bluuebunny/crossref_metadata_2025 huggingface dataset:
JOB VALUES OF PROSPECTIVE CLASSROOM TEACHERS
Authors: Kushel Gerald , Masih Lalit K.
Published: December 2011

Seventy‐seven teachers under training in the Graduate School of Education of Long Island University responded to a Job Values Questionnaire. The subjects were instructed to rank eleven job values in order of preference. Median rankings for the samples were secured and analyzed. The values held in highest regard dealt with an interesting and stimulating job, freedom of expression, helping others, and independence. Implications of the findings are discussed and recommendations are made for further studies.
A STUDY OF THE VALIDITY OF THE GRE BATTERY IN PREDICTING FOUR CRITERIA OF SUCCESS IN DOCTORAL DEGREE PROGRAMS
Authors: Houston Samuel H. , Strohmeyer Eric
Published: December 2011

The predictive validity of Graduate Record Examination (GRE) scores for doctoral degree programs in education at Colorado State College were investigated. The predictor variables included two GRE aptitude scores, three GRE area scores, plus the GRE advanced education score. Criterion variables included: (a) grade point average in doctoral studies; (b) graduation versus dismissal from the program; (c) normative judgment analysis (JAN) rating; and (d) ipsative JAN rating. Except for the normative JAN criterion, multiple correlation coefficients were all statistically significant though weak from a predictive viewpoint.
NEED FOR ACHIEVEMENT: RELATION TO ACADEMIC ACHIEVEMENT AND INVENTORIED NEEDS
Authors: Auvenshine C. D. , Smith David F. , Henaghan Margaret B.
Published: December 2011

Four groups of students were selected on the basis of EPPS need for achievement scores and their grade point averages (GPA). The group included these combinations: high need/high achievement; (b) high need/low achievement; (c) low need/high achievement; and (d) low need/low achievement. Each group was compared with every other group on the EPPS scales and on ACT scores by t‐test. Significant differences were found that form patterns differentiating among the various groups, especially between high‐ and low‐need groups and between high and low achievers within the low‐need group. These differences were on scales of abasement, affiliation, autonomy, deference, intraception, and nurturance.
SOME GENERAL EFFECTS OF A FOUNDATIONS OF EDUCATION COURSE ON SELECTED PERSONALITY VARIABLES OF TEACHER CANDIDATES
Authors: Asbury Frank R. , Ball Robert L. , Costantino Nicholas V.
Published: December 2011

This study describes the effects of systematic treatment, discussion, and concrete exemplification in classroom practice of selected concepts of human behavior on some personality variables of teacher candidates in a foundations of education course. Data were gathered by means of pre‐ and post‐course tests using the Minnesota Teacher Attitude Inventory (MTAI) and the Myers‐Briggs Type Indicator (MBTI). Statistical analysis of the data revealed candidates (a) achieved significantly higher scores on post‐course MTAI measures; (b) made a significant mean movement from judgmental toward perceptive preferences on the MBTI; (c) made a significant mean movement from “Thinking” toward “Feeling” preferences on the MBTI; and (d) failed to change significantly on the Sensing‐Intuiting and Extro‐version‐Introversion scales of the MBTI.
COLLEGE ADVISING: AN ANALYSIS OF ADVISOR‐ADVISEE ROLES
Authors: Witters Lee A. , Miller Harry G.
Published: December 2011

A survey of about 300 students and 14 staff members in one department of a major university revealed some interesting data about advisor‐advisee relationships. The objective was to investigate four areas: (a) student expectations of college advisors, (b) characteristics of good advisors, (c) student roles in advising process, and (d) faculty relationships. The study disclosed that advising was restricted to academic‐educational guidance. Staff members felt a need to expand these relationships to personal, social, and vocational guidance. In view of student demands for more relevant learning experiences, the present system of advising should be reevaluated.
STATUS OF SCHOOL PERSONNEL
Authors: Moses Harold , Delaney Daniel J.
Published: December 2011

This study investigated the status hierarchy of 18 relatively distinct positions or occupations within a school system. It was found that on a rank‐order scale, the counselor ranked sixth, which was below administrators and teachers but above other “special” personnel. A further analysis of the rankings according to sex, age, teaching experience, type of degree, and current position indicated that these variables had little influence on how the counselor position was perceived. It was concluded that the school counselor position has relatively high prestige among school personnel.
Electroactive Electrospun Polyaniline/Poly[(L‐lactide)‐co‐(ε‐caprolactone)] Fibers for Control of Neural Cell Function
Authors: Bhang Suk Ho , Jeong Sung In , Lee Tae‐Jin , Jun Indong , Lee Yu Bin , Kim Byung‐Soo , Shin Heungsoo
Published: December 2011

Blends of PAni and PLCL are electrospun to prepare uniform fibers for the development of electrically conductive, engineered nerve grafts. PC12 cell viability is significantly higher on RPACL fibers than on PLCL‐only fibers, and the electrical conductivity of the fibers affects the differentiation of PC12 cells; the number of cells positively‐stained and their expression level are significantly higher on RPACL fibers. PC12 cell bodies display an oriented morphology with outgrowing neurites. On RPACL fibers, the expression level of paxillin, cdc‐42, and rac is positively affected and proteins including RhoA and ERK exist as more activated state. These results suggest that electroactive fibers may hold promise as a guidance scaffold for neuronal tissue engineering.

