bluuebunny/crossref_metadata_2025 huggingface dataset:
Readiness to adopt a self‐management approach to pain – Are profiles of subscale scores on the Pain Stages of Change Questionnaire useful?
Authors: Fors Terese , Damsgård Elin , Røe Cecilie , Anke Audny
Published: May 2010

The study evaluated the ability of the Pain Stages of Change Questionnaire (PSOCQ) to classify subjects into specific profiles of readiness to adopt a self‐management approach to pain. An analysis was made of whether the five earlier described PSOCQ‐profiles Precontemplation, Contemplation, Non‐contemplative Action, Participation and Ambivalent could be reproduced by two different methods, cluster analysis and visual analysis. The 184 included subjects completed the PSOCQ, the Hopkins Symptom Checklist (HSCL‐25), the Tampa scale of Kinesiophobia (TSK) and five self‐efficacy questions from the arthritis self‐efficacy questionnaire (ASES). Profiles were drawn based on the mean scores of the four subscales in PSOCQ. All the five predefined profiles were identified visually by two coders with an interrater agreement of Kappa 0.731. A 6‐cluster solution generated the four profiles Precontemplation, Contemplation, Non‐contemplative Action and Participation. Discriminant function analysis (DFA) on cluster analysis classified 83.5% of cases in the same group, and DFA on visual classification 72.1% of cases. Fifty‐three percent were classified in the same profile by cluster and visual analysis. The two profiles Precontemplation and Participation seem to identify distinct subgroups that differ in educational level, pain during activity and psychometric measures. Non‐contemplative Action share characteristics with Precontemplation, and the Contemplation group has scores in between. In conclusion, more research on the validity of the PSOCQ is needed. Outcome studies after pain treatment programmes could focus three main states that differ on measures for concurrent validity: Profiles that can be identified as Precontemplation or Non‐contemplative action, Contemplators, and subjects with Participation profiles.
Direct contacts between conserved motifs of different subunits provide major contribution to active site organization in human and mycobacterial dUTPases
Authors: Takács Enikő , Nagy Gergely , Leveles Ibolya , Harmat Veronika , Lopata Anna , Tóth Judit , Vértessy Beáta G.
Published: May 2010

dUTP pyrophosphatases (dUTPases) are essential for genome integrity. Recent results allowed characterization of the role of conserved residues. Here we analyzed the Asp/Asn mutation within conserved Motif I of human and mycobacterial dUTPases, wherein the Asp residue was previously implicated in Mg2+‐coordination. Our results on transient/steady‐state kinetics, ligand binding and a 1.80 Å resolution structure of the mutant mycobacterial enzyme, in comparison with wild type and C‐terminally truncated structures, argue that this residue has a major role in providing intra‐ and intersubunit contacts, but is not essential for Mg2+ accommodation. We conclude that in addition to the role of conserved motifs in substrate accommodation, direct subunit interaction between protein atoms of active site residues from different conserved motifs are crucial for enzyme function.
Dyskeratosis congenita
Authors: Bessler Monica , Wilson David B. , Mason Philip J.
Published: May 2010

Dyskeratosis congenita (DC) was originally defined as a rare inherited bone marrow failure (BMF) syndrome associated with distinct mucocutaneous features. Today DC is defined by its pathogenetic mechanism and mutations in components of the telomere maintenance machinery resulting in excessively short telomeres in highly proliferating tissues. With this new definition the disease spectrum has broadened and ranges from intrauterine growth retardation, cerebellar hypoplasia, and death in early childhood to asymptomatic mutation carriers whose descendants are predisposed to malignancy, BMF, or pulmonary disease. The degree of telomere dysfunction is the major determinant of disease onset and manifestations.
The scaffold protein JIP3 functions as a downstream effector of the small GTPase ARF6 to regulate neurite morphogenesis of cortical neurons
Authors: Suzuki Atsushi , Arikawa Chihiro , Kuwahara Yuji , Itoh Kouichi , Watanabe Masatomo , Watanabe Hiroshi , Suzuki Teruhiko , Funakoshi Yuji , Hasegawa Hiroshi , Kanaho Yasunori
Published: May 2010

