bluuebunny/crossref_metadata_2025 huggingface dataset:
Asian American Adolescents' Willingness to Donate Organs and Engage in Family Discussion about Organ Donation and Transplantation
Authors: Trompeta Joyce A. , Cooper Bruce A. , Ascher Nancy L. , Kools Susan M. , Kennedy Christine M. , Chen Jyu-Lin
Published: April 2012

Context—

Despite the growing need for organ donation among Asian Americans, studies suggest that they are reluctant to donate.

Objective—

To examine the association of attitudes and knowledge about organ donation and transplantation with willingness to donate and willingness to engage in family discussion about organ donation among Asian American adolescents.

Design—

A cross-sectional study.

Setting—

The Big Island of Hawaii.

Participants—

Self-identified Asian American adolescents (Japanese, Chinese, Filipino, Korean), ages 16 to 17 years old, and each adolescent's parent or guardian.

Main Outcome Measures—

Asian American adolescents provided demographic information and completed the Modified Organ Donation Attitude Survey, the Organ Donation and Transplantation Knowledge Survey, and the Suinn-Lew Asian Self-Identity Acculturation Scale. A parent or guardian also provided demographic information. Linear regression analyses were used to examine the associations with willingness to donate and to engage in family discussion about organ discussion.

Results—

Willingness to donate was associated with positive knowledge related to general aspects about organ donation and cultural limitations in receiving an organ transplant, a high level of acculturation, and a low level of negative attitudes ( R2 = 0.402, F = 18.86, P = .005). Asian American adolescents with approving or positive attitudes were likely to engage in family discussion about organ donation ( R2 = 0.195, F =27.93, P = .005). To reinforce and maintain high levels of knowledge and positive attitudes, organ donation education is most likely needed in high schools.
A Department of Motor Vehicles Intervention Yields Moderate Increases in Donor Designation Rates
Authors: Rodrigue James R. , Krouse Jennifer , Carroll Christopher , Giery Kathleen M. , Fraga Yilian , Edwards Elizabeth
Published: April 2012

Context—

Nearly all persons (37% of public) who have a joined an organ donor registry in the United States have done so through their Department of Motor Vehicles (DMV) office, which is an underused venue for organ donation campaigns.

Objective—

To evaluate the effectiveness of a statewide DMV-based intervention to increase donor designation rates.

Design and Setting—

Thirty DMV offices in Florida were randomly assigned to receive usual care (n= 15) or an organ donation intervention (n= 15).

Measurement and Primary Outcome—

Donor designation rates were assessed at baseline (before the intervention), during the intervention, and at follow-up.

Results—

When baseline donor designation rate and region were controlled for, the intervention group showed a significantly higher aggregate monthly donor designation rate than the usual care group during the intervention phase of the study ( P = .02). Donor designation rates did not differ significantly ( P = .13) during the follow-up phase. Lower donor designations rates were significantly associated with DMV service regions with more minorities, less education, and lower income.

Conclusion—

We conclude that a comprehensive DMV-based intervention focused on staff education and direct interactions with the public could yield modest increases in donor designation rates.
Effect of a Study Map Intended to Support Informed Consent in Transplant Research
Authors: Foradori Megan A. , Nolan Marie T.
Published: April 2012

Context—

Research participants' informed consent is integral to the protection of human subjects; studies exploring the enhancement of standard informed consent processes have had mixed success in increasing patients' understanding of complex research protocols.

Objective—

To determine the effect of a “study map,” a flow diagram of a research protocol, on research participants' understanding of research purpose and procedures.

Design—

This study was an experimental posttest-only design using 30 research participants enrolling in a study of decision making and recovery among living kidney donors. Participants were randomly assigned to the standard care group (verbal description with consent documents) or the experimental group (standard of care plus study map). An instrument measured perceived and objective understanding, and the differences between groups were determined by an independent t test.

Discussion—

The high level of comprehension in the control group made detecting improvements in understanding difficult. Objective knowledge and perceived understanding were positively related, suggesting the importance of periodically confirming comprehension with research participants during the informed consent process. Future research should examine the effect of study maps in patients with lower educational levels.

Results—

Knowledge levels were high in all participants (mean objective =3.7 on a 5-point scale, SD= 1.02; mean subjective =9.3 on a 10-point scale, SD= 1.29). There was a significant relationship between objective knowledge and perceived understanding ( r = 0.56, P = .001); however, the study map itself had no significant effect on objective or perceived understanding.
Lessons Learned: Experiences of Gaining Weight by Kidney Transplant Recipients
Authors: Stanfill Ansley , Bloodworth Robin , Cashion Ann
Published: April 2012

Context—

Weight gain after kidney transplantation is a widespread phenomenon, but the question of effective strategies to intervene in patterns that lead to weight gain has not been well studied.

Objective—

To obtain (1) insight into recipients' perceptions of weight gain and (2) information on intervention strategies that recipients think could prevent weight gain.

