bluuebunny/crossref_metadata_2025 huggingface dataset:
Social communication in young children with traumatic brain injury: Relations with corpus callosum morphometry
Authors: Ewing‐Cobbs Linda , Prasad Mary R. , Swank Paul , Kramer Larry , Mendez Donna , Treble Amery , Payne Christa , Bachevalier Jocelyne
Published: July 2011

The purpose of the present investigation was to characterize the relations of specific social communication behaviors, including joint attention, gestures, and verbalization, with surface area of midsagittal corpus callosum (CC) subregions in children who sustained traumatic brain injury (TBI) before 7 years of age. Participants sustained mild (n = 10) or moderate–severe (n = 26) noninflicted TBI. The mean age at injury was 33.6 months; mean age at MRI was 44.4 months. The CC was divided into seven subregions. Relative to young children with mild TBI, those with moderate–severe TBI had smaller surface area of the isthmus. A semi‐structured sequence of social interactions between the child and an examiner was videotaped and coded for specific social initiation and response behaviors. Social responses were similar across severity groups. Even though the complexity of their language was similar, children with moderate–severe TBI used more gestures than those with mild TBI to initiate social overtures; this may indicate a developmental lag or deficit as the use of gestural communication typically diminishes after age 2. After controlling for age at scan and for total brain volume, the correlation of social interaction response and initiation scores with the midsagittal surface area of the CC regions was examined. For the total group, responding to a social overture using joint attention was significantly and positively correlated with surface area of all regions, except the rostrum. Initiating joint attention was specifically and negatively correlated with surface area of the anterior midbody. Use of gestures to initiate a social interaction correlated significantly and positively with surface area of the anterior and posterior midbody. Social response and initiation behaviors were selectively related to regional callosal surface areas in young children with TBI. Specific brainbehavior relations indicate early regional specialization of anterior and posterior CC for social communication.
Assessment of cognition in early dementia
Authors: Silverberg Nina B. , Ryan Laurie M. , Carrillo Maria C. , Sperling Reisa , Petersen Ronald C. , Posner Holly B. , Snyder Peter J. , Hilsabeck Robin , Gallagher Michela , Raber Jacob , Rizzo Albert , Possin Katherine , King Jonathan , Kaye Jeffrey , Ott Brian R. , Albert Marilyn S. , Wagster Molly V. , Schinka John A. , Cullum C. Munro , Farias Sarah T. , Balota David , Rao Stephen , Loewenstein David , Budson Andrew E. , Brandt Jason , Manly Jennifer J. , Barnes Lisa , Strutt Adriana , Gollan Tamar H. , Ganguli Mary , Babcock Debra , Litvan Irene , Kramer Joel H. , Ferman Tanis J.
Published: July 2011

Better tools for assessing cognitive impairment in the early stages of Alzheimer's disease (AD) are required to enable diagnosis of the disease before substantial neurodegeneration has taken place and to allow for detection of subtle changes in the early stages of progression of the disease. The National Institute on Aging and the Alzheimer's Association convened a meeting to discuss state‐of‐the art methods for cognitive assessment, including computerized batteries, as well as new approaches in the pipeline. Speakers described research using novel tests of object recognition, spatial navigation, attentional control, semantic memory, semantic interference, prospective memory, false memory, and executive function as among the tools that could provide earlier identification of individuals with AD. In addition to early detection, there is a need for assessments that reflect real‐world situations so as to better assess functional disability. It is especially important to develop assessment tools that are useful in ethnically, culturally, and linguistically diverse populations as well as in individuals with neurodegenerative disease other than AD.
Knowledge and Use of Antimicrobial Stewardship Resources by Spinal Cord Injury Providers
Authors: Evans Charlesnika T. , Rogers Thea J. , Burns Stephen P. , Lopansri Bert , Weaver Frances M.
Published: July 2011

Objective

To assess the knowledge and the use of antimicrobial stewardship resources, such as hospital antibiograms and infectious disease consultants, by spinal cord injury or disorder (SCI/D) providers.

Design and Setting

Anonymous Internet‐based, cross‐sectional survey.

Participants

A total of 314 SCI/D physicians, nurse practitioners, and physician assistants who prescribe antibiotics were invited to complete a survey.

Main Outcome Measurements

Knowledge of and behaviors related to antibiograms and infectious disease (ID) consults.

Results

A total of 118 providers (80 physicians, 20 nurse practitioners, 18 physician assistants) completed the survey (37.6% response rate). Approximately one‐third of respondents indicated that they did not have access to (11.0%) or were unsure of (28.0%) the existence of facility antibiograms. Half of the providers indicated that they never used antibiograms to determine treatment for their SCI/D patients. Respondent factors associated with viewing facility antibiograms were older age, employment at SCI/D specialty centers, a longer duration since completion of training, and years of SCI/D patient care. Nearly all respondents (95%) indicated that they believed that improving access to antibiotic prescribing data or antibiograms would reduce antibiotic resistance. More than one‐third reported that they never or seldom used ID consults.