MINT‐7892353, MINT‐7892615, MINT‐7892657, MINT‐7892672, MINT‐7892549, MINT‐7892738: Arf6 (uniprotkb:P62331) physically interacts (MI:0915) with JIP3 (uniprotkb:Q9ESN9) by anti tag coimmunoprecipitation (MI:0007)
Metabolism of postsynaptic recombination intermediates
Authors: Adelman Carrie A. , Boulton Simon J.
Published: May 2010

DNA double strand breaks and blocked or collapsed DNA replication forks are potentially genotoxic lesions that can result in deletions, aneuploidy or cell death. Homologous recombination (HR) is an essential process employed during repair of these forms of damage. HR allows for accurate restoration of the damaged DNA through use of a homologous template for repair. Although inroads have been made towards understanding the mechanisms of HR, ambiguity still surrounds aspects of the process. Until recently, relatively little was known concerning metabolism of postsynaptic RAD51 filaments or how synthesis dependent strand annealing intermediates are processed. This review discusses recent findings implicating RTEL1, HELQ and the Caenorhabditis elegans RAD51 paralog RFS‐1 in post‐strand exchange events during HR.
Extracellular superoxide dismutase attenuates release of pulmonary hyaluronan from the extracellular matrix following bleomycin exposure
Authors: Zelko Igor N. , Folz Rodney J.
Published: May 2010

The major pulmonary antioxidant enzyme involved in the protection of the lung interstitium from oxidative stress is extracellular superoxide dismutase (EC‐SOD). It has been previously shown that EC‐SOD knock‐out mice are more susceptible to bleomycin‐induced lung injury, however, the molecular mechanism(s) remains unclear. We report here that bleomycin‐induced lung damage, in EC‐SOD KO mice, is associated with increased hyaluronan release into alveolar fluid. Analysis of hyaluronan synthase gene expression and hyaluronan molecular weight distribution suggested that elevated levels of hyaluronan in the alveolar fluid are mostly due to its release from the interstitium. Our results indicate that EC‐SOD attenuates bleomycin‐induced pulmonary injury, at least in part, by preventing superoxide‐mediated release of hyaluronan into alveolar space.
Telomeres and telomerase in normal and cancer stem cells
Authors: Shay Jerry W. , Wright Woodring E.
Published: May 2010

Differences between normal adult tissue stem cells and cancer stem/initiating cells remain poorly defined. For example, it is controversial if cancer stem cells can become fully quiescent, require a stem cell niche, are better at repairing DNA damage than the bulk of the cancer cells, and if and how they regulate symmetric versus asymmetric cell divisions. This minireview will not only provide our personal views to address some of these outstanding questions, but also present evidence that an understanding of telomere dynamics and telomerase activity in normal and cancer stem cells may provide additional insights into how tumors are initiated, and how they should be monitored and treated.
Zinc accumulation in heterozygous mutants of fumble, the pantothenate kinase homologue of Drosophila
Authors: Gutiérrez Lucia , Sabaratnam Narmatha , Aktar Rubina , Bettedi Lucia , Mandilaras Konstantinos , Missirlis Fanis
Published: May 2010

Coenzyme A (CoA) functions in the intracellular trafficking of acetyl groups. In humans, mutations in the pantothenate kinase‐2 gene, which encodes a key enzyme in CoA biosynthesis, are associated with neurodegeneration and premature death. Diagnosis is based on iron accumulation in the globus pallidus observed by magnetic resonance imaging. We investigated the elemental composition of the fumble mutant, a model of the human disease. Surprisingly, flies carrying a fumble loss‐of‐function allele had a three‐fold increase in total zinc levels per dry weight when compared to control strains, but no change in total iron, copper or manganese levels. Accordingly, zinc supplementation had an adverse impact on the development of fumble mutant larvae, but zinc chelation failed to protect.
An emerging role for bromodomain‐containing proteins in chromatin regulation and transcriptional control of adipogenesis
Authors: Denis Gerald V. , Nikolajczyk Barbara S. , Schnitzler Gavin R.
Published: May 2010

