bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point Defect Clusters and Dislocations in FIB Irradiated Nanocrystalline Aluminum Films: An Electron Tomography and Aberration-Corrected High-Resolution ADF-STEM Study
Authors: Idrissi Hosni , Turner Stuart , Mitsuhara Masatoshi , Wang Binjie , Hata Satoshi , Coulombier Michael , Raskin Jean-Pierre , Pardoen Thomas , Van Tendeloo Gustaaf , Schryvers Dominique 
Published: October 2011

AbstractFocused ion beam (FIB) induced damage in nanocrystalline Al thin films has been characterized using advanced transmission electron microscopy techniques. Electron tomography was used to analyze the three-dimensional distribution of point defect clusters induced by FIB milling, as well as their interaction with preexisting dislocations generated by internal stresses in the Al films. The atomic structure of interstitial Frank loops induced by irradiation, as well as the core structure of Frank dislocations, has been resolved with aberration-corrected high-resolution annular dark-field scanning TEM. The combination of both techniques constitutes a powerful tool for the study of the intrinsic structural properties of point defect clusters as well as the interaction of these defects with preexisting or deformation dislocations in irradiated bulk or nanostructured materials.
Hacking the JPEG/PDF tree format
Authors: Hughes Joseph 
Published: October 2011

AbstractWe have been illustrating the relationships between species and genes as trees for over a century. Whilst in the early years of morphological and molecular phylogenetics, embedding illustrations into manuscripts might have been the most appropriate way to disseminate knowledge, this has resulted in the locking up of phylogenetic hypotheses into the pages of journals and books without an easy way to access this information. As a result, most phylogenetic knowledge is lost upon publication. I will explain the reasons for re-using published trees, discuss ways to liberate this information and avoid these problems in the future.
In silico designing of activator for human IGF2 protein for effective cardiovascular disease therapeutics
Authors: Sandhya rani M , Munikumar Manne , Umamaheswari Amineni 
Published: October 2011

AbstractInsulin like growth factor-II (IGF2) is a member of IGF family, the main role of IGF2 is as a growth hormone during gestation or fetal development. Ischematic stroke, atherosclerosis and pathological cardiac hypertrophy are associated with low circulating levels of IGF2. 5-aza-2’-deoxycytidine increases the activity of IGF2, due to high toxicity of 5aza2’deoxycytidine, some silenced genes are also expressed that cause various cancer diseases. In the present study an in silico approach was used to design the potential activator for IGF2 without side effects to treat cardiovascular diseases. Ligand binding sites were predicted using CASTp for drug target. 361 ligand analogs for 5-aza-2’-deoxycytidine were identified through virtual screening from Ligand.Info database. Docking studies were performed using Schrodinger software (2010) generated 13 lead agonists for human IGF2. Docking complexes of 13 lead agonists and 5aza2’deoxycytidine with IGF2 were compared and four leads with better affinity, ADME properties and lower XPGscore than 5-aza-2’-deoxycytidine were proposed as potential activators. Lead‘1’ (mizoribine), the best ranked activator (XPG score -7.181) having good binding affinity, could be a better drug for cardiovascular diseases and it is forming three hydrogen bonds, two bonds with Thr-58 and one bond with Cys-60, and van der Waal interactions with the binding site residues of IGF2 such as Leu-13, Leu-17 Ile-42, Val-43, Cys-46, Leu-56 and Try -59. Mizoribine decreases the proliferation of vascular smooth muscle cells and the elevated levels of human IGF2 helps in cardiovascular therapies.
Application of Percellome Toxicogenomics to Food Safety
Authors: Kanno J. , Aisaki K. , Igarashi K. , Nakatsu N. , Kodama Y. , Sekita K. , Takagi A. , Kitajima S. 
Published: October 2011

