bluuebunny/crossref_metadata_2025_split huggingface dataset:
A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data
Authors: Pérez‐Cano Laura , Jiménez‐García Brian , Fernández‐Recio Juan 
Published: April 2012

AbstractWe present here an extended protein–RNA docking benchmark composed of 71 test cases in which the coordinates of the interacting protein and RNA molecules are available from experimental structures, plus an additional set of 35 cases in which at least one of the interacting subunits is modeled by homology. All cases in the experimental set have available unbound protein structure, and include five cases with available unbound RNA structure, four cases with a pseudo‐unbound RNA structure, and 62 cases with the bound RNA form. The additional set of modeling cases comprises five unbound‐model, eight model‐unbound, 19 model‐bound, and three model‐model protein–RNA cases. The benchmark covers all major functional categories and contains cases with different degrees of difficulty for docking, as far as protein and RNA flexibility is concerned. The main objective of this benchmark is to foster the development of protein–RNA docking algorithms and to contribute to the better understanding and prediction of protein–RNA interactions. The benchmark is freely available at http://life.bsc.es/pid/protein–rna‐benchmark. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Multi‐LZerD: Multiple protein docking for asymmetric complexes
Authors: Esquivel‐Rodríguez Juan , Yang Yifeng David , Kihara Daisuke 
Published: April 2012

AbstractThe tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly. However, solving protein complex structures by experimental methods is often more difficult than single protein structures. Here, we have developed a novel computational multiple protein docking algorithm, Multi‐LZerD, that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins. A genetic algorithm is applied to explore the conformational space followed by a structure refinement procedure. Benchmark on eleven hetero‐multimeric complexes resulted in near‐native conformations for all but one of them (a root mean square deviation smaller than 2.5Å). We also show that our method copes with unbound docking cases well, outperforming the methodology that can be directly compared with our approach. Multi‐LZerD was able to predict near‐native structures for multimeric complexes of various topologies.Proteins 2012; © 2012 Wiley Periodicals, Inc.
Evaluation of Lymph Nodes in Patients with Colon Cancer Undergoing Colon Resection: A Population‐based Study
Authors: Chang Yun‐Jau , Chang Yao‐Jen , Chen Li‐Ju , Chung Kuo‐Piao , Lai Mei‐Shu 
Published: April 2012

AbstractBackgroundThough lymph node status may predict long‐term outcome of patients with non‐metastatic colon cancer, discordant findings exist among various expressions of lymph node status. The present study was designed to assess the prognostic value among these lymph node evaluations.MethodsThe analysis was based on surgical patients with newly diagnosed colon adenocarcinoma registered in the Taiwan Cancer Database from 2003 to 2005. Exclusion criteria included those patients who had stage IV disease, those whose survival period was <1 month, or those whose lymph node information was unavailable. Studied variables included total number of lymph nodes (LNT), number of positive lymph nodes (LNP), number of negative lymph nodes (LNN), ratio of positive lymph nodes (LNR), and log odds of positive lymph nodes (LODDS).ResultsOf 16,790 newly diagnosed colon cancer patients, there were 9,644 (65.4 ± 13.5 years; male 54.9 %) patients with non‐metastatic disease who met the criteria. Correlation analyses for patients with stage III disease showed that LNR and LODDS were highly correlated, as were LNT and LNN. By the Cox proportional hazard model, LNT was prognostic of long‐term survival in patients with stage II disease, while LNR and LNP were the most powerful prognosticators for patients with stage III disease (p < 0.001). Both the receiver operating characteristics curve analysis and area under the curve indicated that LNR had the best discriminating capability to predict 5‐year survival (0.704, 0.700, and 0.709 for overall, disease‐free, and disease‐specific survival, respectively), followed by LODDS.ConclusionsFor patients undergoing resection for colon cancer, LNR, LODDS, and LNP are better prognostic factors for those with stage III disease than LNT is for patients with stage III disease.
Sense of Community and Informal Social Control Among Lower Income Households: The Role of Homeownership and Collective Efficacy in Reducing Subjective Neighborhood Crime and Disorder
Authors: Lindblad Mark R. , Manturuk Kim R. , Quercia Roberto G. 
Published: April 2012