Transcriptional co‐activators, co‐repressors and chromatin remodeling machines are essential elements in the transcriptional programs directed by the master adipogenic transcription factor PPARγ. Many of these components have orthologs in other organisms, where they play roles in development and pattern formation, suggesting new links between cell fate decision‐making and adipogenesis. This review focuses on bromodomain‐containing protein complexes recently shown to play a critical role in adipogenesis. Deeper understanding of these pathways is likely to have major impact on treatment of obesity‐associated diseases, including metabolic syndrome, cardiovascular disease and Type 2 diabetes. The research effort is urgent because the obesity epidemic is serious; the medical community is ill prepared to cope with the anticipated excess morbidity and mortality associated with diet‐induced obesity.
The impact of anesthesia and mode of delivery on the urinary bladder in the postdelivery period
Authors: Foon Richard , Toozs‐Hobson Philip , Millns Peter , Kilby Mark
Published: May 2010

Objective

To evaluate the effect of regional anesthesia and mode of delivery on the function of the urinary bladder. The primary outcome was the time taken for urinary bladder sensation to return following various modes of delivery and analgesia/anesthesia. The secondary outcome was the volume of urine present in the bladder when sensation returned.

Methods

The study was conducted at the Birmingham Women's Foundation Trust, Birmingham, UK. A total of 120 postnatal patients were studied between January 2007 and March 2008. The volume of urine in the bladder when sensation first returned was measured by release of a clamp for women fitted with an indwelling catheter, and/or estimated using ultrasound.

Results

The median times for sensation to return to the bladder in patients who had a vaginal delivery without epidural analgesia, vaginal delivery with epidural analgesia, and after elective cesarean delivery under spinal anesthesia were 122 minutes (IQR, 112–136 minutes), 234 minutes (IQR, 202–291 minutes), and 374 minutes (IQR, 311–425 minutes), respectively. The median urine volumes were 144 mL (IQR, 112–192 mL), 200 mL (IQR, 136–336 mL), and 152.5 mL (IQR, 125–270 mL), respectively.

Conclusion

These results should be taken into consideration when formulating a postdelivery bladder care protocol.
Transvaginal ultrasound and sonohysterography for assessment of postpartum residual trophoblastic tissue
Authors: Cosmi Erich , Saccardi Carlo , Litta Pietro , Nardelli Giovanni B. , Dessole Salvatore
Published: May 2010

Objective

To compare the accuracy of transvaginal ultrasound and sonohysterography (SHG) in diagnosing residual trophoblastic tissue in postpartum women and to assess the adverse effects and complications of the SHG procedure.

Methods

A prospective study of patients with postpartum bleeding enrolled for clinical symptoms and signs of residual trophoblastic tissue. All women underwent transvaginal ultrasound and SHG. Uterine cavity curettage was performed in all women and the material collected was sent for pathologic examination.

Results

Among 84 patients, transvaginal ultrasound revealed residual trophoblastic tissue in 60 women, whereas SHG detected residual trophoblastic tissue in 48 and blood clots in 12. Pathologic examination confirmed trophoblastic tissue in 48 patients and blood clots in 12. Fifteen (17.9%) patients experienced adverse effects after SHG. Thirteen (15.5%) experienced postprocedural fever that resolved with antibiotics. Two women (2.4%) had severe complications of infection: 1 required surgery for peritonitis, which revealed salpingitis and a pelvic abscess; 1 experienced fever and mild abdominal pain that resolved with antibiotics after 10 days of hospitalization.

Conclusions

Although SHG showed greater accuracy than transvaginal ultrasound in detecting residual trophoblastic tissue, a high proportion of patients experienced adverse effects.
Protocol to the African Charter on the Rights of Women: Implications for access to abortion at the regional level
Authors: Ngwena Charles G.
Published: May 2010

Article 14(2)(c) of the Protocol to the African Charter on the Rights of Women enjoins States Parties to take appropriate measures “to protect the reproductive rights of women by authorising medical abortion in cases of sexual assault, rape, incest, and where continued pregnancy endangers the mental and physical health of the mother or the life of the mother or the foetus.” This paper considers the implications of Article 14 for access to safe, legal abortion. It is submitted that Article 14 has the potential to impact positively on regional abortion law, policy, and practice in 3 main areas. First, it takes forward the global consensus on combating abortion as a major public health danger. Second, it provides African countries with not just an incentive, but also an imperative for reforming abortion laws in a transparent manner. Third, if implemented in the context of a treaty that centers on the equality and non‐discrimination of women, Article 14 has the potential to contribute toward transforming access to abortion from a crime and punishment model to a reproductive health model.
Genetic susceptibility to breast cancer
Authors: Mavaddat Nasim , Antoniou Antonis C. , Easton Douglas F. , Garcia-Closas Montserrat
Published: May 2010