Conclusions

A significant portion of SCI/D providers who prescribe antibiotics do not have access to facility antibiograms or are unaware of their existence and thus could not use them for determining antibiotic treatment. Interventions could include formal education of providers on how to access antibiograms and the use of ID physicians as a resource, as well as providing technologic support, such as electronic facility‐level antibiograms as part of the medical record system, which can be easily identified if a provider is making a decision on an antibiotic.
Evaluation of the McKenzie Intervention for Chronic Low Back Pain by Using Selected Physical and Bio‐Behavioral Outcome Measures
Authors: Al‐Obaidi Saud M. , Al‐Sayegh Nowall A. , Ben Nakhi Huzaifa , Al‐Mandeel Mariam
Published: July 2011

Objectives

To assess the bio‐behavioral and physical performance characteristics of individuals with chronic low back pain who demonstrated the pain centralization phenomenon and received the McKenzie intervention using selected bio‐behavioral and physical performance measures at intake and at 5 weeks and 10 weeks after treatment.

Design

A prospective cohort study with assessment at baseline and 2 follow‐ups after completion of the McKenzie intervention.

Setting

Outpatient orthopedic physical therapy clinics.

Participants

Sixty‐two volunteers with chronic low back pain (28 men, 34 women; average ages 41.9 and 37.1 years, respectively).

Methods

The subjects completed pain and related fear and disability questionnaires, underwent McKenzie mechanical assessment, and executed selected physical performances. They then received the McKenzie intervention.

Main Outcome Measurements

Outcomes measurements were repeated at the end of the 5th and 10th weeks after treatment completion. Pain‐related disability and fear beliefs were assessed by using the Disability Belief Questionnaire and Fear Avoidance Belief Questionnaires, respectively. The time for repeated sit to stand, trunk forward bending, and customary and fast walking were measured by stopwatch. Pain (anticipated versus actual reported) was measured before and immediately after a given physical performance. Descriptive statistics, paired t‐tests, and repeated measures analysis of variance were used.

Results

Significant improvements peaked at the end of the 5th week for all outcome measures (P < .001), with slight increase in bio‐behavioral variables at the end of the 10th week.

Conclusions

McKenzie intervention reduced pain and related fear and disability beliefs and improved physical performances in individuals with chronic low back pain. Improvements in physical performances remained stable 10 weeks after treatment, regardless of the elevation in bio‐behavioral factors.
Can a New Generation Bring about Regime Change?
Authors: Tignor Robert L.
Published: July 2011

Peaceful protests and demonstrations have swept through the Arab world, toppling rulers and advancing programs of radical change. Some enthusiasts for these movements have already proclaimed them a revolution. They predict a new Middle Eastern political and economic order. A new generation of young people—men and women, mainly in their twenties and thirties, using their skills in cyberspace communication and fueled by many frustrations—assembled vast numbers in peaceful protests that have thus far claimed many triumphs. They forced the departures of the long-standing dictators of Egypt and Tunisia and have demanded that the monarchs of Jordan, Morocco, and Bahrain reign rather than rule.
Engendering Democracy
Authors: Moghadam Valentine
Published: July 2011

The year 2011 will forever be known as the year of mass protests for regime change and democratization in the Middle East and North Africa (MENA). Opinions on causes and outcomes have focused on the role of young people, the demands of “the Arab street,” and the possible transition to a liberal, Islamist, or coalition type of governance. Middle East specialists have long been aware of the problems of authoritarian regimes, widening inequalities, high rates of youth unemployment, deteriorating infrastructure and public services, and rising prices attenuated only by subsidies. But something has been missing from recent discussions and analyses. Let us pose it in the form of a number of (socialist-feminist) questions. We have seen that “the Arab street” is not exclusively masculine, but what kind of democratic governance can women's rights groups expect? To what extent will Tunisian women shape the democratic transition and the building of new institutions? In Egypt, will an outcome be—to use a phrase coined by East European feminists in the early 1990s—a “male democracy”? How can a democratic transition benefit working women and the poor?
Military Presidents in Arab States
Authors: Owen Roger
Published: July 2011

The Arab world has experienced a large number of military presidencies since General Bakr Sidki's brief rule in Iraq in 1936. The phenomenon became of great significance beginning with Colonel Jamal ʿAbd al-Nasir's presidency in Egypt in the early 1950s, which established a model for similar regimes in Sudan, Syria, Iraq, Yemen, and, at least initially, Libya under the self-promoted Colonel Muʿammar al-Qadhafi. The president who exchanged his uniform for a suit; an authoritarian style of political management in the name of a revolution against an old, foreign-dominated order; and the legitimacy obtained from laudable achievements in the international and economic sphere: these were all part of al-Nasir's influence and legacy.
MUTUALITY AND IMMEDIACY BETWEENMARJAʿANDMUQALLID: EVIDENCE FROM MALE IN VITRO FERTILIZATION PATIENTS IN SHIʿI LEBANON
Authors: Clarke Morgan , Inhorn Marcia C.
Published: July 2011