Design—

Qualitative focus groups and a 13-question, multiple-choice survey were used.

Setting—

A regional mid-South transplant center.

Participants—

Seven kidney transplant recipients (86% African American, 57% female, mean age 55.0 years) who had gained at least 12% of their total body weight during a 12-month larger observational study.

Main Outcome Measures—

Content from the focus group sessions was analyzed for major and minor themes. The survey results were analyzed with descriptive statistics.

Results—

Identified themes included barriers to healthy eating caused by medications and removal of dietary restrictions. Barriers to physical activity included fear of injuring the new organ and health problems both related and unrelated to transplant. Perceived effects of weight gain included hypertension, diabetes, and embarrassment and concern at the rapid weight gain. Recipients would like an early start to implementation of lifestyle changes. Useful ideas included written materials regarding appropriate physical activities and dietary information, healthy cooking classes, and support groups.
Modelling the Neolithic Transition in the Near East and Europe
Authors: Fort Joaquim , Pujol Toni , Linden Marc Vander
Published: April 2012

For the Neolithic transition in the Near East and Europe, this paper compares the isochrones predicted by computational models to those obtained by interpolating the archaeological data. This comparison reveals that there is a major inconsistency between the predictions of the models and the archaeological data: according to the models, the Neolithic front would have arrived to Greece in less than half the time interval implied by the data. Our main new results are as follows, (a) This inconsistency can be solved by including only Pre Pottery Neolithic B/C (PPNB/C) sites in the Near East; (b) the model that yields the lowest mean error per site in the arrival time of the Neolithic across the Near East and Europe is obtained by allowing for sea travels up to distances of 150 km; and (c) Mountain barriers have a negligible effect on the spread rate of the Neolithic front at the continental scale.
Size and Shape Variation in Late Holocene Projectile Points of Southern Patagonia: A Geometric Morphometric Study
Authors: Charlin Judith , González-José Rolando
Published: April 2012

Since the beginning of systematic archaeological studies in southern Patagonia (Argentina and Chile), projectile points have played an important role as cultural markers. A sequence of projectile point types was established according to their changes in size and shape. These stone tools, along with others cultural evidences, served to differentiate a series of “culturai periods” which were, for decades, the frame of reference to understand the cultural evolution in southernmost Patagonia. Although later researches have questioned several of these assumptions, the classical typology of projectile points continued in use until the present day. The goal of this work is to evaluate size and shape variation in two late Holocene projectile point types, known as Fell, Bird, or Magallanes IV and V points or Patagónicas and Ona points, respectively. These two types are compared using geometric morphometries and multivariate statistical analyses. The reliability in the discrimination between types is tested at the light of reduction. The analyses have shown a major incidence of reduction on shape rather than on size, and on blade rather than on stem. However, in average, types IV and V can be distinguished in terms of size, and stem shape despite reduction. Thus, even though successive cycles of use, damage and resharpening have a great influence over size and shape of projectile points, resharpening techniques are specific enough to maintain the differences of size and shape between types, a pattern that is probably related with functional requirements.
Tracing Social Interaction: Perspectives on Archaic Copper Exchange from the Upper Great Lakes
Authors: Hill Mark A.
Published: April 2012

Compositional analysis of copper is used to explore interaction between the Late Archaic occupants of the Northern Lakes region and their contemporaries in eastern and east-central Wisconsin. Copper artifacts from Burnt Rollways phase sites in northern Wisconsin and the Upper Peninsula are compared with the Middle Archaic Reigh and Late Archaic Riverside sites. Laser ablation inductively coupled plasma mass spectrometry analysis of copper demonstrates differential acquisition of resources between Burnt Rollways and their contemporaries and suggests barriers to social interaction between the Northern Lakes and societies in the Lake Winnebago and western Lake Michigan regions.
Association between single‐nucleotide polymorphisms on chromosome 1p22 and 20q12 and nonsyndromic cleft lip with or without cleft palate: New data in Han Chinese and meta‐analysis
Authors: Huang Enmin , Cheng Hongqiu , Xu Mingyan , Shu Shenyou , Tang Shijie
Published: April 2012

BACKGROUND

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation associated with genetic and environmental risk factors. A recent genome‐wide association study identified two novel susceptibility loci on chromosomes 1p22 and 20q12; however, conflicting results, especially for 1p22, have been reported in Han Chinese population. The aims of this study were to replicate this association with risk of NSCL/P in the southern Han Chinese population and to discern the effect of these loci by a meta‐analysis.

METHODS

To this end, 305 patients with NSCL/P, 356 phenotypically normal controls, and an additional 176 case‐parent trios were recruited. Four of the previously associated single nucleotide polymorphisms (SNPs) were genotyped by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Furthermore, two published datasets were combined with the present results to determine the precise roles of the loci.