Genetic and lifestyle/environmental factors are implicated in the aetiology of breast cancer. This review summarizes the current state of knowledge on rare high penetrance mutations, as well as moderate and low‐penetrance genetic variants implicated in breast cancer aetiology. We summarize recent discoveries from large collaborative efforts to combine data from candidate gene studies, and to conduct genome‐wide association studies (GWAS), primarily in breast cancers in the general population. These findings are compared with results from collaborative efforts aiming to identify genetic modifiers in BRCA1 and BRCA2 carriers. Breast cancer is a heterogeneous disease, and tumours from BRCA1 and BRCA2 carriers display distinct pathological characteristics when compared with tumours unselected for family history. The relationship between genetic variants and pathological subtypes of breast cancer, and the implication of discoveries of novel genetic variants to risk prediction in BRCA1/2 mutation carriers and in populations unselected for mutation carrier status, are discussed.
Distraction osteogenesis of the mandible for airway obstruction in children: Long‐term results
Authors: Tibesar Robert J. , Scott Andrew R. , McNamara Christopher , Sampson Daniel , Lander Timothy A. , Sidman James D.
Published: May 2010

Objective

To determine the long‐term results of distraction osteogenesis of the mandible for upper airway obstruction in children with micrognathia.

Study Design

Case series with chart review.

Setting

Tertiary care children's hospital.

Subjects and Methods

The records of a pediatric otolaryngology practice and tertiary children's hospital were searched for patients treated with bilateral mandibular distraction osteogenesis for upper airway obstruction. Patients were selected if greater than three years of follow‐up data were available. Data were analyzed for airway and feeding outcomes, and long‐term surgical complications were identified.

Results

Thirty‐two patients met study criteria. Of the 11 patients who had tracheotomy prior to distraction, seven were decannulated after the procedure. Seventeen patients needed perioperative gastrostomy. Seven are now able to feed orally. Fifteen patients treated with mandibular distraction were able to avoid gastrostomy tube placement altogether. The complication of open bite deformity was experienced by nine patients (28%). Five of 32 patients (16%) had tooth malformation, tooth loss, or dentigerous cyst formation while an additional three patients (9%) had long‐term facial nerve injury. Nineteen patients (59%) were under three months old at the time of their distraction. Only one of these patients (5.2%) required an additional distraction procedure.

Conclusion

Long‐term follow‐up data on patients treated with mandibular distraction for upper airway obstruction show sustained airway improvement. Additionally, micrognathic children treated with distraction have improved outcomes in oral feeding with a relatively low rate of long‐term complications. It remains important to follow these patients to monitor the need for secondary reconstructive procedures.
Murine complement deficiency ameliorates acute cigarette smoke‐induced nasal damage
Authors: Davis Kara S. , Casey Sarah E. , Mulligan Jennifer K. , Mulligan Ryan M. , Schlosser Rodney J. , Atkinson Carl
Published: May 2010

Objective

Exposure to cigarette smoke is a risk factor for chronic rhinosinusitis. Current literature confirms complement fragments are activated in human nasal mucosa. The mechanism(s) responsible for this activation is unclear. We investigated the effects of cigarette smoke on nasal mucosa in vitro and via a model of cigarette smoke exposure by using animals deficient in complement components.

Study Design

Prospective, controlled animal and in vitro human cell line study.

Setting

University laboratory.

Subjects and Methods

Human respiratory epithelial cells were exposed to five, 10, and 20 percent cigarette smoke extract (CSE) in vitro in the presence or absence of human serum. Complement activation was assessed by enzyme‐linked immunosorbent assay and immunofluorescent techniques. Complement‐deficient (C3–/–, n = 6; factor B–/–, n = 50) and sufficient mice (wild type, n = 10) were exposed to the smoke of four cigarettes per exposure for two exposures per day for three days. Mice were sacrificed 12 hours after the last exposure, and the nasal cavity was surgically removed. Histological characteristics were analyzed by the use of a subjective scale and quantitative image analysis scoring systems.