This article concerns the dominant institution of religious authority within modern Usuli Twelver Shiʿi Islam: themarjaʿiyya. The most senior clerics serve as “sources of emulation” (marājiʿ al-taqlīd), informing the moral conduct of their lay “imitators” (muqallidūn). Despite the importance of this relationship, academic writing on what we call its “affective” qualities, especially from lay perspectives, is limited. We provide ethnographic data from anthropological research into Islamic medical ethics in Lebanon. Interviews in 2003 with infertile Shiʿi patients who were considering controversial assisted reproductive technologies revealed rare insights into which authorities they followed and in what numbers and how this relationship was experienced and drawn upon by those in need. We compare the very different relationships inspired by the two authorities most cited in our study: the late Beirut-based Ayatollah Fadlallah; and the Iranian Ayatollah Khaminaʾi, Hizbullah's patron. From his local base, Fadlallah offered a vivid and responsive persona of a qualitatively distinct type.
A practical approach to the early identification of antidepressant medication non-responders
Authors: Li J. , Kuk A. Y. C. , Rush A. J.
Published: July 2011

Background

The aim of the present study was to determine whether a combination of baseline features and early post-baseline depressive symptom changes have clinical value in predicting out-patient non-response in depressed out-patients after 8 weeks of medication treatment.

Method

We analysed data from the Combining Medications to Enhance Depression Outcomes study for 447 participants with complete 16-item Quick Inventory of Depressive Symptomatology – Self-Report (QIDS-SR16) ratings at baseline and at treatment weeks 2, 4 and 8. We used a multi-time point, recursive subsetting approach that included baseline features and changes in QIDS-SR16 scores from baseline to weeks 2 and 4, to identify non-responders (<50% reduction in QIDS-SR16) at week 8 with a pre-specified accuracy level.

Results

Pretreatment clinical features alone were not clinically useful predictors of non-response after 8 weeks of treatment. Baseline to week 2 symptom change identified 48 non-responders (of which 36 were true non-responders). This approach gave a clinically meaningful negative predictive value of 0.75. Symptom change from baseline to week 4 identified 79 non-responders (of which 60 were true non-responders), achieving the same accuracy. Symptom change at both weeks 2 and 4 identified 87 participants (almost 20% of the sample) as non-responders with the same accuracy. More participants with chronic than non-chronic index episodes could be accurately identified by week 4.

Conclusions

Specific baseline clinical features combined with symptom changes by weeks 2–4 can provide clinically actionable results, enhancing the efficiency of care by personalizing the treatment of depression.
Optimal design of 6-DOF eclipse mechanism based on task-oriented workspace
Authors: Lee Donghun , Kim Jongwon , Seo TaeWon
Published: July 2011

We present a new numerical optimal design for a redundant parallel manipulator, the eclipse, which has a geometrically symmetric workspace shape. We simultaneously consider the structural mass and design efficiency as objective functions to maximize the mass reduction and minimize the loss of design efficiency. The task-oriented workspace (TOW) and its partial workspace (PW) are considered in efficiently obtaining an optimal design by excluding useless orientations of the end-effector and by including just one cross-sectional area of the TOW. The proposed numerical procedure is composed of coarse and fine search steps. In the coarse search step, we find the feasible parameter regions (FPR) in which the set of parameters only satisfy the marginal constraints. In the fine search step, we consider the multiobjective function in the FPR to find the optimal set of parameters. In this step, fine search will be kept until it reaches the optimal set of parameters that minimize the proposed objective functions by continuously updating the PW in every iteration. By applying the proposed approach to an eclipse-rapid prototyping machine, the structural mass of the machine can be reduced by 8.79% while the design efficiency is increased by 6.2%. This can be physically interpreted as a mass reduction of 49 kg (the initial structural mass was 554.7 kg) and a loss of 496 mm3/mm in the workspace volume per unit length. The proposed optimal design procedure could be applied to other serial or parallel mechanism platforms that have geometrically symmetric workspace shapes.
“Tangible as Tissue”: Arnold Gesell, Infant Behavior, and Film Analysis
Authors: Curtis Scott
Published: July 2011

Argument

From 1924 to 1948, developmental psychologist Arnold Gesell regularly used photographic and motion picture technologies to collect data on infant behavior. The film camera, he said, records behavior “in such coherent, authentic and measurable detail that . . . the reaction patterns of infant and child become almost as tangible as tissue.” This essay places his faith in the fidelity and tangibility of film, as well as his use of film as evidence, in the context of developmental psychology's professed need for legitimately scientific observational techniques. It also examines his use of these same films as educational material to promote his brand of scientific child rearing. But his analytic techniques – his methods of extracting data from the film frames – are the key to understanding the complex relationship between his theories of development and his chosen research technology.
Persistent environmental reservoirs on farms as risk factors forCampylobacterin commercial poultry
Authors: ELLIS-IVERSEN J. , RIDLEY A. , MORRIS V. , SOWA A. , HARRIS J. , ATTERBURY R. , SPARKS N. , ALLEN V.
Published: July 2011