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PloGO: Plotting gene ontology annotation and abundance in multi‐condition proteomics experiments
Authors: Pascovici Dana , Keighley Tim , Mirzaei Mehdi , Haynes Paul A. , Cooke Brett
Published: December 2011

We describe the PloGO R package, a simple open‐source tool for plotting gene ontology (GO) annotation and abundance information, which was developed to aid with the bioinformatics analysis of multi‐condition label‐free proteomics experiments using quantitation based on spectral counting. PloGO can incorporate abundance (raw spectral counts) or normalized spectral abundance factors (NSAF) data in addition to the GO annotation, as well as handle multiple files and allow for a targeted collection of GO categories of interest. Our main aims were to help identify interesting subsets of proteins for further analysis such as those arising from a protein data set partition based on the presence and absence or multiple pair‐wise comparisons, as well as provide GO summaries that can be easily used in subsequent analyses. Though developed with label‐free proteomics experiments in mind it is not specific to that approach and can be used for any multi‐condition experiment for which GO information has been generated.
Current–voltage characteristics of cubic Al(Ga)N/GaN double barrier structures on 3C–SiC
Authors: Mietze C. , Lischka K. , As D. J.
Published: December 2011

Resonant tunnelling diodes of cubic Al(Ga)N/GaN were grown by plasma assisted molecular beam epitaxy on 3C‐SiC (001). We observe a pronounced negative differential resistance at about 1.2 V with a peak‐to‐valley ratio (PVR) of 1.3 to 2.7 at room temperature. Experimental data is in good agreement with calculated I–V curves showing only a small deviation of 0.3 V of the resonance peak voltage. We find a decrease of the PVR when the I–V characteristic is measured repeatedly with short time intervals between the voltage‐cycles. However, the I–V characteristics can be recovered fully when the diodes are illuminated by UV‐light indicating charge trapping in our devices. Mesa structures are prepared by reactive ion etching. The size of the top ohmic contacts is (25 × 11) µm2. The Al content of the barrier material is varied between 30% and 100%.
Structural properties of metal‐organic frameworks within the density‐functional based tight‐binding method
Authors: Lukose Binit , Supronowicz Barbara , St. Petkov Petko , Frenzel Johannes , Kuc Agnieszka B. , Seifert Gotthard , Vayssilov Georgi N. , Heine Thomas
Published: December 2011

Density‐functional based tight‐binding (DFTB) is a powerful method to describe large molecules and materials. Metal‐organic frameworks (MOFs), materials with interesting catalytic properties and with very large surface areas, have been developed and have become commercially available. Unit cells of MOFs typically include hundreds of atoms, which make the application of standard density‐functional methods computationally very expensive, sometimes even unfeasible. The aim of this paper is to prepare and to validate the self‐consistent charge‐DFTB (SCC‐DFTB) method for MOFs containing Cu, Zn, and Al metal centers. The method has been validated against full hybrid density‐functional calculations for model clusters, against gradient corrected density‐functional calculations for supercells, and against experiment. Moreover, the modular concept of MOF chemistry has been discussed on the basis of their electronic properties. We concentrate on MOFs comprising three common connector units: copper paddlewheels (HKUST‐1), zinc oxide Zn4O tetrahedron (MOF‐5, MOF‐177, DUT‐6 (MOF‐205)), and aluminum oxide AlO4(OH)2 octahedron (MIL‐53). We show that SCC‐DFTB predicts structural parameters with a very good accuracy (with less than 5% deviation, even for adsorbed CO and H2O on HKUST‐1), while adsorption energies differ by 12 kJ mol−1 or less for CO and water compared to DFT benchmark calculations.
Evolution of physical properties of conjugated systems
Authors: Li Wun‐Fan , Andrzejak Marcin , Witek Henryk A.
Published: December 2011

Evolution of various physical properties of finite conjugated systems with increasing molecular size is studied using the self‐consistent‐charge density‐functional tight‐binding (SCC‐DFTB) method. We usually observe a transition from the finite to the infinite regime for surprisingly short molecular chains containing only 20–30 monomer units of cis‐butadiene, cyclopentadiene, pyrrole, furan, and thiophene. Such a fast convergence of equilibrium geometries, induced atomic charges, electron densities of states (DOS) and energy gaps, dipole and quadrupole moments, and polarizabilities is particularly striking considering the presence of strong π‐conjugation.