Results

In vitro analysis of respiratory cell cultures demonstrated that exposure of serum to CSE resulted in complement activation. Furthermore, immunofluorescent staining for C3d could only be demonstrated in CSE‐exposed cultures. In vivo analysis demonstrated that complement deficiency, either C3 or factor B deficiency, resulted in a significant reduction in histological evidence of damage as compared with wild‐type control mice (wild type vs C3–/–, P = 0.02; wild type vs factor B–/–, P = 0.07; no significant difference between C3–/– vs factor B–/–).

Conclusion

These data demonstrate that cigarette smoke activates the complement system. Furthermore, complement deficiency protected against smoke‐induced mucosal damage in this small series.
Textural and carbon isotopic evidence of monsoonal changes recorded in a composite-type speleothem from Korea since MIS 5a
Authors: Jo Kyoung-nam , Woo Kyung Sik , Cheng Hai , Edwards Lawrence R. , Wang Yongjin , Kim Ryeon , Jiang Xiuyang
Published: May 2010

Textural and stable isotopic records of a composite-type speleothem from Gwaneum Cave in the eastern part of the Korean peninsula show prominent paleoenvironmental changes since MIS (marine oxygen isotope stage) 5a. Based on 230Th/234U dating, the speleothem experienced growth from 90.9 ± 6.5 ka to 1.2 ± 0.5 ka with several hiatuses. Four growth phases (A, B, C and D) are recognized based on speleothem type and texture. Very irregular and laterally discontinuous growth laminae in Phases B and C indicate that the cave coralloids grew over the stalagmite (Phase A) when the supply of dripping water became limited. Variations within the δ13C time series of Phase A are interpreted as responses to millennial-scale fluctuations of the East Asian monsoon intensity during MIS 5a. The monsoonal interpretation is based on the idea that δ13C values reflect the isotopic composition of soil-derived CO2, which, in turn, should relate to monsoon-driven changes in terrestrial productivity above the cave during the MIS 5a. Our reconstruction reveals that the significant monsoonal changes on the Korean peninsula occurred in conjunction with changes in sea level and/or oceanic circulations during the transition period from MIS 5a to MIS 4.
Was ist Katathym Imaginative Psychotherapie?
Authors: Nohr Karin
Published: May 2010

Zusammenfassung. Der Artikel stellt die Katathym Imaginative Psychotherapie als Sonderform des tiefenpsychologischen Vorgehens im Überblick dar. Anhand einer Falldarstellung – einer Krisenintervention als Kurzzeittherapie – wird veranschaulicht, wie die KIP angeleitete Imaginationen für den therapeutischen Prozess nutzt, wie sie diese anregt, begleitet, auswertet und in den Gesprächs- und Verständniszusammenhang einbettet. Dem Patienten ermöglicht das vom Therapeuten durch bestimmte naturhafte Anregungsmotive in ihm angestoßene innere Bildgeschehen eine gefühlsnahe Art der Selbsterkundung. Sie wirkt oft im Sinne eines Aha-Effekts: Der Patient lernt eigene, unvermutete Ressourcen zu entdecken, gerät in aufbauende Regressionen im Dienste des Ich, und er kann mithilfe des Therapeuten seine bewussten und auch unbewusste Konflikte, Wünsche und Ängste auf symbolische, daher zugleich plastische, aber auch von ihm etwas entrückte und dadurch besser erträgliche Weise erforschen oder erstmals wahrnehmen. Es wird hervorgehoben, wie sehr die Imaginationen nicht einfach eine Art Momentaufnahme der Patientenseele darstellen, sondern immer nur das zeigen können, was ein Patient mit seinem Therapeuten zu dem jeweiligen Zeitpunkt des Therapiegeschehens teilen kann (Übertragungs- und Abwehrdimension). Imaginationen können nur fruchtbar wirken im Rahmen einer haltenden und um Verstehen bemühten therapeutischen Beziehung.
Katathymes Kunsterleben: Die weiße Katze von Franz Marc
Authors: Franzen Georg
Published: May 2010