AbstractWe examine the link between homeownership, collective efficacy, and subjective neighborhood crime and disorder. Although prior research suggests that homeownership provides social benefits, the housing downturn and foreclosure crisis, coupled with mounting evidence that people self‐select into housing, raise questions about the role of homeownership. We adjust for respondents’ decision to own or rent using a nationwide sample of lower‐income households. We account for demographic and neighborhood characteristics as well as ratings of individual efficacy. We present a structural equation model that identifies how sense of community and informal social control jointly contribute to collective efficacy. The latent collective efficacy construct mediates the impact of homeownership on resident's perceptions of neighborhood disorder. Such perceptions matter because they have been linked to resident's physical and mental health. Our findings demonstrate that when coupled with sustainable mortgages, homeownership exerts a robust yet indirect effect in reducing subjective neighborhood crime and disorder. Our model also links collective efficacy to neighborhood racial homogeneity, a finding which presents challenges for the study of diversity and community. We discuss sense of community research as well as sustainable mortgages and implications of the foreclosure crisis for the future of homeownership opportunities among lower income households and neighborhoods.
The influence of relational experience and contractual governance on the negotiation strategy in buyer–supplier disputes
Authors: Lumineau Fabrice , Henderson James E. 
Published: April 2012

AbstractThis paper theoretically refines and empirically extends the debate on the type of interplay between relational experience and contractual governance in an under‐researched area: supply chain disputes. We define relational experience as either cooperative or competitive; distinguish between control and coordination functions of contractual governance; and assess their interplay on the negotiation strategy used in disputes. Using a unique data set of buyer–supplier disputes, we find, in particular that increasing contractual control governance weakens the positive effect of cooperative relational experience on cooperative negotiation strategy. However, increasing contractual control governance for a buyer–supplier dyad with competitive relational experience will increase cooperative negotiation strategy. Contractual coordination governance reinforces the positive effect of cooperative relational experience. Through this study, we reach a better understanding ofhowandwhencontractual and relational governance dimensions interact; rather thanwhetherthey act as substitutes or complements as has been studied in prior research. We discuss the implications of these findings for the field of supply chain management.
Functional characterization of mammalian Wntless homolog in mammalian system
Authors: Wang Li‐Ting , Wang Shih‐Jong , Hsu Shih‐Hsien 
Published: April 2012

AbstractWntless (GPR177) protein is a newly identified regulator of Wnt signals in Drosophila, but its cellular function in mammals is still unclear. In this study, we explored the expression pattern and potential cellular function of Wntless in mammalian cells. Wntless mRNA was expressed in many mouse tissues, including the spleen, lung, kidney, thymus, and stomach, and lower levels of expression were detected in the mouse brain and testis. Expression of Wntless protein analyzed by Western blot and immunohistochemical staining was only detected in the submucosa, muscle, ganglia, and nerve cells of murine large intestines. Both immunofluorescence staining and subcellular fraction extraction analysis revealed that endogenous Wntless protein was expressed predominantly in the cytoplasmic organelles with a morphologically dot‐shaped distribution. Furthermore, overexpression of Wntless could be corrected by and may activate the nuclear factor‐κB (NF‐κB) signaling pathway in cancer (HeLa) cells. These results suggest that Wntless plays a role in signaling regulation during the formation of cancer in addition to its role as a retromer protein in mammalian systems.
Soft catheters reduce the risk of intravascular cannulation during epidural block—A retrospective analysis of 1117 cases in a medical center
Authors: Shih Chih‐Kai , Wang Fu‐Yuan , Shieh Chia‐Fang , Huang Jui‐Mei , Lu I‐Cheng , Wu Li‐Chen , Lu David Vi 
Published: April 2012