When an item of food is found to be non-toxic by routine toxicity testing at the maximal applicable dose of 10 g kg−1, the tolerable daily intake is calculated, using a safety factor of 1/100, to be 100 mg kg−1. Thus such a study cannot guarantee the safety of a food which is consumed by the grams or even tens of grams per kg body weight. For other reasons, flavorings are also not subject to routine toxicity testing. In both cases, they normally do not exert detectable histopathological effects on experimental animals at applicable dose ranges. One strategy to cope with this problem is to detect early molecular changes that occur prior to morphological alterations. Our Percellome Toxicogenomics is designed to identify dynamic and extensive networks of genes whose time- and dose-dependent patterns of expression allows its toxic effects to be predicted.
Here, we show that estragole induces genes known to be regulated by PPAR-alpha. The program, which automatically compares over 100 chemicals in our database, identifies clofibrate and di(2-ethylhexyl) phthalate (DEHP) as the two most similar chemicals. Further analysis indicates that DEHP activates both PPAR-alpha and the constitutive androstane receptor (CAR), whereas estragole and clofibrate activate PPAR-alpha but not CAR. Our findings may help elucidate the mechanism(s) of the reported estragole hepatocarcinogenesis.
An advantage of the Percellome method is that the responses obtained in different studies can be compared directly. Judging from the magnitude of the commonly up-regulated genes, estragole appears to be as potent as clofibrate in activating PPAR-alpha signaling.
Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing
Authors: Benichou Jennifer , Ben‐Hamo Rotem , Louzoun Yoram , Efroni Sol 
Published: October 2011

SummaryRecent scientific discoveries fuelled by the application of next‐generation DNA and RNA sequencing technologies highlight the striking impact of these platforms in characterizing multiple aspects in genomics research. This technology has been used in the study of the B‐cell and T‐cell receptor repertoire. The novelty of immunosequencing comes from the recent rapid development of techniques and the exponential reduction in cost of sequencing. Here, we describe some of the technologies, which we collectively refer to as Rep‐Seq (repertoire sequencing), to portray achievements in the field and to present the essential and inseparable role of next‐generation sequencing to the understanding of entities in immune response. The large Rep‐Seq data sets that should be available in the near future call for new computational algorithms to segue the transition from ‘classic’ molecular‐based analysis to system‐wide analysis. The combination of new algorithms with high‐throughput data will form the basis for possible new clinical implications in personalized medicine and deeper understanding of immune behaviour and immune response.
Acculturation in the adaptation of Chinese‐American women to breast cancer: a mixed‐method approach
Authors: Tsai Tzu‐I , Morisky Donald E , Kagawa‐Singer Marjorie , Ashing‐Giwa Kimlin T 
Published: October 2011

Aims.  To explore how and to what extent acculturation and immigration affect Chinese‐American immigrant women’s breast cancer experience.Background.  Acculturation is an important indicator for immigrant health. Less empirical research has been conducted on the association between acculturation and breast cancer experience among Chinese immigrant women in the USA.Design.  A mixed methods study.Methods.  A total of 107 Chinese‐American women with breast cancer completed the structured questionnaire survey, and 16 women completed face‐to‐face in‐depth interviews.Results.  In the quantitative findings, acculturation was related to health beliefs, social support and life stress. Cultural interpretations of the qualitative information are offered to show that breast cancer experience was intertwined with cultural adaptation in a given immigrant environment. Chinese cultural beliefs persistently, even after years of immigration, guide Chinese‐American immigrant women to respond to breast cancer across the meaning of health and illness, family ties and involvement and social interaction.Conclusion.  Our findings show that acculturation is related to health beliefs, social support and life stress in the trajectory of breast cancer adaptation among Chinese‐American immigrant women. Life stresses derived from immigration bring additional difficulties for immigrant women living with cancer.Relevance to clinical practice.  This study pinpoints that traditional cultural beliefs and immigration stress may influence Chinese‐American women to cope with breast cancer. To promote culturally sensitive cancer care for immigrants, healthcare professionals should be aware of and learn intercultural competence. Ethnic social support or outreach healthcare programme may benefit new immigrant families or the immigrant families, who lack social connection, to cope with cancer.
The relationship between attitudes towards different containment measures and their usage in a national sample of psychiatric inpatients
Authors: DACK C. , ROSS J. , BOWERS L. 
Published: October 2011