Zusammenfassung. Ausgehend von einer Kunstbetrachtung mit Patienten einer psychiatrischen Tagesstätte zu einem Gemälde von Franz Marc in der Ausstellung „Marc, Macke und Delaunay” im Sprengel Museum Hannover 2009, werden tiefenpsychologische, imaginative und kunsttherapeutische Aspekte der Kunstbetrachtung beschrieben. Die Begegnung mit dem Kunstwerk wird als Erfahrungsraum beschrieben, der sich über Imaginationen und Assoziationen in der Tiefendimension erschließen lässt.
Coactive Processing of Dimensionally Redundant Targets Within the Auditory Modality?
Authors: Fiedler Anja , Schröter Hannes , Ulrich Rolf
Published: May 2010

Previous reaction time studies have demonstrated coactivation processes within the visual modality for redundant stimuli that differ in two dimensions (e.g., shape and color). The present study provides novel results of analogous processes within the auditory modality. A redundant-target effect (RTE) was obtained in a Go/NoGo experiment using tones that differed in location and/or frequency. Participants were asked to respond to a specific tone location (e.g., left) and/or tone frequency (e.g., 200 Hz) of auditory stimuli. For redundant targets (e.g., a 200 Hz tone presented to the left), an RTE was observed which was too large to be explained by mere statistical facilitation. Therefore, responses to redundant targets were triggered by a combined activation of the target dimensions. The results are consistent with the modular hybrid account of Mordkoff and Yantis (1993) .
Motor Contagion
Authors: Bouquet Cédric A. , Shipley Thomas F. , Capa Rémi L. , Marshall Peter J.
Published: May 2010

Recent theories posit a mirror-matching system mapping observed actions onto one’s own motor system. Determining whether this system makes a distinction between goal-directed and non-goal-directed actions is crucial for the understanding of its function. The present study tested whether motor interference between observed and executed actions, which is thought to be an index of perceptual-motor matching, depends on the presence of goals in the observed action. Participants executed sinusoidal arm movements while observing a video of another person making similar or different movements. In certain conditions, elements representing goals for the observed movement were superimposed on the video displays. Overall, observing an incongruent movement interfered with movement execution. This interference was markedly increased when the observed incongruent movement was directed toward a visible goal, suggesting a greater perceptual-motor matching during observation of goal-directed versus non-goal-directed actions. This finding supports an action-reconstruction model of mirror system function rather than the traditional direct-matching model.
Accessory Stimuli Affect the Emergence of Conflict, Not Conflict Control
Authors: Böckler Anne , Alpay Gamze , Stürmer Birgit
Published: May 2010

Accessory signals that precede stimuli in interference tasks lead to faster overall responses while conflict increases. Two opposing accounts exist for the latter finding: one is based on dual-route frameworks of response preparation and proposes amplification of both direct response activation and indirect response selection processes; the other refers to attentional networks and suggests inhibition of executive attention, thereby hampering conflict control. The present study replicated previous behavioral findings in a Simon task and extended them by electrophysiological evidence. Accessory tones facilitated stimulus classification and attentional allocation in the Simon task as reflected by an increased N1 amplitude and an overall decrease of the N2 amplitude, respectively. The conflict-related N2 amplitude, which is larger in conflict trials compared with nonconflict trials, was not modulated by accessory tones. Moreover, accessory tones did not affect sequence-dependent conflict adaptation. In terms of a dual-route framework present results suggest amplification of both response preparation routes by accessory stimuli. An executive attention approach proposing accessory stimuli to hamper control of conflict is not supported.
How Socially Relevant Visual Characteristics of Avatars Influence Impression Formation
Authors: Weibel David , Stricker Daniel , Wissmath Bartholomäus , Mast Fred W.
Published: May 2010

Like in the real world, the first impression a person leaves in a computer-mediated environment depends on his or her online appearance. The present study manipulates an avatar’s pupil size, eyeblink frequency, and the viewing angle to investigate whether nonverbal visual characteristics are responsible for the impression made. We assessed how participants (N = 56) evaluate these avatars in terms of different attributes. The findings show that avatars with large pupils and slow eye blink frequency are perceived as more sociable and more attractive. Compared to avatars seen in full frontal view or from above, avatars seen from below were rated as most sociable, self-confident, and attractive. Moreover, avatars’ pupil size and eyeblink frequency escape the viewer’s conscious perception but still influence how people evaluate them. The findings have wide-ranging applied implications for avatar design.
Overloading ion‐exchange membranes as a purification step for monoclonal antibodies
Authors: Brown Arick , Bill Jerome , Tully Timothy , Radhamohan Asha , Dowd Chris
Published: May 2010