RESULTS

SNPs (rs6072081, rs13041247, and rs6102085) on 20q12 were found to be strongly associated with NSCL/P (Bonferroni‐corrected and χ2 test; p values < 0.05). Subsequent analysis of the case‐parent trio provided similar results. However, neither the association study nor the trio analysis supported a causative role for SNP rs560426 on 1p22 in NSCL/P susceptibility. Stratified meta‐ analysis combining Chinese samples supported our findings.

CONCLUSIONS

This cross‐validation study confirmed the previous findings that SNPs in 20q12 are associated with NSCL/P in Han Chinese population. We further conclude that rs560426 on 1p22 might not have a major influence on susceptibility to NSCL/P in southern Han Chinese, but future studies with other Han Chinese populations are needed. Birth Defects Research (Part A) 2012. © 2012 Wiley Periodicals, Inc.
Did tillage erosion play a role in millennial scale landscape development?
Authors: Baartman Jantiene E.M. , Temme Arnaud J.A.M. , Schoorl Jeroen M. , Braakhekke Michiel H.A. , Veldkamp Tom (A.)
Published: April 2012

Landscape evolution models (LEMs) quantitatively simulate processes of sedimentation and erosion on millennial timescales. An important aspect of human impact on erosion is sediment redistribution due to agriculture, referred to herein as tillage erosion. In this study we aim to analyse the potential contribution of tillage erosion to landscape development using LEM LAPSUS. The model is calibrated separately for a water erosion process (i) without tillage and (ii) with tillage. The model is applied to the ~250 km2 Torrealvilla case study catchment, SE Spain. We were able to simulate alternating sequences of incision and aggradation, that are important on longer (millennial) timescales. Generally, model results show that tillage erosion adds to deposition in the lower floodplain area, but neither water erosion alone nor water with tillage erosion together could exactly reproduce the observed amounts of erosion and sedimentation for the case study area. In addition, scale effects are apparent. On hillslopes, tillage may contribute importantly to erosion and may fill local depressions. If assessed on the catchment scale, sediments from tillage erosion eventually reach the lower floodplain area where they contribute to deposition. However, water erosion was observed in the model simulations to be the most important process on the catchment scale. This is the first time that tillage erosion has been explicitly included in a landscape evolution model at a millennial timescale and large catchment scale. Copyright © 2012 John Wiley & Sons, Ltd.
Role of regulatory T cells in the promotion of transplant tolerance
Authors: Shalev Itay , Selzner Nazia , Shyu Wendy , Grant David , Levy Gary
Published: April 2012

Liver transplantation is now recognized as the most effective therapy for patients with end-stage acute and chronic liver failure. Despite outstanding short-term graft and patient survival, liver transplantation continues to face several major challenges, including poor long-term graft survival due to chronic rejection and major side effects of long-term immunosuppressive therapy (which is required for the prevention of rejection). The ability to produce a state of tolerance after transplantation would potentially obviate long-term immunosuppression. Self-tolerance and immune homeostasis involve both central and peripheral immunoregulatory mechanisms. To date, studies have shown that many subsets of regulatory T cells (Tregs) control immune responses to foreign and alloantigens. The identification of Tregs that are positive for CD4, CD25, and the transcription factor forkhead box (Foxp3) has resulted in major advances in our understanding of the immunology of rejection and the development of transplant tolerance. In this article, we focus on the importance of Tregs in tolerance induction in experimental models of liver transplantation. Furthermore, we discuss the therapeutic potential of Tregs for the promotion of tolerance in transplant patients and highlight recent clinical trials of Treg-based therapies. Liver Transpl, 2012. © 2012 AASLD.
Multiple phosphorylations of cytochrome c oxidase and their functions
Authors: Helling Stefan , Hüttemann Maik , Ramzan Rabia , Kim Su Hyeon , Lee Icksoo , Müller Thorsten , Langenfeld Elmar , Meyer Helmut E. , Kadenbach Bernhard , Vogt Sebastian , Marcus Katrin
Published: April 2012

Cytochrome c oxidase (COX), the terminal enzyme of the mitochondrial electron transport chain, is regulated by isozyme expression, allosteric effectors such as the ATP/ADP ratio, and reversible phosphorylation. Of particular interest is the “allosteric ATP‐inhibition,” which has been hypothesized to keep the mitochondrial membrane potential at low healthy values (<140 mV), thus preventing the formation of superoxide radical anions, which have been implicated in multiple degenerative diseases. It has been proposed that the “allosteric ATP‐inhibition” is switched on by the protein kinase A‐dependent phosphorylation of COX. The goal of this study was to identify the phosphorylation site(s) involved in the “allosteric ATP‐inhibition” of COX. We report the mass spectrometric identification of four new phosphorylation sites in bovine heart COX. The identified phosphorylation sites include Tyr‐218 in subunit II, Ser‐1 in subunit Va, Ser‐2 in subunit Vb, and Ser‐1 in subunit VIIc. With the exception of Ser‐2 in subunit Vb, the identified phosphorylation sites were found in enzyme samples with and without “allosteric ATP inhibition,” making Ser‐2 of subunit Vb a candidate site enabling allosteric regulation. We therefore hypothesize that additional phosphorylation(s) may be required for the “allosteric ATP‐inhibition,” and that these sites may be easily dephosphorylated or difficult to identify by mass spectrometry.
Mechanistic insight into initiation and chain transfer reaction of CO2/cyclohexene oxide copolymerization catalyzed by zinccobalt double metal cyanide complex catalysts
Authors: Sun Xue‐Ke , Zhang Xing‐Hong , Wei Ren‐Jian , Du Bin‐Yang , Wang Qi , Fan Zhi‐Qiang , Qi Guo‐Rong
Published: April 2012