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Convergence in the size evolution of majority of molecular properties of conjugated systems occurs for surprisingly short molecular chains.
Shape Changes of Pt Nanoparticles Induced by Deposition on Mesoporous Silica
Authors: Giovanetti Lisandro J. , Ramallo‐López José M. , Foxe Michael , Jones Louis C. , Koebel Matthias M. , Somorjai Gabor A. , Craievich Aldo F. , Salmeron Miquel B. , Requejo Félix G.
Published: December 2011

Polyvinylpyrollidone (PVP)‐capped platinum nanoparticles (NPs) are found to change shape from spherical to flat when deposited on mesoporous silica substrates (SBA‐15). Transmission electron microscopy (TEM), small‐angle X‐ray scattering (SAXS), and extended X‐ray absorption fine structure (EXAFS) analyses are used in these studies. The SAXS results indicate that, after deposition, the 2 nm NPs have an average gyration radius 22% larger than in solution, while the EXAFS measurements indicate a decrease in first neighbor co‐ordination number from 9.3 to 7.4. The deformation of these small capped NPs is attributed to interactions with the surface of the SBA‐15 support, as evidenced by X‐ray absorption near‐edge structure (XANES).
Patients Count on It: An Initiative to Reduce Incorrect Counts and Prevent Retained Surgical Items
Authors: Norton Elizabeth K. , Martin Cornelia , Micheli Anne J.
Published: December 2011

Retained surgical items were the most frequently reported sentinel event in 2010, according to The Joint Commission. Perioperative nurse leaders at Children's Hospital Boston, a pediatric teaching hospital, conducted a quality improvement initiative to reduce or eliminate incorrect counts and count discrepancies, which increase the risk of an item being unintentionally retained after surgery. Work included educating the perioperative staff members, standardizing count practices, formally reviewing every reported count discrepancy with the nursing team, and reviewing and revising the count policy for prevention of retained surgical items. The initiative reduced the number of incorrect counts and count discrepancies by 50% between 2009 to 2010. These initiatives continue to be expanded, and the results have been sustained on an ongoing basis.
Stress‐Related Disorders Sourcebook
Authors: Tinkham Michelle
Published: December 2011

Stress‐Related Disorders Sourcebook Amy L. Sutton 3rd Edition 2011, Omnigraphics 632 pages, hardcover
Clinical Issues—January 2012
Authors: Van Wicklin Sharon A.
Published: December 2011

This Month

Venous thromboembolism prophylaxis in pediatric patients

Key words: pediatric patients, venous thromboembolism, prophylaxis.

The Centers for Disease Control and Prevention surgical wound classification system

Key words: surgical wound, wound classification, clean wound, clean‐contaminated wound, contaminated wound, dirty infected wound.

Using the Surgical Wound Classification Decision Tree tool

Key words: surgical wound, wound classification, clean‐contaminated wound, contaminated wound.

Using cotton surgical masks

Key words: allergy, cotton surgical masks, fabric surgical masks, disposable surgical masks.

Using povidone‐iodine solution for surgical skin antisepsis before thyroid procedures

Key words: povidone iodine, thyroid, surgical skin antisepsis.
Implementing AORN Recommended Practices for Surgical Attire
Authors: Braswell Melanie L. , Spruce Lisa
Published: December 2011

Surgical attire is intended to protect both patients and perioperative personnel. AORN published the “Recommended practices for surgical attire” to guide perioperative RNs in establishing protocols for selecting, wearing, and laundering surgical attire. Perioperative RNs should work with vendors and managers to ensure appropriate surgical attire is available, model the correct practices for donning and wearing surgical attire, and teach team members about evidence‐based practices. The recommendation that surgical attire not be home laundered is supported by evidence that perioperative nurses can share with their colleagues and managers to help support appropriate practices. Hospital and ambulatory surgery center scenarios have been included as examples of appropriate execution of these recommended practices.
New scanner data for brand marketers: How neuroscience can help better understand differences in brand preferences
Authors: Venkatraman Vinod , Clithero John A. , Fitzsimons Gavan J. , Huettel Scott A.
Published: December 2011

A core goal for marketers is effective segmentation: partitioning a brand's or product's consumer base into distinct and meaningful groups with differing needs. Traditional segmentation data include factors like geographic location, demographics, and shopping history. Yet, research into the cognitive and affective processes underlying consumption decisions shows that these variables can improve the matching of consumers with products beyond traditional demographic and benefit approaches. We propose, using managing a brand as an example, that neuroscience provides a novel way to establish mappings between cognitive processes and traditional marketing data. An improved understanding of the neural mechanisms of decision making will enhance the ability of marketers to effectively market their products. Just as neuroscience can model potential influences on the decision process—including pricing, choice strategy, context, experience, and memory—it can also provide new insights into individual differences in consumption behavior and brand preferences. We outline such a research agenda for incorporating neuroscience data into future attempts to match consumers to brands.
The Physiological Benefits and Problems Associated with using Standing and Walking Orthoses in Individuals with Spinal Cord Injury—A Meta-analytic Review
Authors: Karimi Taghi Mohammad
Published: December 2011