Campylobacteris the most common known source of human bacterial enteritis in the developed world and poultry is considered the main source. Broilers often become colonized withCampylobacterduring rearing, and then contaminate the farm environment. The objective of this study was to identifyCampylobacter-positive environmental reservoirs on farms, as these pose a risk to broiler flocks becoming colonized withCampylobacter. We considered the temporal aspects of exposure and colonization. A longitudinal study monitored six conventional rearing farms over 2 years. The broiler flocks, catchers' equipment, vehicles, shed surrounds, shed entrance, other equipment, farm entrance, other animals, puddles, dead birds, mains water and drinkers were systematically sampled 2–4 times per flock. A multivariable generalized estimating equation model was used to assess associations between contaminated environmental sites and colonized broiler flocks. The associations were adjusted for confounders and other known risk factors. To further assess temporality of contamination, the sequence of contamination of the different environmental sites and the flocks was established. Contaminated shed entrances and anterooms, contaminated drinkers and shedding ofCampylobacterby other animals such as cattle, dogs, wildlife and rodents were significantly associated with positive flocks. The reservoir of ‘other animals’ was also the reservoir most commonly positive before the flock became colonized. The other sites usually became contaminated after the flock was colonized.
Trends in primary-care consultations, comorbidities, and antibiotic prescriptions for respiratory infections in The Netherlands before implementation of pneumococcal vaccines for infants
Authors: VAN DEURSEN A. M. M. , VERHEIJ T. J. M. , ROVERS M. M. , VEENHOVEN R. H. , GROENWOLD R. H. H. , BONTEN M. J. M. , SANDERS E. A. M.
Published: July 2011

The burden of respiratory infections is mainly seen in primary healthcare. To evaluate the potential impact of new preventive strategies against respiratory infections, such as the implementation of pneumococcal conjugate vaccines for infants in 2006 in The Netherlands, we conducted a baseline retrospective cohort study of electronic primary-care patient records to assess consultation rates, comorbidities and antibiotic prescription rates for respiratory infections in primary care. We found that between 1995 and 2005, overall registered consultation rates for lower respiratory tract infections had increased by 42·4%, upper respiratory infections declined by 4·9%, and otitis media remained unchanged. Concomitantly, there was a steady rise in overall comorbidity (75·7%) and antibiotic prescription rates (67·7%). Since Dutch primary-care rates for respiratory infections changed considerably between 1995 and 2005, these changes must be taken into account to properly evaluate the effect of population-based preventive strategies on primary-care utilization.
Early-life environment influencing susceptibility to cytomegalovirus infection: evidence from the Leiden Longevity Study and the Longitudinal Study of Aging Danish Twins
Authors: MORTENSEN L. H. , MAIER A. B. , SLAGBOM P. E. , PAWELEC G. , DERHOVANESSIAN E. , PETERSEN I. , JAHN G. , WESTENDORP R. G. J. , CHRISTENSEN K.
Published: July 2011

Human cytomegalovirus (CMV) is a common herpesvirus establishing lifelong persisting infection, which has been implicated in immunosenescence and mortality in the elderly. Little is known about how and when susceptibility to CMV infection is determined. We measured CMV seroprevalence in two genetically informative cohorts. From the Leiden Longevity Study (LLS) we selected long-lived sib-pairs (n=844) and their middle-aged offspring and the offspring's partners (n=1452). From the Longitudinal Study of Aging Danish Twins (LSADT) 604 (302 pairs) same-sex monozygotic (MZ) and dizygotic (DZ) twins aged 73–94 years were included (n=302 pairs). Offspring of the long-lived LLS participants had significantly lower seroprevalence of CMV compared to their partners (offspring: 42%vs. partners: 51%,P=0·003). Of 372 offspring living with a CMV-positive partner, only 58% were infected. The corresponding number for partners was 71% (P<0·001). In the LSADT, MZ and DZ twins had high and similar CMV-positive concordance rates (MZ: 90%vs. DZ: 88%,P=0·51) suggesting that shared family environment accounts for the similarity within twin pairs. Our findings suggest that susceptibility to CMV infection – even under continuous within-partnership exposure – appears to be more strongly influenced by early-life environment than by genetic factors and adult environment.
Factors affecting vascular access complications in children undergoing congenital cardiac catheterization
Authors: Roushdy Alaa M. , Abdelmonem Noha , El Fiky Azza A.
Published: July 2011

Background

Complications at the vascular access sites are among the most common adverse events in congenital cardiac catheterization. The use of small-gauge catheters may reduce these events; however, other factors can contribute to the development of vascular complications.

Objectives

To determine factors associated with the development of vascular access complications in children undergoing congenital cardiac catheterization.

Methods

We performed a prospective study of 403 patients who underwent diagnostic (62.5%) or interventional (37.5%) cardiac catheterization over a period of 6 months, and analysed the vascular complications during and immediately after the procedure.

Results

The most common access-related adverse event was transient loss of pulsation (17.6%). Other less common access-related adverse events included subcutaneous haematoma (2%), bleeding (3%), vessel tear (0.2%), and vein thrombosis (0.2%). Patients who had no access-related adverse events had significantly higher age and body weight compared with those who had one or more access problems. Among 81 patients who had vascular access established in unplanned access sites, 30 patients (37%) had lost pulsations. Among the 322 patients who had vascular access established in planned access sites, however, only 41 patients had lost pulsation (13%). In addition, patients who had lost pulsations had significantly longer puncture time compared to those who had normal pulsations (p value 0.01).