Although zinccobalt (III) double metal cyanide complex (ZnCo (III) DMCC) catalyst is a highly active and selective catalyst for carbon dioxide (CO2)/cyclohexene oxide (CHO) copolymerization, the structure of the resultant copolymer is poorly understood and the catalytic mechanism is still unclear. Combining the results of kinetic study and electrospray ionization‐mass spectrometry (ESI‐MS) spectra for CO2/CHO copolymerization catalyzed by ZnCo (III) DMCC catalyst, we disclosed that (1) the short ether units were mainly generated at the early stage of the copolymerization, and were hence in the “head” of the copolymer and (2) all resultant PCHCs presented two end hydroxyl (OH) groups. One end OH group came from the initiation of zinchydroxide (ZnOH) bond and the other end OH group was produced by the chain transfer reaction of propagating chain to H2O (or free copolymer). Adding t‐BuOH (CHO: t‐BuOH = 2:1, v/v) to the reaction system led to the production of fully alternating PCHCs and new active site of ZnOt‐Bu, which was proved by the observation of PCHCs with one end Ot‐Bu (and OCOOt‐Bu) group from ESI‐MS and 13C NMR spectra. Moreover, Zn−OH bond in ZnCo (III) DMCC catalyst was also characterized by the combined results from FT‐IR, TGA and elemental analysis. This work provided new evidences that CO2/CHO copolymerization was initiated by metalOH bond. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Effect of reaction conditions on film morphology of polyaniline composite membranes for gas separation
Authors: Blinova Natalia V. , Stejskal Jaroslav , Fréchet Jean M. J. , Svec Frantisek
Published: April 2012

Composite membranes combining polyaniline as an active layer with a polypropylene support have been prepared using an in situ deposition technique. The protonated polyaniline layer with a thickness in the range of 90–200 nm was prepared using precipitation, dispersion, or emulsion polymerization of aniline with simultaneous deposition on top of the porous polypropylene support, which was immersed in the reaction mixture. Variables such as temperature, concentration of reagents, presence of steric stabilizers, surfactants, and heteropolyacid were found to control both the formation and the quality of the polyaniline layers. Both morphology and thickness of the layers were characterized using scanning electron microscopy. Selective separation of carbon dioxide from its mixture with methane is used to illustrate potential application of these composite membranes. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Interaction structure of the complex between neuroprotective factor humanin and Alzheimer's β‐amyloid peptide revealed by affinity mass spectrometry and molecular modeling
Authors: Maftei Madalina , Tian Xiaodan , Manea Marilena , Exner Thomas E. , Schwanzar Daniel , von Arnim Christine A. F. , Przybylski Michael
Published: April 2012

Humanin (HN) is a linear 24‐aa peptide recently detected in human Alzheimer's disease (AD) brain. HN specifically inhibits neuronal cell death in vitro induced by ß‐amyloid (Aß) peptides and by amyloid precursor protein and its gene mutations in familial AD, thereby representing a potential therapeutic lead structure for AD; however, its molecular mechanism of action is not well understood. We report here the identification of the binding epitopes between HN and Aß(1–40) and characterization of the interaction structure through a molecular modeling study. Wild‐type HN and HN‐sequence mutations were synthesized by SPPS and the HPLC‐purified peptides characterized by MALDI‐MS. The interaction epitopes between HN and Aß(1–40) were identified by affinity‐MS using proteolytic epitope excision and extraction, followed by elution and mass spectrometric characterization of the affinity‐bound peptides. The affinity‐MS analyses revealed HN(5–15) as the epitope sequence of HN, whereas Aß(17–28) was identified as the Aß interaction epitope. The epitopes and binding sites were ascertained by ELISA of the complex of HN peptides with immobilized Aß(1–40) and by ELISA with Aß(1–40) and Aß‐partial sequences as ligands to immobilized HN. The specificity and affinity of the HN‐Aß interaction were characterized by direct ESI‐MS of the HN‐Aß(1–40) complex and by bioaffinity analysis using a surface acoustic wave biosensor, providing a KD of the complex of 610 n m. A molecular dynamics simulation of the HN‐Aß(1–40) complex was consistent with the binding specificity and shielding effects of the HN and Aß interaction epitopes. These results indicate a specific strong association of HN and Aß(1–40) polypeptide and provide a molecular basis for understanding the neuroprotective function of HN. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.
Inter‐specific association and habitat use in a farmland passerine assemblage
Authors: Morales Manuel B. , Guerrero Irene , Oñate Juan J. , Meléndez Leandro
Published: April 2012