AbstractA wet or bloody tap is an inevitable complication while performing epidural block. The influence of different catheters on the incidence of intravascular cannulation during epidural catheterization has not been reported. We observed an initial, relatively different incidence of intravascular cannulation during the placement of different sorts of epidural catheter; hence, a retrospective review was conducted to explore the possible association. We reviewed 1‐year interval anesthetic records of 1117 patients who had undergone epidural anesthesia or received patient‐controlled epidural analgesia. Epidural catheter placement was performed by a loss of resistance technique with an 18‐G Tuohy needle in lateral position. Patients were divided into two groups according to the different types of epidural catheters used (Perifix One, n = 590; Perifix Standard, n = 527). Primary outcome measurement was the incidence of intravascular injection. Other analyzed outcomes included dura puncture, failure rate, and low back pain. The incidence of epiduralintravascular cannulation was significantly lower using the Perifix One catheter (1.5%; 9/590) than using the Perifix Standard (4.6%; 24/527), p = 0.003. The dura puncture rate did not differ significantly between the Perifix One (1.9%; 11/590) and the Perifix Standard (2.5%; 13/527), p = 0.49. Failure rates and low back pain incidence were also comparable between the two groups. Application of the soft epidural catheter (Perifix One) may reduce the incidence of epidural intravascular cannulation. We suggest the use of Perifix One catheter instead of Perifix Standard catheter in daily practice.
Feasibility of First Metatarsophalangeal Joint Injections for Sesamoid Disorders: A Cadaveric Investigation
Authors: Wempe Michael K. , Sellon Jacob L. , Sayeed Yusef A. , Smith Jay 
Published: April 2012

ObjectiveTo determine whether accurately placed first metatarsophalangeal joint (MTPJ) injections consistently deliver injectate to the metatarsosesamoid articulations.DesignProspective anatomic cadaver study.SettingProcedural skills laboratory at a tertiary care academic institution.ParticipantsFive unembalmed cadaveric lower limb specimens, free from trauma, surgery, or major deformity of the medial forefoot.MethodsUltrasound guidance was used to accurately inject the first MTPJs of each cadaveric specimen with diluted, blue‐colored latex. At a minimum of 24 hours after injection, each specimen was dissected to determine whether the latex was present between the metatarsal head and sesamoid bones (metatarsosesamoid articulations).Main Outcome MeasuresThe presence or absence of latex within the first MTPJ and both the tibial and fibular metatarsosesamoid articulations.ResultsIn all 5 cadaveric specimens, ultrasound‐guided first MTPJ injection accurately delivered latex into the first MTPJ. In addition, in each specimen, latex was seen between the metatarsal head and both the fibular and tibial sesamoid bones.ConclusionsAccurate first MTPJ injections reliably deliver latex to the articular surfaces of the metatarsosesamoid articulations. Clinicians administering diagnostic or therapeutic injections for patients with sesamoid disorders should consider injecting the first MTPJ as an alternative to direct metatarsosesamoid articulation injections.
The Low‐Latitude Ionosphere Sensor Network: Initial results
Authors: Valladares C. E. , Chau J. L. 
Published: April 2012

