bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo commitment and functional tissue regeneration using human embryonic stem cell-derived mesenchymal cells
Authors: Hwang Nathaniel S. , Varghese Shyni , Lee H. Janice , Zhang Zijun , Ye Zhaohui , Bae Jongwoo , Cheng Linzhao , Elisseeff Jennifer
Published: December 2008

Development of clinically relevant regenerative medicine therapies using human embryonic stem cells (hESCs) requires production of a simple and readily expandable cell population that can be directed to form functional 3D tissue in an in vivo environment. We describe an efficient derivation method and characterization of mesenchymal stem cells (MSCs) from hESCs (hESCd-MSCs) that have multilineage differentiation potential and are capable of producing fat, cartilage, and bone in vitro. Furthermore, we highlight their in vivo survival and commitment to the chondrogenic lineage in a microenvironment comprising chondrocyte-secreted morphogenetic factors and hydrogels. Normal cartilage architecture was established in rat osteochondral defects after treatment with chondrogenically-committed hESCd-MSCs. In view of the limited available cell sources for tissue engineering applications, these embryonic-derived cells show significant potential in musculoskeletal tissue regeneration applications.
The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA
Authors: Ha Sung Chul , Kim Doyoun , Hwang Hye-Yeon , Rich Alexander , Kim Yang-Gyun , Kim Kyeong Kyu
Published: December 2008

Mammalian DAI (DNA-dependent activator of IFN-regulatory factors), an activator of the innate immune response, senses cytosolic DNA by using 2 N-terminal Z-DNA binding domains (ZBDs) and a third putative DNA binding domain located next to the second ZBD. Compared with other previously known ZBDs, the second ZBD of human DAI (hZβ
DAI
) shows significant variation in the sequence of the residues that are essential for DNA binding. In this article, the crystal structure of the hZβ
DAI
/Z-DNA complex reveals that hZβ
DAI
has a similar fold to that of other ZBDs, but adopts an unusual binding mode for recognition of Z-DNA. A residue in the first β-strand rather than residues in the β-loop contributes to DNA binding, and part of the (α3) recognition helix adopts a 3
10
helix conformation. The role of each residue that makes contact with DNA was confirmed by mutational analysis. The 2 ZBDs of DAI can together bind to DNA and both are necessary for full B-to-Z conversion. It is possible that binding 2 DAIs to 1 dsDNA brings about dimerization of DAI that might facilitate DNA-mediated innate immune activation.
Direct role of structural dynamics in electron-lattice coupling of superconducting cuprates
Authors: Carbone Fabrizio , Yang Ding-Shyue , Giannini Enrico , Zewail Ahmed H.
Published: December 2008

The mechanism of electron pairing in high-temperature superconductors is still the subject of intense debate. Here, we provide direct evidence of the role of structural dynamics, with selective atomic motions (buckling of copper–oxygen planes), in the anisotropic electron-lattice coupling. The transient structures were determined using time-resolved electron diffraction, following carrier excitation with polarized femtosecond heating pulses, and examined for different dopings and temperatures. The deformation amplitude reaches 0.5% of the
c
axis value of 30 Å when the light polarization is in the direction of the copper–oxygen bond, but its decay slows down at 45°. These findings suggest a selective dynamical lattice involvement with the anisotropic electron–phonon coupling being on a time scale (1–3.5 ps depending on direction) of the same order of magnitude as that of the spin exchange of electron pairing in the high-temperature superconducting phase.
Exploring the abuse of robots
Authors: Bartneck Christoph , Hu Jun
Published: December 2008

Robots have been introduced into our society, but their social role is still unclear. A critical issue is whether the robot’s exhibition of intelligent behaviour leads to the users’ perception of the robot as being a social actor, similar to the way in which people treat computers and media as social actors. The first experiment mimicked Stanley Milgram’s obedience experiment, but on a robot. The participants were asked to administer electric shocks to a robot, and the results show that people have fewer concerns about abusing robots than about abusing other people. We refined the methodology for the second experiment by intensifying the social dilemma of the users. The participants were asked to kill the robot. In this experiment, the intelligence of the robot and the gender of the participants were the independent variables, and the users’ destructive behaviour towards the robot the dependent variable. Several practical and methodological problems compromised the acquired data, but we can conclude that the robot’s intelligence had a significant influence on the users’ destructive behaviour. We discuss the encountered problems and suggest improvements. We also speculate on whether the users’ perception of the robot as being “sort of alive” may have influenced the participants’ abusive behaviour.
Revisiting the DARPA communicator data using conversation analysis
Authors: Wallis Peter
Published: December 2008