Conclusion

Factors other than sheath size can contribute to access-related adverse events in children undergoing cardiac catheterization. Obtaining vascular access in unplanned access sites and longer puncture times increases the incidence of lost pulsations after catheterization. Younger age and smaller body weight are also associated with significant increase in access-related adverse events.
A PATRON AMONG PEERS: DEDICATIONS TO HAYDN AND THE ECONOMY OF CELEBRITY
Authors: GREEN EMILY
Published: July 2011

Between 1784 and 1809 more than forty composers dedicated works to Haydn, resulting in the largest group of offerings to a single composer in the eighteenth and nineteenth centuries. Whilst Horst Walter has suggested that certain of these works reveal the ways in which composers received Haydn's style, a study of the larger collection of dedications illuminates the broader nature of Haydn's fame and the ways in which other composers and their publishers both contributed to and capitalized on that fame. Making Haydn into a kind of pseudo-patron, the title-pages, advertisements and dedicatory epistles for these works allow for an exchange of various types of capital ranging from the material to the symbolic, ultimately enabling both dedicator and dedicatee to improve their reputations in the eyes of the consuming public.
ALIGNMENT, ABSORPTION, ANIMATION: PANTOMIME BALLET IN THE LOMBARD ILLUMINISMO
Authors: LOCKHART ELLEN
Published: July 2011

This article investigates the theme of statuary animation within pantomime and language reform, particularly in Milan between the 1760s and the 1790s. Its focal point is a little-known work created by Florentine choreographer Gasparo Angiolini for the new Teatro alla Scala in 1782: his didactic ‘philosophical ballet’La vendetta spiritosa, based on theTraité des sensationsby Étienne Bonnot de Condillac (in Venice the work was given asLa vendetta ingegnosa o La statua di Condilliac[sic]). During the last decades of his career, informed by French linguistic theory and by Milanese writers such as the Verri brothers and Cesare Beccaria, Angiolini aimed to create an unmediated music-gestural language that could overcome linguistic and even political boundaries. The project had significant implications for the use of representative sound, both in music and in language. I examine the development of the impulse towards gestural mimesis and through-composition within scores for thedanza parlante, including by Angiolini himself.
HAYDN'S FORGOTTEN QUARTETS: THREE OF THE ‘PARIS’ SYMPHONIES ARRANGED FOR STRING QUARTET
Authors: JONES DAVID WYN
Published: July 2011

In 1787 Artaria, Haydn's publisher in Vienna, issued three versions of The Seven Last Words: the original orchestral version, a quartet arrangement prepared by the composer and a keyboard arrangement sanctioned by him. A year later, in September 1788, Artaria issued three of the recent ‘Paris’ Symphonies, Nos 84, 85 and 86, in an arrangement for quartet. While the quartet version of The Seven Last Words has always been accepted as part of the canon, the three quartet arrangements of the symphonies have been ignored. Sympathetic consideration of a range of evidence, including the bibliographical, historical and text-critical, suggests that Haydn may have been the author of these three quartets.
Discovery of Lower Cretaceous synmetamorphic thrust tectonics in French Lesser Antilles (La Désirade Island, Guadeloupe): Implications for Caribbean geodynamics
Authors: Corsini M. , Lardeaux J. M. , Verati C. , Voitus E. , Balagne M.
Published: July 2011

Located east of Guadeloupe, the island of La Désirade exhibits the oldest rocks of the Lesser Antilles arc and the eastern Caribbean plate. An old magmatic basement is composed of (1) late Jurassic ophiolitic complex with meta‐basaltic pillow lavas and interbedded radiolarites, (2) acid igneous complex comprising meta‐quartz‐diorite and meta‐rhyolitic lavas flows, and (3) meta‐diabasic/microdioritic dyke swarm complex. We present and discuss the discovery of synmetamorphic thrust tectonics in this island. Based on detailed structural analysis we evidenced two main compressive events. The first event (D1) is characterized by pervasive folding associated with thrust development. In the northeastern part of the island, a major thrust fault, the Grand Abaque Thrust, has been discovered which displaces for several kilometers the acid igneous complex onto the ophiolitic unit. The second deformation event (D2) is featured by a main pervasive cleavage S2 observed at the regional scale associated with upright folding (F2) and by the development of two sets of conjugated steeply dipping strike‐slip shear zones, dextral 130°N and sinistral 20°N striking, respectively. Microstructural observations indicate that Greenschist facies metamorphism is clearly contemporaneous with the development of D1 and D2 superimposed tectonic structures. Ar/Ar geochronology was performed on two bulk of adularia minerals sampled in the northeast volcanic complex within a deformed zone related to a D2 event. These analyses yield well‐defined and concordant plateau ages at 106.2 ± 1.7 Ma and 107.2 ± 1.8 Ma. Thus, shortening and thickening tectonics occurred during Lower Cretaceous (Albian). In the available framework of Caribbean geodynamics, the synmetamorphic thrust tectonics we discovered in the French Lesser Antilles is related to the collision between an Aptian‐Albian oceanic plateau and the Andean‐Cordilleran east‐dipping subduction zone. Our results support subduction polarity reversal during Lower Cretaceous.
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0
Authors: Fricke W. Florian , White James , Arze Cesar , Matalka Malcolm , Team The CloVR , White Owen , Angiuoli Samuel
Published: July 2011

