatory elements using reporter constructs in transgenic C. elegans.