The state of the art in human computer conversation leaves something to be desired and, indeed, talking to a computer can be down-right annoying. This paper describes an approach to identifying “opportunities for improvement” in these systems by looking for abuse in the form of swear words. The premise is that humans swear at computers as a sanction and, as such, swear words represent a point of failure where the system did not behave as it should. Having identified where things went wrong, we can work backward through the transcripts and, using conversation analysis (CA) work out how things went wrong. Conversation analysis is a qualitative methodology and can appear quite alien — indeed unscientific — to those of us from a quantitative background. The paper starts with a description of Conversation analysis in its modern form, and then goes on to apply the methodology to transcripts of frustrated and annoyed users in the DARPA Communicator project. The conclusion is that there is at least one species of failure caused by the inability of the Communicator systems to handle mixed initiative at the discourse structure level. Along the way, I hope to demonstrate that there is an alternative future for computational linguistics that does not rely on larger and larger text corpora.
Prosthetic gods
Authors: Cavanagh Thomas B.
Published: December 2008

Computer-facilitated self-service technologies (SSTs) have become ubiquitous in today’s consumer-focused world. Yet, few human–computer interactions elicit such dramatically polarizing emotional reactions from users as those involving SSTs. ATMs, pay-at-the-pump gas stations, and self-scanning retail registers tend to produce both passionate supporters and critics. While negative comments often center on unpleasant personal user experiences, the actual “abuse” related to such systems is really much deeper and more complex. SSTs carry with them a number of potentially insidious consequences, including the exploitation of consumers as uncompensated temporary workers; the sacrifice of our inherent humanity to delegate both skills and cognition to electronic helpers; and the enabling of a new type of posthuman consumer identity, where each transaction is completed by a cyborg entity constructed of the human on one side and the electronic mechanism on the other. As a result, we may ultimately lose the boundary between the human and the machine.
Naturally occurring gestures in a human–robot teaching scenario
Authors: Otero Nuno , Nehaniv Chrystopher L. , Syrdal Dag Sverre , Dautenhahn Kerstin
Published: December 2008

This paper describes our general framework for the investigation of how human gestures can be used to facilitate the interaction and communication between humans and robots. Two studies were carried out to reveal which “naturally occurring” gestures can be observed in a scenario where users had to explain to a robot how to perform a home task. Both studies followed a within-subjects design: participants had to demonstrate how to lay a table to a robot using two different methods — utilizing only gestures or gestures and speech. The first study enabled the validation of the COGNIRON coding scheme for human gestures in Human–Robot Interaction (HRI). Based on the data collected in both studies, an annotated video corpus was produced and characteristics such as frequency and duration of the different gestural classes have been gathered to help capture requirements for the designers of HRI systems. The results from the first study regarding the frequencies of the gestural types suggest an interaction between the order of presentation of the two methods and the actual type of gestures produced. However, the analysis of the speech produced along with the gestures did not reveal differences due to ordering of the experimental conditions. The second study expands the issues addressed by the first study: we aimed at extending the role of the interaction partner (the robot) by introducing some positive acknowledgement of the participants’ activity. The results show no significant differences in the distribution of gestures (frequency and duration) between the two explanation methods, in contrast to the previous study. Implications for HRI are discussed focusing on issues relevant for the design of the robot’s communication skills to support the interaction loop with humans in home scenarios.
Lexical representation of second language words
Authors: Schwartz Ana I. , Yeh Li-Hao , Shaw Moira P.
Published: December 2008

The goal of the present study was to examine whether cross-language activation of a bilingual’s native language influences the processing of lexical ambiguity within a second language. Highly proficient Spanish-English bilinguals performed a semantic verification task in which sentence frames were followed by the presentation of the final word of the sentence (the prime word). Participants then decided whether a follow-up target word was related to the meaning of the sentence. On critical trials the sentences ended in a semantically ambiguous word that was either a cognate with Spanish (e.g., novel), or a noncognate control matched on frequency and length (e.g., fast). The preceding sentence context biased the subordinate meaning (e.g., new; refrain from eating) and targets were related to the irrelevant, dominant meaning (e.g., BOOK; SPEED). Mean reaction times and error rates were greater when the prime words were ambiguous cognates than when they were ambiguous noncognates. This suggests that the semantic representations from the native language were coactivated and increased the lexical competition from the shared, dominant meaning. Implications for second language vocabulary acquisition and current models of reading are discussed.
Cross-language lexical processes and inhibitory control
Authors: Linck Jared A. , Hoshino Noriko , Kroll Judith F.
Published: December 2008