The present study examined the overloading of ion‐exchange membrane adsorbers, a form of frontal chromatography, as the final purification step in the production of mAbs (monoclonal antibodies) produced from CHO (Chinese‐hamster ovary) cells. Preferential binding of impurities over antibody product was exploited using commercially available cation‐ and anion‐exchange membranes. Three different antibody feedstreams previously purified over Protein A and ion‐exchange column chromatography were tested. Feedstream conductivity and pH were adjusted to induce product and impurity adsorption. Membranes were then overloaded in a normal flow mode, resulting in retention of impurities and breakthrough of purified antibody. Although some amount of the product also binds to the membranes (usually ≤30 g mAb/l membrane), yields of ≥99% were achieved by marginalizing the losses, typically by loading more than 3 kg mAb/l membrane. Analyses of the purified pools show consistent removal of impurities despite strong mAb–ligand interactions and high membrane loadings. The clearance of host cell proteins was affected by pH and conductivity, but was unaffected by flow rate, membrane properties or scale. The importance of the present study lies in our demonstration of an alternative use of ion‐exchange membranes for fast, effective and high yielding purification of mAbs.
The complexity and evolution of the plastid-division machinery
Authors: Maple Jodi , Møller Simon Geir
Published: May 2010

Plastids are vital organelles, fulfilling important metabolic functions that greatly influence plant growth and productivity. In order to both regulate and harness the metabolic output of plastids, it is vital that the process of plastid division is carefully controlled. This is essential, not only to ensure persistence in dividing plant cells and that optimal numbers of plastids are obtained in specialized cell types, but also to allow the cell to act in response to developmental signals and environmental changes. How this control is exerted by the host nucleus has remained elusive. Plastids evolved by endosymbiosis and during the establishment of a permanent endosymbiosis they retained elements of the bacterial cell-division machinery. Through evolution the photosynthetic eukaryotes have increased dramatically in complexity, from single-cell green algae to multicellular non-vascular and vascular plants. Reflected with this is an increasing complexity of the division machinery and recent findings also suggest increasing complexity in the molecular mechanisms used by the host cell to control the process of plastid division. In the present paper, we explore the current understanding of the process of plastid division at the molecular and cellular level, with particular respect to the evolution of the division machinery and levels of control exerted on the process.
Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol
Authors: Richardson Des R. , Lane Darius J. R. , Becker Erika M. , Huang Michael L.-H. , Whitnall Megan , Rahmanto Yohan Suryo , Sheftel Alex D. , Ponka Prem
Published: May 2010

The mitochondrion is well known for its key role in energy transduction. However, it is less well appreciated that it is also a focal point of iron metabolism. Iron is needed not only for heme and iron sulfur cluster (ISC)-containing proteins involved in electron transport and oxidative phosphorylation, but also for a wide variety of cytoplasmic and nuclear functions, including DNA synthesis. The mitochondrial pathways involved in the generation of both heme and ISCs have been characterized to some extent. However, little is known concerning the regulation of iron uptake by the mitochondrion and how this is coordinated with iron metabolism in the cytosol and other organelles (e.g., lysosomes). In this article, we discuss the burgeoning field of mitochondrial iron metabolism and trafficking that has recently been stimulated by the discovery of proteins involved in mitochondrial iron storage (mitochondrial ferritin) and transport (mitoferrin-1 and -2). In addition, recent work examining mitochondrial diseases (e.g., Friedreich's ataxia) has established that communication exists between iron metabolism in the mitochondrion and the cytosol. This finding has revealed the ability of the mitochondrion to modulate whole-cell iron-processing to satisfy its own requirements for the crucial processes of heme and ISC synthesis. Knowledge of mitochondrial iron-processing pathways and the interaction between organelles and the cytosol could revolutionize the investigation of iron metabolism.
Biased gene transfer mimics patterns created through shared ancestry
Authors: Andam Cheryl P. , Williams David , Gogarten J. Peter
Published: May 2010