We studied the pattern of inter‐specific association of breeding territories in a passerine assemblage of dry cereal farmland in central Spain and evaluated the role of the presence of heterospecifics in the habitat use patterns exhibited by different species. Bird territories showed a non‐random inter‐specific spatial aggregation pattern. We studied territory abundance variation in the three more abundant species: the corn bunting, the crested lark, and the fan‐tailed warbler. Crested lark and fan‐tailed warbler territories were more abundant in plots where corn bunting territories were present and vice versa, while their respective abundances did not vary with the breeding presence of the other species. We used landscape and agricultural management variables to analyze the relationships between habitat and each species’ breeding territories by means of classification trees. While the corn bunting showed a marked pattern of nesting habitat use, the crested lark and the fan‐tailed warbler exhibited a much more generalist one. Corn Bunting presence was affected negatively by intensification‐related variables, such as field size and percent cover of cereal crops. Similarly, the presence of crested larks was negatively related to high yielding areas. However, when the presence of hetero‐specific territories was considered, the presence of corn bunting territories was the most important variable explaining the occurrence of breeding fan‐tailed warblers, and the second most important in the case of the crested lark. These results suggest that inter‐specific attraction could play a role in the formation of farmland bird assemblages, while adding further evidence for the detrimental effect of agricultural intensification at the community level.
Plasticity of PDZ domains in ligand recognition and signaling
Authors: Ivarsson Ylva
Published: April 2012

The PDZ domain is a protein–protein interacting module that plays an important role in the organization of signaling complexes. The recognition of short intrinsically disordered C‐terminal peptide motifs is the archetypical PDZ function, but the functional repertoire of this versatile module also includes recognition of internal peptide sequences, dimerization and phospholipid binding. The PDZ function can be tuned by various means such as allosteric effects, changes of physiological buffer conditions and phosphorylation of PDZ domains and/or ligands, which poses PDZ domains as dynamic regulators of cell signaling. This review is focused on the plasticity of the PDZ interactions.
Soziales Kapital und Gesundheit im städtischen Raum
Authors: Dragano Nico
Published: April 2012

Einleitung

Das Zusammenleben in Städten schafft eigene soziale Realitäten. Daraus kann sich soziales Kapital bilden, das je nach Ausprägung die Gesundheit günstig oder ungünstig beeinflussen kann. Soziales Kapital äußert sich etwa in Vertrauen und sozialem Rückhalt, beides psychische Ressourcen mit gesundheitsförderlicher Wirkung. Ebenfalls nachgewiesen sind Effekte die durch kollektives Verhalten, die Akzeptanz von gesundheitsbezogenen Normen oder durch praktische Formen der Nachbarschaftshilfe entstehen.
The efficacy of dental therapy for an adult case of Henoch–Schönlein purpura
Authors: Abe Masanobu , Mori Yoshiyuki , Saijo Hideto , Hoshi Kazuto , Ohkubo Kazumi , Ono Takehito , Takato Tsuyoshi
Published: April 2012

Henoch–Schönlein purpura (HSP) is a disease that involves palpable purpura on the skin, joint pain, and gastrointestinal problems. An acute bacterial infection is one of the causes of HSP. Odontogenic infectious diseases have also been implicated in causing HSP. However, there are only a few reports describing the correlation between HSP and odontogenic infectious diseases. The present study describes a case in which a patient was cured of HSP following dental treatment.
Multikulturelle Überzeugungen
Authors: Hachfeld Axinja , Schroeder Sascha , Anders Yvonne , Hahn Adam , Kunter Mareike
Published: April 2012

Zusammenfassung: In letzter Zeit wurden vermehrt Initiativen gestartet, Lehrende mit Migrationshintergrund zu gewinnen, unter der Annahme, dass sie über mehr Kompetenzen für das Unterrichten in kulturell heterogenen Kontexten verfügen. Jedoch ist empirisch ungeklärt, ob sich Lehrkräfte in ihrer professionellen Kompetenz für das Unterrichten von Kindern mit Migrationshintergrund unterscheiden und ob mögliche Unterschiede allein auf den Migrationshintergrund zurückzuführen sind. Ausgehend vom COACTIV-Modell der professionellen Kompetenz von Lehrkräften untersuchte die vorliegende Studie an 433 Mathematiklehramtsanwärter(inne)n mit und ohne Migrationshintergrund Selbstwirksamkeitserwartungen, Enthusiasmus und Vorurteile für das Unterrichten von Schüler(inne)n mit Migrationshintergrund vergleichend und testete, ob multikulturelle Überzeugungen (MKÜ) eine vermittelnde Rolle spielen. Ergebnisse aus Strukturgleichungsmodellen bestätigen letzteres: Lehramtsanwärter(innen) mit Migrationshintergrund berichteten ausgeprägtere MKÜ, die wiederum Selbstwirksamkeitserwartungen und Enthusiasmus positiv und Vorurteile negativ beeinflussten.
A formalism for scattering of complex composite structures. II. Distributed reference points
Authors: Svaneborg Carsten , Pedersen Jan Skov
Published: April 2012