Spinal cord injury (SCI) patients use two transportation systems that include orthosis and wheelchair. It was claimed that standing and walking bring some benefits for SCI patients, such as decreasing bone osteoporosis, preventing pressure sores, and improving various physiological functions. The main question posted here is as follows: Is there enough evidence to support the effect of walking with orthosis on the health status of the patients with SCI? A review of the relevant literature was carried out in Bioengineering Unit of Strathclyde University. The benefits of orthoses were evaluated. Evidence reported in the literature regarding the effectiveness of orthoses for improving the health condition of SCI patients is conflicting. The benefits that were mentioned in various research studies regarding using the orthosis include decreasing bone osteoporosis, preventing joint deformity, improving bowl and bladder function, improving digestive system function, decreasing muscle spasm, improving independent living, improving respiratory and cardiovascular systems function. Improvement of independence living and physiological health of the patients are the only two benefits that are supported by strong evidence. Unfortunately, conflicting results in the literature have led to criticism of most hypotheses based on theoretical grounds, with the effects of using orthoses on the health status remaining a matter of considerable debate.
Relationship Between Disability and Health‐Related Quality of Life and Caregiver Burden in Patients With Upper Limb Poststroke Spasticity
Authors: Doan Quan V. , Brashear Allison , Gillard Patrick J. , Varon Sepideh F. , Vandenburgh Amanda M. , Turkel Catherine C. , Elovic Elie P.
Published: December 2011

Objective

To evaluate the relationship between disability and both health‐related quality of life (HRQoL) and caregiver burden in patients with upper limb poststroke spasticity.

Design

Multicenter open‐label study.

Setting

Thirty‐five sites in North America.

Participants

Patients (N = 279) with upper limb poststroke spasticity.

Methods

Post hoc analyses of data from an open‐label study were performed to estimate HRQoL and caregiver burden at study baseline across levels of disability in 4 problem domains: hygiene, dressing, limb posture, and pain. Disability severity in these areas was determined by using the 4‐point Disability Assessment Scale rated by the physicians.

Main Outcome Measurements

HRQoL measured by the patient‐reported EuroQol 5 Dimensions questionnaire and the Stroke‐Adapted Sickness Impact Profile and caregiver burden.

Results

At study baseline, increasing disability in the hygiene, dressing, and pain domains of the Disability Assessment Scale was associated with diminishing HRQoL scores (P < .002) measured by the EuroQol 5 Dimensions. By using the Stroke‐Adapted Sickness Impact Profile, greater disability scores in all problem domains were significantly associated with higher overall dysfunction scores (P ≤ .05). Within the physical dimension of the Stroke‐Adapted Sickness Impact Profile, significant associations also were observed in all domains. At baseline, caregiver burden was significantly related to increasing levels of hygiene and dressing domain severity (P ≤ .05). Caregiver assistance requirement increased from approximately 9.0‐28.2 hours per week in the hygiene domain and 3.3‐32.1 hours per week in the dressing domain as disability increased from “none” to “severe.”

Conclusions

In patients with upper limb poststroke spasticity, increasing disability in the hygiene, dressing, and pain domains of the Disability Assessment Scale were associated with diminishing HRQoL. Furthermore, these patients required caregiver assistance proportionally related to the severity of their disability in the hygiene and dressing domains.
Comparing Identification of Standardized and Regionally Valid Vowels
Authors: Wright Richard , Souza Pamela
Published: December 2011

Purpose

In perception studies, it is common to use vowel stimuli from standardized recordings or synthetic stimuli created using values from well-known published research. Although the use of standardized stimuli is convenient, unconsidered dialect and regional accent differences may introduce confounding effects. The goal of this study was to examine the effect of regional accent variation on vowel identification.

Method

The authors analyzed formant values of 8 monophthong vowels produced by 12 talkers from the region where the research took place and compared them with standardized vowels. Fifteen listeners with normal hearing identified synthesized vowels presented in varying levels of noise and at varying spectral distances from the local-dialect values.

Results

Acoustically, local vowels differed from standardized vowels, and distance varied across vowels. Perceptually, there was a robust effect of accent similarity such that identification was reduced for vowels at greater distances from local values.

Conclusions

Researchers and clinicians should take care in choosing stimuli for perception experiments. It is recommended that regionally validated vowels be used instead of relying on standardized vowels in vowel perception tasks.
Effects of the Menstrual Cycle and Oral Contraception on Singers' Pitch Control
Authors: Lã Filipa M. B. , Sundberg Johan , Howard David M. , Sa-Couto Pedro , Freitas Adelaide
Published: December 2011

Purpose

Difficulties with intonation and vibrato control during the menstrual cycle have been reported by singers; however, this phenomenon has not yet been systematically investigated.

Method

A double-blind randomized placebo-controlled trial assessing effects of the menstrual cycle and use of a combined oral contraceptive pill (OCP) on pitch control in singing is presented. Audio-electrolaryngograph recordings were made and blood samples were taken from 9 singers in each of the 3 phases of the menstrual cycle both under the placebo and the OCP conditions for a total of 6 months. Participants sang an exercise consisting of an ascending octave followed by a descending major triad, starting on pitches F4 and B4. Pitch control was assessed in terms of the octave’s deviations from pure intonation and of the vibrato rate and extent.

Results

Significant differences were found between the 3 phases of the cycle regarding octave size only for pitch F5 during OCP use. Significant vibrato rate differences between placebo and OCP conditions were found only for pitch F5.