Accessible summary
The Attitudes to Containment Questionnaire has good construct validity.
Patients have separate attitudes towards different containment measures rather than an overall attitude towards containment in general.
High levels of intramuscular medication use on wards were associated with lower approval ratings from patients towards a number of other containment measures.
The use of IM medication has a negative impact on attitudes towards all measures of containment regardless of whether a patient has personally experienced it or has just witnessed it.
AbstractThe aims of this report were to explore the relationships between patients' approval of containment measures, their levels of usage and patients' individual experience of each measure. Additionally the psychometric properties of the Attitudes to Containment Measures Questionnaire (ACMQ) were tested. A cross‐sectional design was used. The ACMQ was completed by 1361 patients across 136 acute psychiatric wards from three regions in England that participated in the ‘City 128’ study. Staff on each ward completed the Patient‐Staff Conflict Checklist – Shift Report at the end of each shift to log how often each containment measure was used. Frequency of patient reported containment correlated with rates reported by staff. Patients had separate attitudes to each containment measure rather than an attitude towards containment in general. High frequency of coerced intramuscular (IM) medication use was associated with negative attitudes to nearly all types of containment. The ACMQ has good construct validity. In wards where high levels of IM medication are used, all patients have lower approval ratings for a number of other containment measures. This suggests that IM medication has a negative impact not only on those subjected to it but also patients who witness it. Measures to reduce the negative impact of IM medication are discussed.
Serotonin‐immunoreactive neurons and mast cells in the mouse esophagus suggest involvement of serotonin in both motility control and neuroimmune interactions
Authors: Hempfling C. , Neuhuber W. L. , Wörl J. 
Published: October 2011

AbstractBackground  Serotonin is a major transmitter in the gastrointestinal tract, but little is known about the serotonergic system in the esophagus.Methods  The aim of this study was to use multilabel immunofluorescence to characterize serotonin‐positive nerve cell bodies and fibers and their relationship with other neuronal and non‐neuronal elements in the mouse esophagus. Antibodies against serotonin, vesicular acetylcholine transporter (VAChT), choline acetyltransferase (ChAT), protein gene product 9.5 (PGP 9.5), and α‐bungarotoxin (α‐BT), were used.Key Results  Serotonin‐containing perikarya represented ∼10% of all PGP 9.5‐positive myenteric neurons. Serotonin‐positive varicose nerve fibers were found in the lamina muscularis mucosae and present on ∼13% of α‐BT–labeled motor endplates in addition to VAChT‐immunoreactive motor terminals. As ChAT‐positive neurons of the compact formation of the nucleus ambiguus were negative for serotonin, serotonin‐positive varicosities on motor endplates are presumed to be of enteric origin. On the other hand, cholinergic ambiguus neurons were densely supplied with serotonin‐positive varicosities. The tela submucosa and tunica adventitia contained large numbers of serotonin‐positive mast cells, a few of which were in close association with serotonin‐positive nerve fibers.Conclusions & Inferences  The mouse esophagus is endowed with a rich serotonin‐positive intrinsic innervation, including enteric co‐innervation of striated muscles. Serotonin may modulate vagal motor innervation of esophageal‐striated muscles not only at the central level via projections of the raphe nuclei to the nucleus ambiguus but also at the peripheral level via enteric co‐innervation. In addition, mast cells represent a non‐neuronal source of serotonin, being involved in neuroimmune processes.
Variability of cold‐water coral mounds in a high sediment input and tidal current regime, Straits of Florida
Authors: CORREA THIAGO B.S. , GRASMUECK MARK , EBERLI GREGOR P. , REED JOHN K. , VERWER KLAAS , PURKIS SAM 
Published: October 2011