Recently, we developed a formalism for the scattering from linear and acyclic branched structures build of mutually non-interacting sub-units. [C. Svaneborg and J. S. Pedersen, J. Chem. Phys. 136, 104105 (2012)]10.1063/1.3682778 We assumed each sub-unit has reference points associated with it. These are well-defined positions where sub-units can be linked together. In the present paper, we generalize the formalism to the case where each reference point can represent a distribution of potential link positions. We also present a generalized diagrammatic representation of the formalism. Scattering expressions required to model rods, polymers, loops, flat circular disks, rigid spheres, and cylinders are derived, and we use them to illustrate the formalism by deriving the generic scattering expression for micelles and bottle-brush structures and show how the scattering is affected by different choices of potential link positions and sub-unit choices.
Structures of small bismuth cluster cations
Authors: Kelting Rebecca , Baldes Alexander , Schwarz Ulrike , Rapps Thomas , Schooss Detlef , Weis Patrick , Neiss Christian , Weigend Florian , Kappes Manfred M.
Published: April 2012

The structures of bismuth cluster cations in the range between 4 and 14 atoms have been assigned by a combination of gas phase ion mobility and trapped ion electron diffraction measurements together with density functional theory calculations. We find that above 8 atoms the clusters adopt prolate structures with coordination numbers between 3 and 4 and highly directional bonds. These open structures are more like those seen for clusters of semiconducting-in-bulk elements (such as silicon) rather than resembling the compact structures typical for clusters of metallic-in-bulk elements. An accurate description of bismuth clusters at the level of density functional theory, in particular of fragmentation pathways and dissociation energetics, requires taking spin-orbit coupling into account. For n = 11 we infer that low energy isomers can have fragmentation thresholds comparable to their structural interconversion barriers. This gives rise to experimental isomer distributions which are dependent on formation and annealing histories.
Kinetic model for dependence of thin film stress on growth rate, temperature, and microstructure
Authors: Chason E. , Shin J. W. , Hearne S. J. , Freund L. B.
Published: April 2012

During deposition, many thin films go through a range of stress states, changing from compressive to tensile and back again. In addition, the stress depends strongly on the processing and material parameters. We have developed a simple analytical model to describe the stress evolution in terms of a kinetic competition between different mechanisms of stress generation and relaxation at the triple junction where the surface and grain boundary intersect. The model describes how the steady state stress scales with the dimensionless parameter D/LR where D is the diffusivity, R is the growth rate, and L is the grain size. It also explains the transition from tensile to compressive stress as the microstructure evolves from isolated islands to a continuous film. We compare calculations from the model with measurements of the stress dependence on grain size and growth rate in the steady state regime and of the evolution of stress with thickness for different temperatures.
A molecular dynamics study of the lateral free energy profile of a pair of cholesterol molecules as a function of their distance in phospholipid bilayers
Authors: Andoh Yoshimichi , Oono Kimiko , Okazaki Susumu , Hatta Ichiro
Published: April 2012

Free energy profile of a pair of cholesterol molecules in a leaflet of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayers in the liquid-crystalline phase has been calculated as a function of their lateral distance using a combination of NPT-constant atomistic molecular dynamics calculations (P = 1 atm and T = 310.15 K) and the thermodynamic integration method. The calculated free energy clearly shows that the two cholesterol molecules form a dimer separated by a distance of 1.0−1.5 nm in POPC bilayers. Well depth of the free energy profile is about 3.5 kJ/mol, which is comparable to the thermal energy kBT at 310.15 K. This indicates that the aggregation of cholesterol molecules in the bilayers depends on the temperature as well as the concentration of the system. The free energy function obtained here may be used as a reference when coarse grained potential model is investigated for this two-component system. Local structure of POPC molecules around two cholesterol molecules has also been investigated.
Growth-induced hormone dilution can explain the dynamics of plant root cell elongation
Authors: Band Leah R. , Úbeda-Tomás Susana , Dyson Rosemary J. , Middleton Alistair M. , Hodgman T. Charlie , Owen Markus R. , Jensen Oliver E. , Bennett Malcolm J. , King John R.
Published: April 2012