Conclusion

OCP use may have an effect on pitch control in singers. Possible explanations point to a complex interaction between hormonal milieu and pitch control, enhancing the need for longitudinal studies.
Auditory Long Latency Responses to Tonal and Speech Stimuli
Authors: Swink Shannon , Stuart Andrew
Published: December 2011

Purpose

The effects of type of stimuli (i.e., nonspeech vs. speech), speech (i.e., natural vs. synthetic), gender of speaker and listener, speaker (i.e., self vs. other), and frequency alteration in self-produced speech on the late auditory cortical evoked potential were examined.

Method

Young adult men (
n
= 15) and women (
n
= 15), all with normal hearing, participated. P1–N1–P2 components were evoked with the following stimuli: 723-Hz tone bursts; naturally produced male and female /a/ tokens; synthetic male and female /a/ tokens; an /a/ token self-produced by each participant; and the same /a/ token produced by the participant but with a shift in frequency.

Results

In general, P1–N1–P2 component latencies were significantly shorter when evoked with the tonal stimulus versus speech stimuli and natural versus synthetic speech (
p
< .05). Women had significantly shorter latencies for only the P2 component (
p
< .05). For the tonal versus speech stimuli, P1 amplitudes were significantly smaller, and N1 and P2 amplitudes were significantly larger (
p
< .05). There was no significant effect of gender on the P1, N1, or P2 amplitude (
p
> .05).

Conclusion

These findings are consistent with the notion that spectrotemporal characteristics of nonspeech and speech stimuli affect P1–N1–P2 latency and amplitude components.
New Measures of Masked Text Recognition in Relation to Speech-in-Noise Perception and Their Associations With Age and Cognitive Abilities
Authors: Besser Jana , Zekveld Adriana A. , Kramer Sophia E. , Rönnberg Jerker , Festen Joost M.
Published: December 2011

Purpose

In this research, the authors aimed to increase the analogy between Text Reception Threshold (TRT; Zekveld, George, Kramer, Goverts, & Houtgast, 2007) and Speech Reception Threshold (SRT; Plomp & Mimpen, 1979) and to examine the TRT’s value in estimating cognitive abilities that are important for speech comprehension in noise.

Method

The authors administered 5 TRT versions, SRT tests in stationary (SRT
STAT
) and modulated (SRT
MOD
) noise, and 2 cognitive tests: a reading span (RSpan) test for working memory capacity and a letter–digit substitution test for information-processing speed. Fifty-five adults with normal hearing (18–78 years,
M
= 44 years) participated. The authors examined mutual associations of the tests and their predictive value for the SRTs with correlation and linear regression analyses.

Results

SRTs and TRTs were well associated, also when controlling for age. Correlations for the SRT
STAT
were generally lower than for the SRT
MOD.
The cognitive tests were correlated to the SRTs only when age was not controlled for. Age and the TRTs were the only significant predictors of SRT
MOD
. SRT
STAT
was predicted by level of education and some of the TRT versions.

Conclusions

TRTs and SRTs are robustly associated, nearly independent of age. The association between SRTs and RSpan is largely age dependent. The TRT test and the RSpan test measure different nonauditory components of linguistic processing relevant for speech perception in noise.
Interferometric scanning microscopy for the study of disordered materials
Authors: Kumar D. , Treacy M. M. J.
Published: December 2011

We demonstrate an interferometric optical technique that probes pair-pair correlations in disordered materials. Fraunhofer diffraction patterns, using coherent double-probe illumination, exhibit Young’s interference fringes whose strength is influenced by structural correlations between the two probed regions. Fourier transforms of diffraction patterns exhibit holographic sidebands, and the strength of correlations is proportional to the sideband intensity. Autoregression analysis of the correlation strength provides a direct measure of the characteristic ordering length scales. This technique is extendable in principle to x-ray and electron probes for studying materials at atomic length scales.
Nucleation and propagation of voids in microbumps for 3 dimensional integrated circuits
Authors: Hsu Hsueh-Hsien , Huang Shin-Yi , Chang Tao-Chih , Wu Albert T.
Published: December 2011

The shrinking solder dimensions greatly impact the reliability of devices and increase entire failure modes. Limited solder volumes can be consumed completely and transformed into intermetallic compound (IMC) microbumps. Microvoids surface when microbumps are formed and may be attributed to a mismatch of the thermal expansion coefficient between the constituents. After thermal aging at 150 °C, the stress induced by the growth of IMCs relaxes and enhances propagation of the cracks along the middle of the bumps. The brittle nature of the IMC showed minimal resistance to cracks and incurred a failure mode.
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites
Authors: Berkholz Donald S. , Driggers Camden M. , Shapovalov Maxim V. , Dunbrack Roland L. , Karplus P. Andrew
Published: December 2011