The Low‐Latitude Ionospheric Sensor Network (LISN) is a distributed observatory designed to nowcast the state and dynamics of the low‐latitude ionosphere and to develop forecasts of the electric fields, densities, and equatorial spread F over the South American continent. The LISN observatory consists of three different types of instruments: GPS receivers, fluxgate magnetometers, and vertical incidence pulsed ionospheric radar (VIPIR) ionosondes. This report provides a succinct summary of recent observations obtained using the LISN GPS receivers and complemented with measurements from other instruments and GPS receivers that operate in South America. More specifically, the following are shown here: (1) observations of total electron content (TEC) enhancements that occur near local midnight, (2) maps of TEC perturbations associated with the passage of traveling ionospheric disturbances over South America, and (3) statistics of TEC depletions for 2 years of low solar activity. Near‐midnight TEC enhancements consist of sudden increases in TEC that occur after sunset at low latitudes on 30% of the days. These TEC enhancements last for several hours and can have amplitudes between 1 and 50 TEC units. On 11–12 March 2011 the largest TEC enhancement was observed in South America at times when the Jicamarca incoherent scatter radar operated and observed peak densities above 106 el/cc at 300 km altitude. It is suggested that a combination of zonal electric fields and meridional neutral winds are able to redistribute the plasma along the field lines and create regions of enhanced TEC. Maps of TEC perturbations associated with the passage of gravity waves (GWs) over South America have been used to measure the phase velocity and direction of propagation of GWs. The large number of GPS receivers over South America has allowed us to record bubble events for every day during 2008 and 2009. It was found that the number of TEC depletion detections varies with a periodicity of 28 days. It is mentioned how these new observations and the installation of the last four VIPIR ionosondes will lead to new discoveries in the near future.
Age or Experience? The Influence of Age at Implantation and Social and Linguistic Environment on Language Development in Children With Cochlear Implants
Authors: Szagun Gisela , Stumper Barbara 
Published: April 2012

Purpose
The authors investigated the influence of social environmental variables and age at implantation on language development in children with cochlear implants.

Method

Participants were 25 children with cochlear implants and their parents. Age at implantation ranged from 6 months to 42 months (
M
age
= 20.4 months,
SD
= 22.0 months). Linguistic progress was assessed at 12, 18, 24, and 30 months after implantation. At each data point, language measures were based on parental questionnaire and 45-min spontaneous speech samples. Children’s language and parents' child-directed language were analyzed.

Results
On all language measures, children displayed considerable vocabulary and grammatical growth over time. Although there was no overall effect of age at implantation, younger and older children had different growth patterns. Children implanted by age 24 months made the most marked progress earlier on, whereas children implanted thereafter did so later on. Higher levels of maternal education were associated with faster linguistic progress; age at implantation was not. Properties of maternal language input, mean length of utterance, and expansions were associated with children’s linguistic progress independently of age at implantation.

Conclusions
In children implanted within the sensitive period for language learning, children’s home language environment contributes more crucially to their linguistic progress than does age at implantation.
Influences of Sentence Length and Syntactic Complexity on the Speech Motor Control of Children Who Stutter
Authors: MacPherson Megan K. , Smith Anne 
Published: April 2012

Purpose
To investigate the potential effects of increased sentence length and syntactic complexity on the speech motor control of children who stutter (CWS).

Method
Participants repeated sentences of varied length and syntactic complexity. Kinematic measures of articulatory coordination variability and movement duration during perceptually fluent speech were analyzed for 16 CWS and 16 typically developing children (CTD) between 4 and 6 years of age. Behavioral data from a larger pool of children were also examined.

Results
For both groups, articulatory coordination variability increased with sentence length. For syntactically simple sentences, CWS had higher coordination variability than CTD. There was no group difference in coordination variability for complex sentences. Coordination variability increased significantly with complexity for CTD, whereas that of CWS remained at the high level demonstrated for simple sentences. There was a trend for higher overall coordination variability in CWS compared with CTD. For both groups, movement duration was greater for syntactically complex, as compared with simple, sentences.