The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Mothur – a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;C) Qiime – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac) for within-(alpha diversity) and between-(beta diversity) sample analysis;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyrotagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.
Agenda of the "BioSharing workshop - Bringing catalogues of bio-resource and standards together"
Authors: Sansone Susanna-Assunta , Rocca-Serra Philippe , Field Dawn , Gaudet Pascale
Published: July 2011

This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were twofold:1. Ensure that BioSharing (www.biosharing.org), a catalogue of minimal information checklists, terminologies and exchange formats (hereafter called standards) and policies, complements and links to existing catalogues of tools and databases, and also to publications and related material;2. Outline the technical implementations of the bioDBcore checklist (www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to ensure (bi-directional) linking to the BioSharing catalogue.Location: University of Oxford, UK.Date: June 8th and 9th 2011
Structural and biophysical insight into cholesteryl ester-transfer protein
Authors: Hall Justin , Qiu Xiayang
Published: July 2011

CETP (cholesteryl ester-transfer protein) is essential for neutral lipid transfer between HDL (high-density lipoprotein) and LDL (low-density lipoprotein) and plays a critical role in the reverse cholesterol transfer pathway. In clinical trials, CETP inhibitors increase HDL levels and reduce LDL levels, and therefore may be used as a potential treatment for atherosclerosis. In this review, we cover the analysis of CETP structure and provide insights into CETP-mediated lipid transfer based on a collection of structural and biophysical data.
Dual host-defence functions of SPLUNC2/PSP and synthetic peptides derived from the protein
Authors: Gorr Sven-Ulrik , Abdolhosseini Mahsa , Shelar Anuradha , Sotsky Julie
Published: July 2011

PSP (parotid secretory protein)/SPLUNC2 (short palate, lung and nasal epithelium clone 2) is expressed in human salivary glands and saliva. The protein exists as an N-glycosylated and non-glycosylated form and both appear to induce agglutination of bacteria, a major antibacterial function for salivary proteins. Both forms of PSP/SPLUNC2 bind LPS (lipopolysaccharide), suggesting that the protein may also play an anti-inflammatory role. Based on the predicted structure of PSP/SPLUNC2 and the location of known antibacterial and anti-inflammatory peptides in BPI (bactericidal/permeability-increasing protein) and LBP (LPS-binding protein), we designed GL13NH2 and GL13K, synthetic peptides that capture these proposed functions of PSP/SPLUNC2. GL13NH3 agglutinates bacteria, leading to increased clearance by macrophages and reduced spread of infection in a plant model. GL13K kills bacteria with a minimal inhibitory concentration of 5–10 μg/ml, kills bacteria in biofilm and retains activity in 150 mM NaCl and 50% saliva. Both peptides block endotoxin action, but only GL13K appears to bind endotoxin. The peptides do not cause haemolysis, haemagglutination in serum, inhibit mammalian cell proliferation or induce an inflammatory response in macrophages. These results suggest that the GL13NH2 and the modified peptide GL13K capture the biological activity of PSP/SPLUNC2 and can serve as lead compounds for the development of novel antimicrobial and anti-inflammatory peptides.
LBP/BPI proteins and their relatives: conservation over evolution and roles in mutualism
Authors: Krasity Benjamin C. , Troll Joshua V. , Weiss Jerrold P. , McFall-Ngai Margaret J.
Published: July 2011

LBP [LPS (lipopolysaccharide)-binding protein] and BPI (bactericidal/permeability-increasing protein) are components of the immune system that have been principally studied in mammals for their involvement in defence against bacterial pathogens. These proteins share a basic architecture and residues involved in LPS binding. Putative orthologues, i.e. proteins encoded by similar genes that diverged from a common ancestor, have been found in a number of non-mammalian vertebrate species and several non-vertebrates. Similar to other aspects of immunity, such as the activity of Toll-like receptors and NOD (nucleotide-binding oligomerization domain) proteins, analysis of the conservation of LBPs and BPIs in the invertebrates promises to provide insight into features essential to the form and function of these molecules. This review considers state-of-the-art knowledge in the diversity of the LBP/BPI proteins across the eukaryotes and also considers their role in mutualistic symbioses. Recent studies of the LBPs and BPIs in an invertebrate model of beneficial associations, the Hawaiian bobtail squid Euprymna scolopes' alliance with the marine luminous bacterium Vibrio fischeri, are discussed as an example of the use of non-vertebrate models for the study of LBPs and BPIs.
Role of oxidative stress and antioxidant enzymes in Crohn's disease
Authors: Iborra Marisa , Moret Inés , Rausell Francisco , Bastida Guillermo , Aguas Mariam , Cerrillo Elena , Nos Pilar , Beltrán Belén
Published: July 2011