Many recent studies demonstrate that both languages are active when bilinguals and second language (L2) learners are reading, listening, or speaking one language only. The parallel activity of the two languages has been hypothesized to create competition that must be resolved. Models of bilingual lexical access have proposed an inhibitory control mechanism to effectively limit attention to the intended language (e.g., Green, 1998). Critically, other recent research suggests that a lifetime of experience as a bilingual negotiating the competition across the two languages confers a set of benefits to cognitive control processes more generally (e.g., Bialystok, Craik, Klein, & Viswanathan, 2004). However, few studies have examined the consequences of individual differences in inhibitory control for performance on language processing tasks. The goal of the present work was to determine whether there is a relation between enhanced executive function and performance for L2 learners and bilinguals on lexical comprehension and production tasks. Data were analyzed from two studies involving a range of language processing tasks, a working memory measure, and also the Simon task, a nonlinguistic measure of inhibitory control. The results demonstrate that greater working memory resources and enhanced inhibitory control are related to a reduction in cross-language activation in a sentence context word naming task and a picture naming task, respectively. Other factors that may be related to inhibitory control are identified. The implications of these results for models of bilingual lexical comprehension and production are discussed.
NT‐proBNP is increased in healthy pregnancies compared to non‐pregnant controls
Authors: FRANZ MAXIMILIAN B. , FRANZ MAXIMILIAN B. , ANDREAS MARTIN , SCHIESSL BARBARA , ZEISLER HARALD , NEUBAUER ANNA , KASTL STEFAN P. , HESS GEORG , RHOMBERG FRANZISKA , ZDUNEK DIETMAR , MAURER GERALD , SCHLEMBACH DIETMAR , HEINZE GEORG , SZEKERES THOMAS , GOTTSAUNER‐WOLF MICHAEL
Published: December 2008

Serum concentrations of the amino‐terminal pro‐B‐type natriuretic peptide (NT‐proBNP) may be used to monitor cardiac function during pregnancy but normal values are not established for this purpose. Therefore, we investigated NT‐proBNP in normotensive healthy pregnancies compared to a non‐pregnant control group. Serum NT‐proBNP was measured in 94 normotensive, healthy pregnant women (32±6 years) every five weeks beginning from 12th gestational week (GW) in a longitudinal study and compared to a non‐pregnant control group of 521 women (32±7 years). Pooled median serum NT‐proBNP levels (25th; 75th percentile) were significantly higher in pregnant women compared to non‐pregnant women (56 (33; 95) pg/ml vs. 38 (22; 62) pg/ml (p<0.001)). NT‐proBNP increased during pregnancy to 73 (51; 124) pg/ml in the 11+6 to 15+6 GW (p<0.001). However, NT‐proBNP levels from 23+0 GW towards term were comparable to non‐pregnant controls. NT‐proBNP is significantly elevated in healthy pregnancies until mid‐pregnancy. As preeclampsia and gestational hypertension are associated with increased NT‐proBNP, our results have to be considered in future diagnostic approaches using NT‐proBNP for these pathologic conditions.
Stillbirths and infant deaths among migrants in industrialized countries
Authors: GISSLER MIKA , ALEXANDER SOPHIE , MACFARLANE ALISON , SMALL RHONDA , STRAY‐PEDERSEN BABILL , ZEITLIN JENNIFER , ZIMBECK MEGAN , GAGNON ANITA ,   FOR THE ROAM COLLABORATION (REPRODUCTIVE OUTCOMES AND MIGRATION: AN INTERNATIONAL RESEARCH COLLABORATION)
Published: December 2008

Introduction. The relation of migration to infant outcomes is unclear. There are studies which show that some migrant groups have similar or even better outcomes than those from the receiving country. Equally, raised risk of adverse outcomes for other migrant groups has been reported. Objective. We sought to determine (1) if migrants in western industrialized countries have consistently higher risks of stillbirth, neonatal mortality, or infant mortality, (2) if there are migrant sub‐groups at potentially higher risk, and (3) what might be the explanations for any risk differences found. Design and Setting. Systematic review of the literature on perinatal health outcomes among migrants in western industrialized countries. Methods and Main outcome measures. Drawing on a larger systematic review of perinatal outcomes and migration, we reviewed studies including mortality outcomes (stillbirths and infant deaths). Results. Eligible studies gave conflicting results. Half (53%) reported worse mortality outcomes, one third (35%) reported no differences and a few (13%) reported better outcomes for births to migrants compared to the receiving country population. Refugees were the most vulnerable group. For non‐refugees, non‐European migrants in Europe and foreign‐born blacks in the United States had the highest excess mortality. In general, adjustment of background factors did not explain the increased mortality rate among migrants. Regarding causes of death, higher preterm birth rates explained the increased mortality figures among some migrant groups. The increased mortality from congenital anomalies may be related to restricted access to screening, but also to differing attitudes to screening and termination of pregnancy. Conclusions. Mortality risk among babies born to migrants is not consistently higher, but appears to be greatest among refugees, non‐European migrants to Europe, and foreign‐born blacks in the US. To understand this variation better, more information is needed about migrant background, such as length of time in receiving country and receiving country language fluency. Additional data on demographic, health care, biological, medical, and socioeconomic risk factors should be gathered and analyzed in greater detail.
Effectiveness of subcutaneous injection of sterile water to the lower back for pain relief in labor
Authors: KUSHTAGI PRALHAD , BHANU BASVANAHALLI THIMMEGOUDA
Published: December 2008