The planarity of peptide bonds is an assumption that underlies decades of theoretical modeling of proteins. Peptide bonds strongly deviating from planarity are considered very rare features of protein structure that occur for functional reasons. Here, empirical analyses of atomic-resolution protein structures reveal that
trans
peptide groups can vary by more than 25° from planarity and that the true extent of nonplanarity is underestimated even in 1.2 Å resolution structures. Analyses as a function of the
φ
,
ψ
-backbone dihedral angles show that the expected value deviates by ± 8° from planar as a systematic function of conformation, but that the large majority of variation in planarity depends on tertiary effects. Furthermore, we show that those peptide bonds in proteins that are most nonplanar, deviating by over 20° from planarity, are not strongly associated with active sites. Instead, highly nonplanar peptides are simply integral components of protein structure related to local and tertiary structural features that tend to be conserved among homologs. To account for the systematic
φ
,
ψ
-dependent component of nonplanarity, we present a conformation-dependent library that can be used in crystallographic refinement and predictive protein modeling.
CLARE: Cracking the LAnguage of Regulatory Elements
Authors: Taher Leila , Narlikar Leelavati , Ovcharenko Ivan
Published: December 2011

Summary:  CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.

Availability: CLARE is freely accessible at http://clare.dcode.org/.

Contact:  taherl@ncbi.nlm.nih.gov; ovcharen@nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
LaTcOm: a web server for visualizing rare codon clusters in coding sequences
Authors: Theodosiou Athina , Promponas Vasilis J.
Published: December 2011

Summary: We present LaTcOm, a new web tool, which offers several alternative methods for ‘rare codon cluster’ (RCC) identification from a single and simple graphical user interface. In the current version, three RCC detection schemes are implemented: the recently described %MinMax algorithm and a simplified sliding window approach, along with a novel modification of a linear-time algorithm for the detection of maximally scoring subsequences tailored to the RCC detection problem. Among a number of user tunable parameters, several codon-based scales relevant for RCC detection are available, including tRNA abundance values from Escherichia coli and several codon usage tables from a selection of genomes. Furthermore, useful scale transformations may be performed upon user request (e.g. linear, sigmoid). Users may choose to visualize RCC positions within the submitted sequences either with graphical representations or in textual form for further processing.

Availability: LaTcOm is freely available online at the URL http://troodos.biol.ucy.ac.cy/latcom.html.

Contact:  vprobon@ucy.ac.cy

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effect of Amoxicillin/Clavulanate on Gastrointestinal Motility in Children
Authors: Gomez Roberto , Fernandez Sergio , Aspirot Ann , Punati Jaya , Skaggs Beth , Mousa Hayat , Di Lorenzo Carlo
Published: December 2011

Aim:

The aim of the present study was to evaluate the effect of amoxicillin/clavulanate (A/C) on gastrointestinal motility.

Methods:

Twenty consecutive pediatric patients referred for antroduodenal manometry received 20 mg/kg of A/C into the small bowel lumen. In 10 patients (group A), A/C was given 1 hour after and in 10 (group B), 1 hour before ingestion of a meal. Characteristics of the migrating motor complex, including presence, frequency, amplitude, and propagation of duodenal phase III and phase I duration and phase II motility index (MI), were evaluated 30 minutes before and after A/C administration.

Results:

There were no statistically significant differences in age and sex between the 2 groups. Manometry studies were considered normal in 8 patients in each group. In group A, 2 patients developed duodenal phase III after receiving A/C, and no significant difference was found in the MI before and after the drug administration. In group B, 9 patients developed duodenal phase III (P < 0.05 vs group A). All phase III occurred within a few minutes from the medication administration. Most duodenal phase III contractions were preceded by an antral component during fasting but never after the medication was administered in either of the 2 groups (P < 0.001 vs fasting). In group B, the duration of duodenal phase I was shorter after drug administration (P < 0.05). There was no significant difference in duodenal phase II MI before and after A/C administration for the 2 study groups.

Conclusions:

In children, administration of A/C directly into the small bowel before a meal induces phase III‐type contractions in the duodenum, with characteristics similar to those present in the fasting state. These data suggest the possible use of A/C as a prokinetic agent. Further studies are needed to clarify its specific mechanism of action and the group of patients most likely to benefit from its use.
Methotrexate Modulates Tight Junctions Through NF‐κB, MEK, and JNK Pathways
Authors: Beutheu Youmba Stéphanie , Belmonte Liliana , Galas Ludovic , Boukhettala Nabile , Bôle‐Feysot Christine , Déchelotte Pierre , Coëffier Moïse
Published: December 2011

Objectives:

Chemotherapy often induces intestinal mucositis, which is associated with an increase in intestinal permeability; however, underlying mechanisms remain incompletely understood. Thus, we aimed to study the regulation of 3 tight junction (TJ) proteins, claudin‐1, occludin, and zonula occludens‐1, after anticancer treatment.

Methods:

Methotrexate (MTX) was subcutaneously injected for 3 consecutive days in Sprague‐Dawley rats to induce intestinal mucositis and was applied on Caco‐2 cell monolayers. TJ protein expression and cellular distribution were studied by Western blot and microscopy, respectively. In Caco‐2 cells, the paracellular permeability was evaluated by both transepithelial electrical resistance and flux of fluorescein isothiocyanate‐dextran marker. Cytokine production and signaling pathways were also assessed.