There is increasing interest in oxidative stress being a potential aetiological factor and/or a triggering factor in Crohn's disease, rather than a concomitant occurrence during the pathogenesis of the disease. Recent research has shown that the immune mononuclear cells of Crohn's disease patients are induced to produce hydrogen peroxide (H2O2). Similarly, the regulation of antioxidant enzymes during disease in these cells has been unravelled, showing that SOD (superoxide dismutase) activity and GPx (glutathione peroxidase) activity is increased during active disease and returns to normal in remission phases. However, catalase remains constantly inhibited which supports the idea that catalase is not a redox-sensitive enzyme, but a regulator of cellular processes. ROS (reactive oxygen species) can be produced under the stimulus of different cytokines such as TNFα (tumour necrosis factor α). It has been shown in different experimental models that they are also able to regulate apoptosis and other cellular processes. The status of oxidative stress elements in Crohn's disease and their possible implications in regulating cellular processes are reviewed in the present paper.
Role of Toll-like receptors in liver health and disease
Authors: Broering Ruth , Lu Mengji , Schlaak Joerg F.
Published: July 2011

TLRs (Toll-like receptors), as evolutionarily conserved germline-encoded pattern recognition receptors, have a crucial role in early host defence by recognizing so-called PAMPs (pathogen-associated molecular patterns) and may serve as an important link between innate and adaptive immunity. In the liver, TLRs play an important role in the wound healing and regeneration processes, but they are also involved in the pathogenesis and progression of various inflammatory liver diseases, including autoimmune liver disease, alcoholic liver disease, non-alcoholic steatohepatitis, fibrogenesis, and chronic HBV (hepatitis B virus) and HCV (hepatitis C virus) infection. Hepatitis viruses have developed different evading strategies to subvert the innate immune system. Thus recent studies have suggested that TLR-based therapies may represent a promising approach in the treatment in viral hepatitis. The present review focuses on the role of the local innate immune system, and TLRs in particular, in the liver.
The influence of carbon nanotube structure on complex permittivity and determination of filler density by microwave techniques
Authors: Xiao Ting , Yang He Lin , Zhang Guo Ping
Published: July 2011

The influence of carbon nanotube geometry and morphology on complex permittivity (both ɛ′ and ɛ″) was investigated. In a dilute complex system, it was found that single walled carbon nanotubes (SWNTs) composites can obtain a higher relative dielectric permittivity due to the largest length/diameter aspect ratio (A. R.). Although the A. R. did make a difference, the variation of permittivity could be slightly influenced by the structure in microwave frequencies. Motivated by the idea that the permittivity of carbon nanotubes (CNTs) composites is mostly related to the volume fraction, a process which can determine the sequence of CNTs density is proposed. The influence of the functional group on CNTs was investigated based on dielectric measurements of CNTs-paraffin nanocomposites. The experimental results denoted that the variation of both ɛ′ and ɛ″ in the coiled CNTs (CCNTs) composites shown less frequency dependence.
Study of Si-based three-dimensional photonic crystals infiltrated with liquid crystal within a one-dimensional effective model
Authors: Chang L. , Liao C.-Z. , Wu G. Y.
Published: July 2011

In this work, we study Si-based three-dimensional photonic crystals infiltrated with liquid crystal (LC), within a one-dimensional effective medium model. Two specific systems of diamond crystal structure compatible with the mature Si technology are considered, namely, (i) diamond-1 which is composed of LC spheres embedded in the Si background, and (ii) diamond-2 which is the inverse of the foregoing structure, with Si spheres immersed in the LC background. For each system, the study is carried out with the LC being in the isotropic/nematic phase. The one-dimensional effective medium model employed in the study is an improved version of the conventional mean field theory (MFT). While retaining partially the typical advantage of MFT, e.g., physical transparency, analytical capability, and computational efficiency, it goes beyond the conventional MFT by taking into account the modulation of dielectric constant in the direction of wave propagation. As such, it improves greatly the poor numerical accuracy inherent in the MFT. We find a partial gap between the 2nd and 3rd bands, with the gap-to-midgap ratio being a few percents. Moreover, the edge of partial gap may be shifted by about 1% (in relative unit) when optical, thermal, or electrical means are applied to alter the phase of LC or rotate the axis of nematic molecules.
Generalization of the Bollobás-Riordan polynomial for tensor graphs
Authors: Tanasa Adrian
Published: July 2011

Tensor models are used nowadays for implementing a fundamental theory of quantum gravity. We define here a polynomial \documentclass[12pt]{minimal}\begin{document}$\mathcal T$\end{document}T encoding the supplementary topological information. This polynomial is a natural generalization of the Bollobás-Riordan polynomial (used to characterize matrix graphs) and is different from the Gurău polynomial [R. Gurău, Ann. Henri Poincare 11, 565 (2010)]10.1007/s00023-010-0035-6, defined for a particular class of tensor graphs, the colorable ones. The polynomial \documentclass[12pt]{minimal}\begin{document}$\mathcal T$\end{document}T is defined for both colorable and non-colorable graphs and it is proved to satisfy the deletion/contraction relation. A non-trivial example of a non-colorable graphs is analyzed.
Polarization fatigue in ferroelectric vinylidene fluoride and trifluoroethylene copolymer thin films
Authors: Zhu GuoDong , Gu Yin , Yu Hao , Fu ShaoSong , Jiang YuLong
Published: July 2011