The analgesic efficacy of subcutaneous injection of sterile water compared to isotonic saline was investigated in a randomized, controlled study on a total of 100 women in the active phase of labor and who complained of low back pain. Pain perception was rated on a numerical rating scale before and at 10 and 45 minutes after the injection. The initial pain score was the same in both groups and pain relief was expressed by both groups irrespective of the solution injected, but the sterile water group had significantly higher relief scores compared to those receiving saline. This was not influenced by maternal age, parity, education, body mass index, cervical dilatation at intervention or fetal size, suggesting that subcutaneous injection of sterile water to the lower back provides relief from back pain during labor.
Cause without a Rebel: Kazakhstan's Unionist Nationalism in the USSR and CIS
Authors: Hale Henry E.
Published: December 2008

Why would elites or masses in an ethnically distinct region ever opt for “alien rule” over national independence? While separatist movements tend to create the most drama and make the most headlines, mass media and most scholarly accounts pay far less attention to ethnic groups opting to stay in a union state dominated by other groups. Yet such unionist groups are surely more numerous than the separatist ones. Indeed, in the neighborhood of almost every separatist region in a given multi-ethnic state, one can find one or more unionist groups, such as the Yoruba during Nigeria's Biafran Civil War, the Ingush as Chechnya battled the Russian Federation, and the Kannadigas at the peak of Kashmir's struggle for independence from India. Sometimes, unionist groups advocate political integration despite seeming to have every reason to seek secession. Such groups are neglected by analysts only at great cost, because it is precisely these groups that are likely to hold the key to understanding how distinct groups can come to live together in peace.
The Role of Islam in Chechen National Identity
Authors: Swirszcz Joanna
Published: December 2008

Uncovering the importance of Islam in Chechen national identity is not necessarily difficult. Alexei Malashenko has noted that Chechen identity today cannot be considered outside the context of Islamic tradition. Chechnya today is not an independent Muslim state. Its embracing of Islam came about during a time of colonization, when Chechens were struggling to halt Russian encroachment on their lands. Many works pertaining to Islam in Chechnya suggest that, at the time of Russian advancement in the eighteenth century, most Chechens were “nominally” Muslim. This has been attributed to the geographic isolation of the Caucasus. While the rugged mountainous landscape and thick forests which cover the region provided protection from invaders, it also hindered interaction among the various mountain peoples as well as the strength of outside religious influence. Soon after their defeat to the tsarist Russians, the Bolshevik Revolution occurred and Chechens spent the following 80 years under Soviet rule. After the fall of the Soviet Union, the Republic of Chechnya declared independence alongside the full-fledged Soviet Socialist Republics, though their independence was not recognized by the UN. The Chechen victory over the Russian Federation in the first war in 1994–1996 has been considered a remarkable military defeat. However, a weak economy, high unemployment, and criminality caused the young nation to fall into a state of lawlessness and radicalism, eventually causing it to suffer a defeat to the Russians in the second war, which began in 1999. The present day is characterized by exhaustion and a desire for peace, a desire that ultimately has meant deference to Russian rule.
Social Capital, Civic Engagement and the Performance of Local Self-Government in Azerbaijan
Authors: Hasanov Rafail Musa oglu
Published: December 2008

Eight years of municipal reform in Azerbaijan reflect a lack of social capital in communities. Without building social capital, achieving effectiveness of governance, as well as political stability and economic progress, in the country appears bleak.

This paper seeks to study factors such as the set of informal values, tolerance, social trust, norms and networks of voluntary associations which contribute to social capital formation within the communities of Azerbaijan. As a way of exploring the problem, we have focused on one specific area of governance-the construction of infrastructural services (i.e. roads, housing and communal services, water supply, and sewerage) in Baku, the country's capital, and in Khachmaz and Masalli, both of which are districts of Azerbaijan. The aim is to highlight and clarify the effectiveness of municipal governments in different communities of Azerbaijan from the standpoint of civic engagement and its role in this process.
Association of lumbar arterial stenosis with low back symptoms: A cross-sectional study using two-dimensional time-of-flight magnetic resonance angiography
Authors: Korkiakoski A. , Niinimäki J. , Karppinen J. , Korpelainen R. , Haapea M. , Natri A. , Tervonen O.
Published: December 2008

Background: Recent studies indicate that diminished blood flow may cause low back symptoms and intervertebral disc degeneration.

Purpose: To explore the association between lumbar arterial stenosis as detected by two-dimensional time-of-flight magnetic resonance angiography (2D TOF-MRA) and lumbar pain symptoms in an occupational cohort of middle-aged Finnish males.

Material and Methods: 228 male subjects aged 36 to 55 years (mean 47 years) were imaged with 2D TOF-MRA. Additionally, 20 randomly selected subjects were scanned with contrast-enhanced MRA (ceMRA). In each subject, the first (L1) to fourth (L4) segmental lumbar arteries were evaluated for lumbar artery stenosis using a dichotomic scale. One subject was excluded because of poor image quality, reducing the study population to 227 subjects. Logistic regression analysis was used to evaluate the association between arterial stenosis in 2D TOF-MRA and low back pain and sciatica symptoms (intensity, duration, frequency).