AbstractCold‐water coral mound morphology and development are thought to be controlled primarily by current regime. This study, however, reveals a general lack of correlation between prevailing bottom current direction and mound morphology (i.e. footprint shape and orientation), as well as current strength and mound size (i.e. footprint area and height). These findings are based on quantitative analyses of a high‐resolution geophysical dataset collected with an Autonomous Underwater Vehicle from three cold‐water coral mound sites at the toe of slope of Great Bahama Bank. The three sites (80 km2 total) have an average of 14 mounds km−2, indicating that the Great Bahama Bank slope is a major coral mound region. At all three sites living coral colonies are observed on the surface of the mounds, documenting active mound growth. Morphometric analysis shows that mounds at these sites vary significantly in height (1 to 83 m), area (81 to 6 00 000 m2), shape (mound aspect ratio 0·1 to 1) and orientation (mound longest axis 0 to 180°). The Autonomous Underwater Vehicle measured bottom current data depict a north–south flowing current that reverses approximately every six hours. The tidal nature of this current and its intermittent deviations during reversals are interpreted to contribute to the observed mound complexity. An additional factor contributing to the variability in mound morphometrics is the sediment deposition rate that varies among and within sites. At most locations sedimentation rate lags slightly behind mound growth rate, causing mounds to develop into large structures. Where sedimentation rates are higher than mound growth rates, sediment partially or completely buries mounds. The spatial distribution and alignment of mounds can also be related to gravity mass deposits, as indicated by geomorphological features (for example, slope failure and linear topographic highs) in the three‐dimensional bathymetry. In summary, variability in sedimentation rates, current regime and underlying topography produce extraordinarily high variability in the distribution, development and morphology of coral mounds on the Great Bahama Bank slope.
A comparison of Nd model ages and U–Pb zircon ages of Grenville granitoids: constraints on the evolution of the Laurentian margin from 1.5 to 1.0 Ga
Authors: McNutt Robert H. , Dickin Alan P. 
Published: October 2011

Terra Nova, 24, 7–15, 2012AbstractConcordance and discordance between Nd model ages and U–Pb ages is still widely misunderstood in the geological community. In the SW Grenville Province, plutonic orthogneisses often yield TDM ages significantly older than U–Pb crystallization ages, but this can be understood in a model where a series of crustal Nd isotope evolution lines departs at intervals from the depleted mantle (DM) evolution line. Seven samples with concordant U–Pb and Nd model ages have initial ε Nd on the DM line, attributed to melting of juvenile crust generated in an Elzevirian back‐arc rift zone. In contrast, plutons with discordant U–Pb and Nd model ages lie near crustal evolution lines defined by suites of basement gneisses on the flanks of the rift zone. This study shows that Nd data from large suites of geographically constrained, undated grey gneiss provide a crustal evolution framework for orogen‐scale interpretation of more scattered but precisely dated plutons.
DOES A FITTED ABDOMINAL CORSET MAKES COLONOSCOPY MORE TOLERABLE?
Authors: TOROS AHMET BURAK , ERSOZ FEYZULLAH , OZCAN OZHAN 
Published: October 2011

Background and Aim:  The present study evaluated the usefulness of a fitted abdominal corset for colonoscopy, enabling proper compression of the abdomen during the entire examination.Methods:  Patients undergoing colonoscopy were subjected to either traditional methods or to using a fitted abdominal corset. Two hundred and sixteen patients were divided into two groups: group 1 (conventional colonoscopy) and group 2 (colonoscopy with abdominal corset). Cecal intubation rate and time need for manual compression and change of position were recorded. At the end of each colonoscopic examination, the patient evaluated pain by an 11‐point visual analog scale from 0 to 10 (0: no pain, 10: worst pain).Results:  Cecal intubation time was shorter, the need for extra manual compression and change of position decreased and patients felt less pain during the procedure as denoted by lower visual analog scale scores in the group using a fitted abdominal corset, when compared to the group without a corset, in a statistically proven manner.Conclusion:  Our data confirm the usefulness of the abdominal corset in decreasing the degree of patient pain and it makes colonoscopy easier and quicker with less manipulation, so we propose using a fitted abdominal corset during routine colonoscopic procedures.
Mozart'sObviouslyCorruptMinuet
Authors: GJERDINGEN ROBERT O. 
Published: October 2011

ABSTRACTThe Romantic and Modern reception and reinterpretation of eighteenth‐century music stretches over a period much longer than that of the eighteenth century itself, in the process forming its own authenticity and norms. Modern editors of eighteenth‐century music must occasionally grapple with musical texts which appear to violate either the earlier or later standards. A minuet whose text seemed ‘obviously corrupt’ to the official editors of Mozart's keyboard sonatas would probably have seemed highly artful yet utterly normative to Mozart or his audiences. A focus on the norms of musical phrases was proposed by the Victorian author Violet Paget, writing under the pseudonym Vernon Lee. Her immersion in eighteenth‐century music at an early age, along with her training in the Italian tradition, gave her a unique position from which to comment on the differences between the musical culture of her own time and that of Mozart and his Italian models.
A figurative proverb test for dementia: rapid detection of disinhibition, excuse and confabulation, causing discommunication
Authors: YAMAGUCHI Haruyasu , MAKI Yohko , YAMAGUCHI Tomoharu 
Published: October 2011