Results:

In MTX‐treated rats, the cellular distribution of the 3 TJ proteins was altered and claudin‐1 and occludin expression was reduced during the acute phase of mucositis compared with controls. During the recovery phase, these parameters were restored. In vitro, MTX treatment led to an increase in proinflammatory cytokine production at the apical side but did not affect Caco‐2 cell apoptosis and necrosis. Increase in paracellular permeability was associated with altered occludin and zonula occludens‐1 expression and cellular distribution. All of these alterations were prevented by MEK1 and 2, JNK, and NF‐κB inhibitors.

Conclusions:

MTX treatment induced an increase in intestinal permeability partially related to alteration of TJs protein expression and cellular distribution that may be mediated by MAPK and NF‐κB pathways. These are potential targets to limit the adverse effects of chemotherapy.
Factors Associated With Nonadherence to Thiopurines in Adolescent and Adult Patients With Inflammatory Bowel Disease
Authors: Kamperidis N. , Goodhand J.R. , Chowdhury F.A. , Koodun Y. , Direzke N.C. , Naik S. , Sanderson I.R. , Croft N.M. , Langmead F.L. , Irving P.M. , Rampton D.S. , Lindsay J.O.
Published: December 2011

Objectives:

We hypothesised that nonadherence to thiopurines is more common in adolescents than in adults with inflammatory bowel disease.

Methods:

We sought factors associated with thiopurine nonadherence defined by thiopurine metabolite levels.

Results:

Multivariate logistic regression confirmed that adolescents (odds ratio [OR] 4.6 [95% confidence interval [CI] 1.9–11.5]; P < 0.01) compared with adults, patients with Crohn disease (OR 3.3 [CI 1.1–10.5] P = 0.04) compared with ulcerative colitis, and patients living in more socially deprived areas (OR 1.03 [CI 1.0–1.1] P = 0.02) were more likely to be nonadherent to thiopurines.

Conclusions:

Adolescents are more frequently nonadherent than adults: prospective studies are required to determine the reasons for nonadherence in adolescents.
Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle
Authors: Kudo Yuko , Oki Kaihei , Watanabe Koichi
Published: December 2011

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as

Lactobacillus delbrueckii

, the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of

L. delbrueckii

. Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of

L. delbrueckii

were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T  = DSM 24966T).
Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum
Authors: Tani Akio , Sahin Nurettin , Kimbara Kazuhide
Published: December 2011

A pink-pigmented, facultatively methylotrophic bacterium, strain 23eT, was isolated from the leaves ofGnaphalium spicatum(cudweed). The cells of strain 23eTwere Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23eTwas related toMethylobacterium organophilumATCC 27886T(97.1 %) andMethylobacterium marchantiaeJT1T(97 %), and the phylogenetic similarities to all otherMethylobacteriumspecies with validly published names were less than 97 %. Major cellular fatty acids were C18 : 1ω7c, C16 : 00and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA andcpn60gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23eTfrom the phylogenetically closest relatives. We propose that strain 23eTrepresents a novel species within the genusMethylobacterium, for which the nameMethylobacterium gnaphaliisp. nov. is proposed. The type strain is 23eT( = DSM 24027T = NBRC 107716T).
A Data-Driven Integrative Model of Sepal Primordium Polarity in Arabidopsis
Authors: La Rota Camilo , Chopard Jérôme , Das Pradeep , Paindavoine Sandrine , Rozier Frédérique , Farcot Etienne , Godin Christophe , Traas Jan , Monéger Françoise
Published: December 2011

Flower patterning is determined by a complex molecular network but how this network functions remains to be elucidated. Here, we develop an integrative modeling approach that assembles heterogeneous data into a biologically coherent model to allow predictions to be made and inconsistencies among the data to be found. We use this approach to study the network underlying sepal development in the young flower of Arabidopsis thaliana. We constructed a digital atlas of gene expression and used it to build a dynamical molecular regulatory network model of sepal primordium development. This led to the construction of a coherent molecular network model for lateral organ polarity that fully recapitulates expression and interaction data. Our model predicts the existence of three novel pathways involving the HD-ZIP III genes and both cytokinin and ARGONAUTE family members. In addition, our model provides predictions on molecular interactions. In a broader context, this approach allows the extraction of biological knowledge from diverse types of data and can be used to study developmental processes in any multicellular organism.
Electrodeposition of iron‐enriched nanocrystalline Fe‐Ni alloy foil from chloride‐sulfate solutions
Authors: Yang Xiyun , Duan Xitao , Yuan Haiwei
Published: December 2011

Purpose

The purpose of this paper is to obtain iron‐enriched Fe‐Ni alloy foil on Ti substrates with good quality from a chloride‐sulfate bath used in a normal DC plating mode. The effects of iron content on the hardness, surface morphology and microstructure of the foil were clarified.

Design/methodology/approach

Fe‐Ni alloy foil was prepared by electrodeposition in a chloride‐sulfate based solution. The effects of current density, temperature, stirring rate and sodium propargyl sulfonate concentration on the iron contents of the Fe‐Ni alloy foils were studied. The phase composition and surface morphology with various iron contents were characterized by X‐ray diffraction (XRD) and atomic force microscopy (AFM), respectively. Cathodic polarization curves were used to evaluate the role of sodium propargyl sulfonate (PS).