Results: Comparing 2D TOF-MRA and ceMRA images, the kappa value (95% confidence interval) was 0.52 (0.31–0.73). The intraobserver reliability kappa value for 2D TOF-MRA was 0.85 (0.77–0.92), and interobserver kappa was 0.57 (0.49–0.65). The sensitivity of 2D TOF-MRA in detecting stenosis was 0.58, the accuracy 0.89, and the specificity 0.94. In 97 (43%) subjects all arteries were normal, whereas 130 (57%) had at least one stenosed artery. The left L4 artery was most often affected. The degree of arterial stenosis was associated with intensity of low back and sciatic pain, and sciatica pain duration during the past 3 months.

Conclusion: 2D TOF-MRA is an acceptable imaging method for arterial stenosis compared to ceMRA. Arterial stenosis was associated with subjective pain symptoms, indicating a role of decreased nutrition in spinal disorders.
Effect of radiation monitoring method and formula differences on estimated physician dose during percutaneous coronary intervention
Authors: Chida K. , Morishima Y. , Masuyama H. , Chiba H. , Katahira Y. , Inaba Y. , Mori I. , Maruoka S. , Takahashi S. , Kohzuki M. , Zuguchi M.
Published: December 2008

Background: Currently, one or two dosimeters are used to monitor radiation exposure in most cardiac laboratories. In addition, several different formulas are used to convert exposure data into an effective dose (ED).

Purpose: To clarify the effect of monitoring methods and formula selection on the estimated ED for physicians during percutaneous coronary interventions (PCIs).

Material and Methods: The ED of physicians during cardiac catheterization was determined using an optically stimulated luminescence dosimeter (Luxel badge). Two Luxel badges were worn: one beneath a personal lead apron (0.35-mm lead equivalent) at the chest and one outside of the apron at the neck.

Results: The difference in the average ED of seven physicians was approximately fivefold (range 1.13–5.43 mSv/year) using the six different formulas in the clinical evaluation. The estimated physician ED differed markedly according to both the monitoring method and formula selected.

Conclusion: ED estimation is dependent on both the monitoring method and the formula used. Therefore, it is important that comparisons among laboratories are based on the same monitoring method and same formula for calculating the ED.
Differentiation of primary central nervous system lymphoma and high-grade glioma with dynamic susceptibility contrast-enhanced perfusion magnetic resonance imaging
Authors: Liao Weihua , Liu Yunhai , Wang Xiaoyi , Jiang Xinya , Tang Beisha , Fang Jiasheng , Chen Changqing , Hu Zhongliang
Published: December 2008

Background: Preoperative differentiation of primary central nervous system lymphomas (PCNSLs) from other tumors is important for presurgical staging, intraoperative management, and postoperative treatment. Dynamic susceptibility contrast-enhanced perfusion magnetic resonance imaging (DSC perfusion MRI) can provide in vivo assessment of the microvasculature in intracranial mass lesions.

Purpose: To determine the utility of DSC perfusion MRI in the differentiation of PCNSLs and high-grade gliomas, as well as their pathological and physiological differences.

Material and Methods: Nine patients with pathologically proven PCNSLs and 11 patients with high-grade gliomas were examined using a 1.5T MRI scanner. DSC perfusion MRI was performed by gradient-echo echo-planar imaging (GE-EPI). The maximum rCBV ratio, the signal intensity–time curves, and the percentage of signal intensity recovery were obtained. The maximum relative cerebral blood volume (rCBV) ratio and the percentage of signal intensity recovery of PCNSLs were compared with those of high-grade gliomas by using Student's t test. Microvessel density (MVD) was evaluated using immunohistochemical staining of surgical specimens with anti-CD34, and MVDs of the two tumor groups were compared by using Student's t test.

Results: The maximum rCBV ratio of primary intracranial lymphomas was 1.72±0.59, while that of high-grade gliomas was 4.86±2.18. PCNSLs tended to have relatively low perfusion compared to high-grade gliomas ( P=0.001), and the MVD labeled by anti-CD34 of PCNSLs was much lower than that of gliomas ( P<0.001). The signal intensity–time curve of primary intracranial lymphomas was different from that of high-grade gliomas. The percentage of signal intensity recovery was significantly greater in PCNSLs compared with that of high-grade gliomas ( P<0.001).

Conclusion: The difference in DSC perfusion MRI characteristics between PCNSLs and high-grade gliomas is determined by their different vascularities and different patterns of contrast agent leakage. This difference may be helpful in the diagnosis and preoperative differentiation between PCNSLs and high-grade gliomas, which sometimes may have similar conventional MR imaging appearance.
Value of perineural edema/inflammation detected by fat saturation sequences in lumbar magnetic resonance imaging of patients with unilateral sciatica
Authors: Şirvanci M. , Kara B. , Duran C. , Ozturk E. , Karatoprak O. , Onat L. , Ulusoy O. L. , Mutlu A.
Published: December 2008

Background: Routine lumbar spine magnetic resonance imaging (MRI) may not show any evidence of the cause of sciatica in some cases. The relationship between nerve root compression detected on lumbar MRI and sciatica is also sometimes uncertain.