AbstractBackground:  Communicative disability is regarded as a prominent symptom of demented patients, and many studies have been devoted to analyze deficits of lexical‐semantic operations in demented patients. However, it is often observed that even patients with preserved lexical‐semantic skills might fail in interactive social communication. Whereas social interaction requires pragmatic language skills, pragmatic language competencies in demented subjects have not been well understood. We propose here a brief stress‐free test to detect pragmatic language deficits, focusing on non‐literal understanding of figurative expression. We hypothesized that suppression of the literal interpretation was required for figurative language interpretation.Methods:  We examined 69 demented subjects, 13 subjects with mild cognitive impairment and 61 healthy controls aged 65 years or more. The subjects were asked the meaning of a familiar proverb categorized as a figurative expression. The answers were analyzed based on five factors, and scored from 0 to 5. To consider the influence of cognitive inhibition on proverb comprehension, the scores of the Stroop Colour–Word Test were compared concerning correct and incorrect answers for each factor, respectively. Furthermore, the characteristics of answers were considered in the light of excuse and confabulation qualitatively.Results:  The proverb comprehension scores gradually decreased significantly as dementia progressed. The literal interpretation of the proverb, which showed difficulties in figurative language comprehension, was related to disinhibition. The qualitative analysis showed that excuse and confabulation increased as the dementia stage progressed.Conclusions:  Deficits in cognitive inhibition partly explains the difficulties in interactive social communication in dementia. With qualitative analysis, asking the meaning of a proverb can be a brief test applied in a clinical setting to evaluate the stage of dementia, and to illustrate disinhibition, confabulation and excuse, which might cause discommunication and psychosocial maladjustment in demented patients.
Protease inhibitor levels in periodontal health and disease
Authors: Kretschmar S. , Yin L. , Roberts F. , London R. , Flemmig T. T. , Arushanov D. , Kaiyala K. , Chung W. O. 
Published: October 2011

Kretschmar S, Yin L, Roberts F, London R, Flemmig TT, Arushanov D, Kaiyala K, Chung WO. Protease inhibitor levels in periodontal health and disease. J Periodont Res 2012; 47: 228–235. © 2011 John Wiley & Sons A/SBackground and Objective:  Our previous study showed that protease inhibitors were attenuated by the periodontal pathogen Porphyromonas gingivalis in cultured gingival epithelial cells. We hypothesize that fewer protease inhibitors would be present in more advanced periodontal disease sites, where the level of P. gingivalis may be high. The goal of this study was to investigate the relationship between the protease inhibitor [secretory leukocyte protease inhibitor (SLPI), elastase‐specific inhibitor (ELAFIN) and squamous cell carcinoma antigen (SCCA)] levels in gingival crevicular fluid and the number of P. gingivalis micro‐organisms in subgingival plaque.Material and Methods:  Plaque samples from subjects without (n = 18) and with moderate to advanced periodontitis (n = 41) were used to quantify P. gingivalis using real‐time PCR. Protease inhibitor levels in the gingival crevicular fluid of all the subjects were determined by ELISA.Results:  P. gingivalis was detected in 68.3% of patients with periodontitis, while 16.7% of subjects without periodontitis had a detectable level of P. gingivalis. Patients with periodontitis and P. gingivalis in their plaque exhibited lower SLPI and ELAFIN levels (p < 0.001) compared with control subjects without periodontitis. Secretory leukocyte protease inhibitor was also reduced (p < 0.05) in gingival crevicular fluid of periodontitis patients without a detectable level of P. gingivalis. Periodontitis patients with high vs. low levels of P. gingivalis exhibited reciprocal mean levels of SLPI and ELAFIN concentrations.Conclusion:  The reduced concentrations of SLPI and ELAFIN may contribute to the loss of host protective capacity and increase susceptibility to breakdown from chronic infection. The work of this investigation may aid in finding diagnostic and prognostic markers in periodontal health and disease and may also help in finding pharmacological targets directed against periodontal inflammation.