In the elongation zone of the
Arabidopsis thaliana
plant root, cells undergo rapid elongation, increasing their length by ∼10-fold over 5 h while maintaining a constant radius. Although progress is being made in understanding how this growth is regulated, little consideration has been given as to how cell elongation affects the distribution of the key regulating hormones. Using a multiscale mathematical model and measurements of growth dynamics, we investigate the distribution of the hormone gibberellin in the root elongation zone. The model quantifies how rapid cell expansion causes gibberellin to dilute, creating a significant gradient in gibberellin levels. By incorporating the gibberellin signaling network, we simulate how gibberellin dilution affects the downstream components, including the growth-repressing DELLA proteins. We predict a gradient in DELLA that provides an explanation of the reduction in growth exhibited as cells move toward the end of the elongation zone. These results are validated at the molecular level by comparing predicted mRNA levels with transcriptomic data. To explore the dynamics further, we simulate perturbed systems in which gibberellin levels are reduced, considering both genetically modified and chemically treated roots. By modeling these cases, we predict how these perturbations affect gibberellin and DELLA levels and thereby provide insight into their altered growth dynamics.
Genomic landscape of human allele-specific DNA methylation
Authors: Fang Fang , Hodges Emily , Molaro Antoine , Dean Matthew , Hannon Gregory J. , Smith Andrew D.
Published: April 2012

DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for full-genome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species.
Probabilistic suffix array: efficient modeling and prediction of protein families
Authors: Lin Jie , Adjeroh Donald , Jiang Bing-Hua
Published: April 2012

Motivation: Markov models are very popular for analyzing complex sequences such as protein sequences, whose sources are unknown, or whose underlying statistical characteristics are not well understood. A major problem is the computational complexity involved with using Markov models, especially the exponential growth of their size with the order of the model. The probabilistic suffix tree (PST) and its improved variant sparse probabilistic suffix tree (SPST) have been proposed to address some of the key problems with Markov models. The use of the suffix tree, however, implies that the space requirement for the PST/SPST could still be high.

Results: We present the probabilistic suffix array (PSA), a data structure for representing information in variable length Markov chains. The PSA essentially encodes information in a Markov model by providing a time and space-efficient alternative to the PST/SPST. Given a sequence of length N, construction and learning in the PSA is done in O(N) time and space, independent of the Markov order. Prediction using the PSA is performed in O(mlog N|Σ|) time, where m is the pattern length, and Σ is the symbol alphabet. In terms of modeling and prediction accuracy, using protein families from Pfam 25.0, SPST and PSA produced similar results (SPST 89.82%, PSA 89.56%), but slightly lower than HMMER3 (92.55%). A modified algorithm for PSA prediction improved the performance to 91.7%, or just 0.79% from HMMER3 results. The average (maximum) practical construction space for the protein families tested was 21.58±6.32N (41.11N) bytes using the PSA, 27.55±13.16N (63.01N) bytes using SPST and 47±24.95N (140.3N) bytes for HMMER3. The PSA was 255 times faster to construct than the SPST, and 11 times faster than HMMER3.

Availability:  http://www.csee.wvu.edu/~adjeroh/projects/PSA

Contact:  don@csee.wvu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty
Authors: Yang Haixuan , Nepusz Tamás , Paccanaro Alberto
Published: April 2012

Motivation: Several measures have been recently proposed for quantifying the functional similarity between gene products according to well-structured controlled vocabularies where biological terms are organized in a tree or in a directed acyclic graph (DAG) structure. However, existing semantic similarity measures ignore two important facts. First, when calculating the similarity between two terms, they disregard the descendants of these terms. While this makes no difference when the ontology is a tree, we shall show that it has important consequences when the ontology is a DAG—this is the case, for example, with the Gene Ontology (GO). Second, existing similarity measures do not model the inherent uncertainty which comes from the fact that our current knowledge of the gene annotation and of the ontology structure is incomplete. Here, we propose a novel approach based on downward random walks that can be used to improve any of the existing similarity measures to exhibit these two properties. The approach is computationally efficient—random walks do not need to be simulated as we provide formulas to calculate their stationary distributions.

Results: To show that our approach can potentially improve any semantic similarity measure, we test it on six different semantic similarity measures: three commonly used measures by Resnik (1999), Lin (1998), and Jiang and Conrath (1997); and three recently proposed measures: simUI, simGIC by Pesquita et al. (2008); GraSM by Couto et al. (2007); and Couto and Silva (2011). We applied these improved measures to the GO annotations of the yeast Saccharomyces cerevisiae, and tested how they correlate with sequence similarity, mRNA co-expression and protein–protein interaction data. Our results consistently show that the use of downward random walks leads to more reliable similarity measures.

Availability: We have developed a suite of tools that implement existing semantic similarity measures and our improved measures based on random walks. The tools are implemented in Matlab and are freely available from: http://www.paccanarolab.org/papers/GOsim/

Contact:  alberto@cs.rhul.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations
Authors: Stanhope Stephen A. , Abney Mark
Published: April 2012

Summary: Mixed model-based approaches to genome-wide association studies (GWAS) of binary traits in related individuals can account for non-genetic risk factors in an integrated manner. However, they are technically challenging. GLOGS (Genome-wide LOGistic mixed model/Score test) addresses such challenges with efficient statistical procedures and a parallel implementation. GLOGS has high power relative to alternative approaches as risk covariate effects increase, and can complete a GWAS in minutes.