Conclusions
Results indicate more variable speech motor coordination during fluent speech production in many CWS as compared with CTD. Disproportionate effects of length and complexity on coordination variability and duration were not found for CWS. Considerable individual differences in performance were observed.
An Alternative Programme
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter focuses on the British Broadcasting Corporation's (BBC) introduction of an alternative programme in September 1939 after it was restricted to only one programme at the start of World War 2. It explains that while the Air Ministry was adamant on the subject of a single programme, the BBC Control Board did not drop the subject which quickly began to be linked with the question of how best to entertain British Expeditionary Forces (BEF) stationed in France. It highlights the Air Ministry's approval of the use of 342-meter wavelength for BBC's programmes for BEF.
Britain and France
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter focuses on British broadcasting in France during the months of June and July 1940. It explains that during this period, there was a need for urgent action in relation to France, which passed quickly from friendship and alliance to non-belligerence and tacit hostility after the German blitzkrieg attack. It discusses the British Broadcasting Corporation's (BBC) first use of the term French Armistice in its broadcast to France during this period. It also highlights Charles De Gaulle's decision to broadcast his message to Occupied France from London.
‘Sounds of War’
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter examines the pattern of broadcasting after the autumn of 1940 and the second winter of the World War 2. It discusses how broadcasting responded to Germany's victory in East Africa and Iraq and to the deployment of German troops to North Africa in February 1941. It highlights Haw-Haws' decision to reveal his true identity to the British public as being William Joyce and describes the government's reaction to learning Haw-Haw's identity. It mentions the British government's disappointment with the British Broadcasting Corporation for failing to provide an up-to-date war broadcast which led British audience to listen to Haw-Haw.
The Pattern of Programmes
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter examines the changes in the patterns of radio programming of the British Broadcasting Corporation (BBC). It explains that during the war, familiar old issues continued to be raised such as whether Happidrome should be broadcast in the Forces programme opposite the religious service. BBC continued to be judged by most of its listeners in terms of the home programmes it provided. This provides a detailed description of the reorganization of BBC's programming.
Politics, Religion, and Society
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter focuses on the British Broadcasting Corporation's (BBC) wartime broadcasting about politics, religion, and society. It describes the criticisms of listeners to BBC broadcasters, including J.B. Priestly, for expressing their opinion about politics. It explains that that in 1942 the borderline between religion and politics seemed to be one of the most dangerous frontiers argued about. It discusses the dilemma of the BBC on whether to maintain free access to the microphone or exercise discipline in what the government believed were the interests of the nation.
A Year of Climax
Authors: Briggs Asa 
Published: April 2012

Abstract
This chapter discusses the British Broadcasting Corporation's (BBC) programming after the defeat of Germany. It explains that the BBC had begun to consider as early as October 1943 what form its programmes should take immediately following an armistice with Germany. It highlights BBC Director-General William Haley's plan to seek balance rejoicing, thanksgiving, tribute, and warning; and describes the talks prepared for the autumn of 1944 which included ‘full employment’ and ‘reconstruction’.
Therapy of acute spinal cord injury
Authors: Young Wise 
Published: April 2012

AbstractClinical and laboratory approaches to spinal cord injury maintain the traditional pessimism first expressed in the Edwin Smith Papyrus, which regarded the possibility of recovery from spinal cord injury as being so remote that it recommended letting spinal-injured warriors die. For example, most clinical categorizations of spinal injury segregate patients into two distinct groups: ‘complete’ and ‘incomplete’. The former are assumed not to recover. Medical care focuses on preservation and protection of peripheral organs, while surgical procedures continue to be oriented towards the stabilization of spinal fractures and the prevention of further spinal cord injury. Rehabilitative care of the spinal-injured emphasizes making the best use of residual function.
An introduction to functional magnetic resonance imaging of the brain
Authors: Matthews Paul M. 
Published: April 2012

AbstractThis chapter provides an overview of functional magnetic resonance imaging (fMRI) methods and applications, highlighting key concepts and strategies, and includes the full range of techniques by which physiological changes accompanying brain activity are defined. It focuses on the changes in blood oxygenation and flow that have been used for the functional magnetic resonance imaging methods. Direct imaging of the blood flow response using perfusion MRI is also discussed. The study furthermore deals with elegant methods that have been developed and allow an extension of this simple concept for one-dimensional imaging into methods for multi-slice two-dimensional or three-dimensional imaging. It outlines the major issues in statistical analysis for fMRI and addresses ways in which the data can be prepared for analysis to minimize artefacts and maximize sensitivity for the detection of activation changes. Finally, the chapter discusses the various applications of fMRI in neuroscience.