Purpose: To ascertain whether axial (and, when necessary, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted MRI findings can be used to study the level of sciatica in patients with a non-yielding routine MRI examination.

Material and Methods: A total of 215 patients with unilateral sciatica underwent MRI. All patients were asked to complete pain drawing forms describing their pain dermatomal distributions. Perineural edema/inflammation corresponding to the pain location indicated by the pain drawings was sought on short-tau inversion recovery or fat-saturated T2-weighted images.

Results: Routine MRI findings revealed that 110 of the 215 patients had nerve root compromise related to the patients’ symptoms. Routine MRI could not ascertain the cause of these symptoms in the remaining 105 patients. In 31 (29.5%) of these 105 patients, short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images revealed perineural edema/inflammation surrounding the nerve roots related to the pain locations indicated in the pain drawings.

Conclusion: Axial (and, when required, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images may be helpful for revealing additional findings in cases of unexplained sciatica in standard magnetic resonance imaging. However, the value of this imaging may be not great enough to justify routine use of these additional sequences to study the level of sciatica.
Respiratory-gated positron emission tomography and breath-hold computed tomography coupling to reduce the influence of respiratory motion: Methodology and feasibility
Authors: Daouk J. , Fin L. , Bailly P. , Meyer M.-E.
Published: December 2008

Background: Respiratory motion causes uptake in positron emission tomography (PET) images of chest and abdominal structures to be blurred and reduced in intensity.

Purpose: To compare two respiratory-gated PET binning methods (based on frequency and amplitude analyses of the respiratory signal) and to propose a “BH-based” method based on an additional breath-hold computed tomography (CT) acquisition.

Material and Methods: Respiratory-gated PET consists in list-mode (LM) acquisition with simultaneous respiratory signal recording. A phantom study featured rectilinear movement of a 0.5-ml sphere filled with 18F-fluorodeoxyglucose (18F-FDG) solution, placed in a radioactive background (sphere-to-background contrast 6:1). Two patients were also examined. Three figures of merit were calculated: the target-to-background ratio profile (TBRP) in the axial direction through the uptake (i.e., the sphere or lesion), full-width-at-half-maximum (FWHM) values, and maximized standard uptake values (SUVmax).

Results: In the phantom study, the peak TBRP was 0.9 for non-gated volume, 1.83 for BH-based volume, and varied between 1.13 and 1.73 for Freq-based volumes and between 1.34 and 1.66 for Amp-based volumes. A reference volume (REF-static) was also acquired for the phantom (in a static, “expiratory” state), with a peak TBRP at 1.88. TBRPs were computed for patient data, with higher peak values for all gated volumes than for non-gated volumes.

Conclusion: Respiratory-gated PET acquisition reduces the blurring effect and increases image contrast. However, Freq-based and Amp-based volumes are still influenced by inappropriate attenuation correction and misregistration of mobile lesions on CT images. The proposed BH-based method both reduces motion artifacts and improves PET-CT registration.
Short article: The role of working memory in tactile selective attention
Authors: Dalton Polly , Lavie Nilli , Spence Charles
Published: December 2008

Load theory suggests that working memory controls the extent to which irrelevant distractors are processed (e.g., Lavie, Hirst, De Fockert, & Viding, 2004). However, so far this proposal has only been tested in vision. Here, we examine the extent to which tactile selective attention also depends on working memory. In Experiment 1, participants focused their attention on continuous target vibrations while attempting to ignore pulsed distractor vibrations. In Experiment 2, targets were always presented to a particular hand, with distractors being presented to the other hand. In both experiments, a high (vs. low) load in a concurrent working memory task led to greater interference by the tactile distractors. These results establish the role of working memory in the control of tactile selective attention, demonstrating for the first time that the principles of load theory also apply to the tactile modality.
Prediction of RNA secondary structure using generalized centroid estimators
Authors: Hamada Michiaki , Kiryu Hisanori , Sato Kengo , Mituyama Toutai , Asai Kiyoshi
Published: December 2008

Motivation: Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding of the base-pairing probabilities has an advantage with respect to prediction accuracy over the conventionally utilized minimum free energy methods. However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures.

Results: We propose novel estimators which improve the accuracy of secondary structure prediction of RNAs. The proposed estimators maximize an objective function which is the weighted sum of the expected number of the true positives and that of the true negatives of the base pairs. The proposed estimators are also improved versions of the ones used in previous works, namely CONTRAfold for secondary structure prediction from a single RNA sequence and McCaskill-MEA for common secondary structure prediction from multiple alignments of RNA sequences. We clarify the relations between the proposed estimators and the estimators presented in previous works, and theoretically show that the previous estimators include additional unnecessary terms in the evaluation measures with respect to the accuracy. Furthermore, computational experiments confirm the theoretical analysis by indicating improvement in the empirical accuracy. The proposed estimators represent extensions of the centroid estimators proposed in Ding et al. and Carvalho and Lawrence, and are applicable to a wide variety of problems in bioinformatics.