Availability: Source code and documentation are provided at http://www.bioinformatics.org/~stanhope/GLOGS.

Contact:  sstanhop@bsd.uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Saccharothrix hoggarensis sp. nov., an actinomycete isolated from Saharan soil
Authors: Boubetra Dalila , Zitouni Abdelghani , Bouras Noureddine , Mathieu Florence , Lebrihi Ahmed , Schumann Peter , Spröer Cathrin , Klenk Hans-Peter , Sabaou Nasserdine
Published: April 2012

An actinomycete, designated SA181T, was isolated from Saharan soil in the Hoggar region (south Algeria) and was characterized taxonomically by using a polyphasic approach. The morphological and chemotaxonomic characteristics of the isolate were consistent with the genus

Saccharothrix

, and 16S rRNA gene sequence analysis confirmed that strain SA181T was a novel member of the genus

Saccharothrix

. DNA–DNA hybridization values between strain SA181T and its closest phylogenetic neighbours, the type strains of

Saccharothrix longispora

,

Saccharothrix texasensis

and

Saccharothrix xinjiangensis

, were clearly below the 70 % threshold. The genotypic and phenotypic data showed that the isolate represents a novel species of the genus

Saccharothrix

, for which the name Saccharothrix hoggarensis sp. nov. is proposed, with the type strain SA181T ( = DSM 45457T  = CCUG 60214T).
Oligosphaera ethanolica gen. nov., sp. nov., an anaerobic, carbohydrate-fermenting bacterium isolated from methanogenic sludge, and description of Oligosphaeria classis nov. in the phylum

Lentisphaerae
Authors: Qiu Yan-Ling , Muramatsu Mizuho , Hanada Satoshi , Kamagata Yoichi , Guo Rong-Bo , Sekiguchi Yuji
Published: April 2012

A mesophilic, obligately anaerobic, carbohydrate-fermenting bacterium, designated 8KG-4T, was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from salted vegetable production processes. Cells of strain 8KG-4T were non-motile, spherical and 0.7–1.5 µm in diameter (mean, 1.0 µm). Spore formation was not observed under any culture conditions tested. The strain grew optimally at 37 °C (range for growth 25–40 °C) and pH 7.0 (range, pH 6.5–7.5), and could grow fermentatively on glucose, ribose, xylose, galactose and sucrose. The main end products of glucose fermentation were acetate, ethanol and hydrogen. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe(III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.1 mol%. 16S rRNA gene sequence analysis revealed that the isolate represented a previously uncultured lineage at the subphylum level within the phylum

Lentisphaerae

known as ‘WWE2 subgroup I’. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. Respiratory quinones were not detected. The most abundant polar lipid of strain 8KG-4T was phosphatidylethanolamine. A novel genus and species, Oligosphaera ethanolica gen. nov., sp. nov., is proposed to accommodate strain 8KG-4T ( = JCM 17152T = DSM 24202T  = CGMCC 1.5160T). In addition, we formally propose Oligosphaeria classis nov. and the subordinate taxa Oligosphaerales order nov. and Oligosphaeraceae fam. nov.
The Plastid Genome-Encoded Ycf4 Protein Functions as a Nonessential Assembly Factor for Photosystem I in Higher Plants
Authors: Krech Katharina , Ruf Stephanie , Masduki Fifi F. , Thiele Wolfram , Bednarczyk Dominika , Albus Christin A. , Tiller Nadine , Hasse Claudia , Schöttler Mark A. , Bock Ralph
Published: April 2012

Photosystem biogenesis in the thylakoid membrane is a highly complicated process that requires the coordinated assembly of nucleus-encoded and chloroplast-encoded protein subunits as well as the insertion of hundreds of cofactors, such as chromophores (chlorophylls, carotenoids) and iron-sulfur clusters. The molecular details of the assembly process and the identity and functions of the auxiliary factors involved in it are only poorly understood. In this work, we have characterized the chloroplast genome-encoded ycf4 (for hypothetical chloroplast reading frame no. 4) gene, previously shown to encode a protein involved in photosystem I (PSI) biogenesis in the unicellular green alga Chlamydomonas reinhardtii. Using stable transformation of the chloroplast genome, we have generated ycf4 knockout plants in the higher plant tobacco (Nicotiana tabacum). Although these mutants are severely affected in their photosynthetic performance, they are capable of photoautotrophic growth, demonstrating that, different from Chlamydomonas, the ycf4 gene product is not essential for photosynthesis. We further show that ycf4 knockout plants are specifically deficient in PSI accumulation. Unaltered expression of plastid-encoded PSI genes and biochemical analyses suggest a posttranslational action of the Ycf4 protein in the PSI assembly process. With increasing leaf age, the contents of Ycf4 and Y3IP1, another auxiliary factor involved in PSI assembly, decrease strongly, whereas PSI contents remain constant, suggesting that PSI is highly stable and that its biogenesis is restricted to young leaves.