In recent years polarization fatigue in ferroelectric polymers has attracted much attention due to their potential use in nonvolatile memories, though the mechanism is still an open question. Here we mainly focus on the experimental observations on two physical phenomena occurring during fatigue process: The frequency dependence of the fatigue rate and the change in the coercive field with increased fatigue cycles. The frequency dependence of fatigue rate shows that at lower fatigue frequencies the rate obeys a universal scaling behavior with respect to N/f, where N is the fatigue cycles and f is the fatigue frequency, while at much higher frequencies this scaling behavior is broken and the fatigue rate is N/f dependent. In addition, both the increase and the decrease of the coercive field are observed, which indicates that the change in the coercive field should be dominated by different mechanisms. Based on the understanding of the crucial influence of space charges on electrical fatigue, we give a detailed discussion on both phenomena.
Mobility and fill factor correlation in geminate recombination limited solar cells
Authors: Andersson L. Mattias , Müller Christian , Badada Bekele H. , Zhang Fengling , Würfel Uli , Inganäs Olle
Published: July 2011

Empirical data for the fill factor as a function of charge carrier mobility for two different polymer:fullerene systems is presented and analyzed. The results indicate that charge extraction depth limitations and space charge effects are inconsistent with the observed behavior, and the decrease in the fill factor is, instead, attributed to the field-dependent charge separation and geminate recombination. A solar cell photocurrent limited by the Onsager-Braun charge transfer exciton dissociation is shown to be able to accommodate the experimental observations. Charge dissociation limited solar cells always benefit from increased mobilities, and the negative contribution from the reduced charge separation is shown to be much more important for the fill factor in these material systems than any adverse effects from charge carrier extraction depth limitations or space charge effects due to unbalanced mobilities. The logarithmic dependence of the fill factor on the mobility for such a process is also shown to imply that simply increasing the mobilities is an impractical way to reach very high fill factors under these conditions since unrealistically high mobilities are required. A more controlled morphology is, instead, argued to be necessary for high performance.
Interfacial, optical properties and band offsets of HfTiON thin films with different nitrogen concentrations
Authors: Liu M. , Fang M. , Wang X. J. , Luo Y. Y. , Wang H. M. , Kang S. H. , Zhang L. D. , Fang Q.
Published: July 2011

The effect of nitrogen concentration on the interfacial and optical properties, as well as band offsets of HfTiO thin films by rf sputtering HfTi alloy target has been systematically investigated. The results indicate that an interfacial layer is unavoidably formed between HfTiON thin films and Si substrate, and the main content of the interfacial layer is silicate. No silicide is formed in the interfacial layer which is partly responsible for the poor electrical properties of high-k gate dielectrics. The optical properties of HfTiON films change, such as the refractive index decreases, while the extinction coefficient increases with the increase of N content, due to the defects increase in the films. The results also indicate that the bandgap and VB offset reduce with the introduction of N into HfTiO thin films. The CB offset of the HfTiON thin films is almost unchanged indicating that the N concentration has little effect on CB offset. However, the bandgap and band offsets are all higher than 1 eV, the sufficient band offsets still makes sputtering-derived HfTiON films by HfTi alloy target a promising high-k gate dielectric for future complementary metal oxide semiconductor technology.
Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method
Authors: Nagata Takeshi , Fedorov Dmitri G. , Ishimura Kazuya , Kitaura Kazuo
Published: July 2011

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order Møller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H2O)64 and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.
Nanoparticle Brownian motion and hydrodynamic interactions in the presence of flow fields
Authors: Uma B. , Swaminathan T. N. , Radhakrishnan R. , Eckmann D. M. , Ayyaswamy P. S.
Published: July 2011

We consider the Brownian motion of a nanoparticle in an incompressible Newtonian fluid medium (quiescent or fully developed Poiseuille flow) with the fluctuating hydrodynamics approach. The formalism considers situations where both the Brownian motion and the hydrodynamic interactions are important. The flow results have been modified to account for compressibility effects. Different nanoparticle sizes and nearly neutrally buoyant particle densities are also considered. Tracked particles are initially located at various distances from the bounding wall to delineate wall effects. The results for thermal equilibrium are validated by comparing the predictions for the temperatures of the particle with those obtained from the equipartition theorem. The nature of the hydrodynamic interactions is verified by comparing the velocity autocorrelation functions and mean square displacements with analytical and experimental results where available. The equipartition theorem for a Brownian particle in Poiseuille flow is verified for a range of low Reynolds numbers. Numerical predictions of wall interactions with the particle in terms of particle diffusivities are consistent with results, where available.