Availability: Supporting information and the CentroidFold software are available online at: http://www.ncrna.org/software/centroidfold/.

Contact:  hamada-michiaki@aist.go.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Probabilistic assignment of formulas to mass peaks in metabolomics experiments
Authors: Rogers Simon , Scheltema Richard A. , Girolami Mark , Breitling Rainer
Published: December 2008

Motivation: High-accuracy mass spectrometry is a popular technology for high-throughput measurements of cellular metabolites (metabolomics). One of the major challenges is the correct identification of the observed mass peaks, including the assignment of their empirical formula, based on the measured mass.

Results: We propose a novel probabilistic method for the assignment of empirical formulas to mass peaks in high-throughput metabolomics mass spectrometry measurements. The method incorporates information about possible biochemical transformations between the empirical formulas to assign higher probability to formulas that could be created from other metabolites in the sample. In a series of experiments, we show that the method performs well and provides greater insight than assignments based on mass alone. In addition, we extend the model to incorporate isotope information to achieve even more reliable formula identification.

Availability: A supplementary document, Matlab code, data and further information are available from http://www.dcs.gla.ac.uk/inference/metsamp.

Contact:  srogers@dcs.gla.ac.uk
All hits all the time: parameter-free calculation of spaced seed sensitivity
Authors: Mak Denise Y.F. , Benson Gary
Published: December 2008

Motivation: Standard search techniques for DNA repeats start by identifying small matching words, or seeds, that may inhabit larger repeats. Recent innovations in seed structure include spaced seeds and indel seeds which are more sensitive than contiguous seeds. Evaluating seed sensitivity requires (i) specifying a homology model for alignments and (ii) assigning probabilities to those alignments. Optimal seed selection is resource intensive because all alternative seeds must be tested. Current methods require that the model and its probability parameters be specified in advance. When the parameters change, the entire calculation has to be rerun.

Results: We show how to eliminate the need for prior parameter specification by exploiting a simple observation: given a homology model, the alignments hit by a particular seed remain the same regardless of the probability parameters. Only the weights assigned to those alignments change. Therefore, if we know all the hits, we can easily (and quickly) find optimal seeds. We describe an efficient preprocessing step, which is computed once per seed. Then we show several increasingly efficient methods to find the optimal seed when given specific probability parameters. Indeed, we show how to determine exactly which seeds can never be optimal under any set of probability parameters. This leads to the startling observation that out of thousands of seeds, only a handful have any chance of being optimal. We then show how to identify optimal seeds and the boundaries within probability space where they are optimal.

Contact:  dyfmak@bu.edu
Mediation of Endogenousβ‐Endorphin in the Plasma Glucose‐Lowering Action of Herbal Products Observed in Type 1‐Like Diabetic Rats
Authors: Liu I. M. , Cheng J. T.
Published: December 2008

Recently, there have been advances in the development of new substances effective in managing diabetic disorders. Opioid receptors couple multiple systems to result in various biological effects, although opioids are best known for analgesia. In the present review, we used our recent data to describe the advance in plasma glucose‐lowering action of herbal products, especially the mediation ofβ‐endorphin in glucose homeostasis of insulin‐deficient diabetes. In type 1‐like streptozotocin‐induced diabetic rats, we identified many products purified from herbs that show a dose‐dependent plasma glucose‐lowering action. Increase inβ‐endorphin secretion from the adrenal gland may activate peripheral opioidμ‐receptors (MOR) to enhance the expression of muscle glucose transporters and/or to reduce hepatic gluconeogenesis at the gene level, thereby leading to improved glucose utilization in peripheral tissues for amelioration of severe hyperglycemia. It has also been observed that stimulation ofα1‐adrenoceptors (α1‐ARs) in the adrenal gland by some herbal products is responsible for the increase inβ‐endorphin secretion via a phospholipase C‐protein kinase dependent pathway. However, an increase inβ‐endorphin secretion from the adrenal gland by herbal products can function via another receptor. New insights into the mediation of endogenousβ‐endorphin activation of peripheral MOR by herbal products for regulation of glucose homeostasis without the presence of insulin have been established. Therefore, an increase inβ‐endorphin secretion and/or direct stimulation of peripheral MOR via an insulin‐independent action might serve as the potential target for development of a therapeutic agent or promising adjuvant in intensive plasma glucose control.
Mechanisms and behavioural functions of structural coloration in cephalopods
Authors: Mäthger Lydia M , Denton Eric J , Marshall N. Justin , Hanlon Roger T
Published: December 2008