Findings

Nanocrystalline Fe‐Ni alloy foil containing up to 64 wt. percent iron can be obtained from a chloride‐sulfate based solution. The foil converts from a face‐centered cubic (fcc) Fe3Ni2 phase to a mixture of fcc and body‐centered cubic (bcc) Fe7Ni3 with increase in iron content from 55.0 wt. percent to 63.5 wt. percent. AFM studies revealed that the foil had a fine grain structure with a roughness of 30 nm and grain size of 30 nm. With iron increasing to 63.5 wt. percent some islands appeared on the surface. This structure was related to the development of a (200) fiber texture in the BCC phase. Sodium propargyl sulfonate accelerates the discharge of nickel and inhibits the discharge of Fe.

Practical implications

The foil has many industrial applications in the area of memory devices for computers, laser components and precise instruments.

Originality/value

The paper presents a process to produce a foil with iron up to 64 wt. percent from a chloride‐sulfate based solution used in normal DC mode. The dependence of microstructure and surface morphology on iron contents also is presented. Until now, there has been little research or reports on this subject.
Multi‐faceted views on a Lean Six Sigma application
Authors: Assarlind Marcus , Gremyr Ida , Bäckman Kristoffer
Published: December 2011

Purpose

As Lean and Six Sigma have become established as influential concepts in the process improvement area, observers, researchers and managers are awaiting the next step, which many feel could take the form of a combination of the two concepts, known as Lean Six Sigma. A considerable amount of literature has been produced regarding the possible benefits of combining Lean and Six Sigma, which has led to greater support for the idea. The purpose of this paper is to explore an application of Lean Six Sigma in practical improvement work.

Design/methodology/approach

The empirical study was conducted through interviews, meetings, document analysis and observations over a period of four months.

Findings

Based on this paper, it seems unfeasible to apply one standardised approach to improvements in one company. Continuous smaller improvements and larger improvement projects demand different formulas. It seems that using both Lean and Six Sigma in parallel is appropriate but this should be done through clever cross‐fertilisation.

Research limitations/implications

This paper shows one possible way of working with one improvement concept in one company. It does not claim to present the only possible way of combining Lean and Six Sigma nor does it suggest universal applicability. Further research on other possible combinations would therefore be valuable.

Practical implications

This paper provides an outline of how to structure a combination of Lean and Six Sigma. It can provide valuable insights to managers who wish to structure their improvement processes.

Originality/value

This paper expands the theoretical foundation for combining Lean and Six Sigma by studying and analysing a practical application of the concept. Apart from the paper's value for managers, it can also help researchers understand the compatibility of Lean and Six Sigma.
Application of Six Sigma DMAIC methodology in a transactional environment
Authors: Antony Jiju , Singh Bhuller Anmol , Kumar Maneesh , Mendibil Kepa , Montgomery Douglas C.
Published: December 2011

Purpose

Communication and Information Management (CIM) is crucial for any organisation and effectiveness of CIM can result in significant improvement to the bottom line and customer satisfaction. The purpose of this paper is to investigate and streamline the communication and information system within an “infrastructure support service” company using Six Sigma methodology.

Design/methodology/approach

The research involved a triangulation approach of case study and use of survey instrument to find a solution to the problem.

Findings

The paper highlights a significant concern with regard to CIM within all the business units of the group. The effectiveness of the present CIM system for the whole group is below industry average with regard to accuracy and timeliness of CIM, resulting in an inefficient management reporting system. Operating in a highly competitive and time‐bound environment, correct and real time reporting is paramount. The main reasons for the ineffectiveness of CIM across the group can be attributed to two main factors; data management and communication systems being used. The paper also illustrates an appreciation of the use of Six Sigma within a transactional environment.

Originality/value

This study is a novel application of Six Sigma methodology within the communication and information management system.
Does investment improve when firms go private?
Authors: Straska Miroslava , Waller Gregory , Yu Yao
Published: December 2011

Purpose

This paper aims to examine whether investment efficiency improves after publicly‐traded firms are taken private.

Design/methodology/approach

The analysis uses univariate comparisons and regression analysis of panel data.

Findings

Before going private, firms' investment ratios and investment opportunities are similar to investment ratios and investment opportunities of peer firms. However, after going private, the investment ratios significantly decrease to levels significantly below the investment ratios of peer firms. Additionally, investment becomes less sensitive to investment opportunities and more sensitive to operating profits and cash holdings. Finally, cash becomes more sensitive to cash‐flow after going private. These results suggest that firms become more financially constrained, under‐invest relative to their industry peers, and invest less efficiently after going private.

Originality/value

Improvements in investment efficiency are often cited as a contributing factor to the value gains associated with going‐private transactions. However, whether investment efficiency improves when firms go private remains unanswered by prior research. In theory, investment efficiency should improve if private firms are shielded from the market pressure for short‐term earnings and better able to invest for long‐term value creation. Conversely, it is possible that the high levels of debt associated with these transactions impose financial constraints that reduce investment efficiency. The results of this study suggest that investment efficiency does not improve after going private.