Octopus, squid and cuttlefish are renowned for rapid adaptive coloration that is used for a wide range of communication and camouflage. Structural coloration plays a key role in augmenting the skin patterning that is produced largely by neurally controlled pigmented chromatophore organs. While most iridescence and white scattering is produced by passive reflectance or diffusion, some iridophores in squid are actively controlled via a unique cholinergic, non-synaptic neural system. We review the recent anatomical and experimental evidence regarding the mechanisms of reflection and diffusion of light by the different cell types (iridophores and leucophores) of various cephalopod species. The structures that are responsible for the optical effects of some iridophores and leucophores have recently been shown to be proteins. Optical interactions with the overlying pigmented chromatophores are complex, and the recent measurements are presented and synthesized. Polarized light reflected from iridophores can be passed through the chromatophores, thus enabling the use of a discrete communication channel, because cephalopods are especially sensitive to polarized light. We illustrate how structural coloration contributes to the overall appearance of the cephalopods during intra- and interspecific behavioural interactions including camouflage.
Neuroactive conducting scaffolds: nerve growth factor conjugation on active ester-functionalized polypyrrole
Authors: Lee Jae Young , Lee Joo-Woon , Schmidt Christine E.
Published: December 2008

Electrically conductive and biologically active scaffolds are desirable for enhancing adhesion, proliferation and differentiation of a number of cell types such as neurons. Hence, the incorporation of neuroactive molecules into electroconductive polymers via a specific and stable method is essential for neuronal tissue engineering applications. Traditional conjugation approaches dramatically impair conductivities and/or stabilities of the scaffolds and ligands. In this study, we developed copolymers (PPy-NSE) of
N
-hydroxyl succinimidyl ester pyrrole and regular pyrrole, which can be immobilized with nerve growth factor (NGF) without significantly hindering electroconductivity. The presence of active ester groups was confirmed using reflectance infrared spectroscopy and X-ray photoelectron spectroscopy (XPS) from the copolymers prepared from different monomer compositions. We selected PPy-NSE
50
(polymerized from a 50 : 50 monomer ratio of pyrrole : pyrrole-NSE) for further modification with NGF because this copolymer retains good conductivity (approx. 8 S cm
−1
) and presents active ester groups for NGF immobilization. We tethered NGF on the PPy-NSE
50
surface, and found that PC12 cells extended neurites similarly to cells cultured in NGF-containing medium. XPS and enzyme-linked immunosorbent assay confirmed that NGF immobilized via the active ester on the PPy-NSE
50
film was stable for up to 5 days in phosphate-buffered saline solution. Also, application of an external electrical potential to NGF-immobilized PPy films did not cause a significant release of NGF nor reduce their neurotrophic activity. This novel scaffold, providing electroconductive and neurotrophic activities, has potential for neural applications, such as tissue engineering scaffolds and biosensors.
Predicting undetected infections during the 2007 foot-and-mouth disease outbreak
Authors: Jewell C. P. , Keeling M. J. , Roberts G. O.
Published: December 2008

Active disease surveillance during epidemics is of utmost importance in detecting and eliminating new cases quickly, and targeting such surveillance to high-risk individuals is considered more efficient than applying a random strategy. Contact tracing has been used as a form of at-risk targeting, and a variety of mathematical models have indicated that it is likely to be highly efficient. However, for fast-moving epidemics, resource constraints limit the ability of the authorities to perform, and follow up, contact tracing effectively. As an alternative, we present a novel real-time Bayesian statistical methodology to determine currently undetected (occult) infections. For the UK foot-and-mouth disease (FMD) epidemic of 2007, we use real-time epidemic data synthesized with previous knowledge of FMD outbreaks in the UK to predict which premises might have been infected, but remained undetected, at any point during the outbreak. This provides both a framework for targeting surveillance in the face of limited resources and an indicator of the current severity and spatial extent of the epidemic. We anticipate that this methodology will be of substantial benefit in future outbreaks, providing a compromise between targeted manual surveillance and random or spatially targeted strategies.
Deformable wing kinematics in the desert locust: how and why do camber, twist and topography vary through the stroke?
Authors: Walker Simon M. , Thomas Adrian L. R. , Taylor Graham K.
Published: December 2008

Here, we present a detailed analysis of the wing kinematics and wing deformations of desert locusts (Schistocerca gregaria, Forskål) flying tethered in a wind tunnel. We filmed them using four high-speed digital video cameras, and used photogrammetry to reconstruct the motion of more than 100 identified points. Whereas the hindwing motions were highly stereotyped, the forewing motions showed considerable variation, consistent with a role in flight control. Both wings were positively cambered on the downstroke. The hindwing was cambered through an ‘umbrella effect’ whereby the trailing edge tension compressed the radial veins during the downstroke. Hindwing camber was reversed on the upstroke as the wing fan corrugated, reducing the projected area by 30 per cent, and releasing the tension in the trailing edge. Both the wings were strongly twisted from the root to the tip. The linear decrease in incidence along the hindwing on the downstroke precisely counteracts the linear increase in the angle of attack that would otherwise occur in root flapping for an untwisted wing. The consequent near-constant angle of attack is reminiscent of the optimum for a propeller of constant aerofoil section, wherein a linear twist distribution allows each section to operate at the unique angle of attack maximizing the lift to drag ratio. This implies tuning of the structural, morphological and kinematic parameters of the hindwing for efficient aerodynamic force production.