In phylogenetic reconstruction, two types of bacterial tyrosyl-tRNA synthetases (TyrRS) form distinct clades with many bacterial phyla represented in both clades. Very few taxa possess both forms, and maximum likelihood analysis of the distribution of TyrRS types suggests horizontal gene transfer (HGT), rather than an ancient duplication followed by differential gene loss, as the contributor to the evolutionary history of TyrRS in bacteria. However, for each TyrRS type, phylogenetic reconstruction yields phylogenies similar to the ribosomal phylogeny, revealing that frequent gene transfer has not destroyed the expected phylogeny; rather, the expected phylogenetic signal was reinforced or even created by HGT. We show that biased HGT can mimic patterns created through shared ancestry by in silico simulation. Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative gene positions, bothtyrRStypes occupy equivalent positions in closely related genomes, rejecting the loss hypothesis. Although the two types of bacterial TyrRS are only distantly related and only rarely coexist in a single genome, they have many features in common with alleles that are swapped between related lineages. We propose to label these functionally similar homologs as homeoalleles. We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.
Machine learning based prediction for peptide drift times in ion mobility spectrometry
Authors: Shah Anuj R. , Agarwal Khushbu , Baker Erin S. , Singhal Mudita , Mayampurath Anoop M. , Ibrahim Yehia M. , Kangas Lars J. , Monroe Matthew E. , Zhao Rui , Belov Mikhail E. , Anderson Gordon A. , Smith Richard D.
Published: May 2010

Motivation: Ion mobility spectrometry (IMS) has gained significant traction over the past few years for rapid, high-resolution separations of analytes based upon gas-phase ion structure, with significant potential impacts in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics techniques, such as in the elucidation of secondary structure information, identification of post-translational modifications, as well as higher identification rates with reduced experiment times. The high throughput nature of this technique benefits from accurate calculation of cross sections, mobilities and associated drift times of peptides, thereby enhancing downstream data analysis. Here, we present a model that uses physicochemical properties of peptides to accurately predict a peptide's drift time directly from its amino acid sequence. This model is used in conjunction with two mathematical techniques, a partial least squares regression and a support vector regression setting.

Results: When tested on an experimentally created high confidence database of 8675 peptide sequences with measured drift times, both techniques statistically significantly outperform the intrinsic size parameters-based calculations, the currently held practice in the field, on all charge states (+2, +3 and +4).

Availability: The software executable, imPredict, is available for download from http:/omics.pnl.gov/software/imPredict.php

Contact:  rds@pnl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
FuncBase : a resource for quantitative gene function annotation
Authors: Beaver John E. , Taşan Murat , Gibbons Francis D. , Tian Weidong , Hughes Timothy R. , Roth Frederick P.
Published: May 2010

Summary: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. For example, a custom Cytoscape viewer shows functional linkage graphs relevant to the gene or function of interest. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases.

Availability: FuncBase as well as all underlying data and annotations are freely available via http://func.med.harvard.edu/

Contact:  fritz_roth@hms.harvard.edu
Exercise training for systolic heart failure: Cochrane systematic review and meta‐analysis
Authors: Davies Edward J. , Moxham Tiffany , Rees Karen , Singh Sally , Coats Andrew J.S. , Ebrahim Shah , Lough Fiona , Taylor Rod S.
Published: May 2010

Aims

To determine the effect of exercise training on clinical events and health‐related quality of life (HRQoL) of patients with systolic heart failure.

Methods and results

We searched electronic databases including Medline, EMBASE, and Cochrane Library up to January 2008 to identify randomized controlled trials (RCTs) comparing exercise training and usual care with a minimum follow‐up of 6 months. Nineteen RCTs were included with a total of 3647 patients, the majority of whom were male, low‐to‐medium risk, and New York Heart Association class II–III with a left ventricular ejection fraction of <40%. There was no significant difference between exercise and control in short‐term (≤12 months) or longer‐term all‐cause mortality or overall hospital admissions. Heart failure‐related hospitalizations were lower [relative risk: 0.72, 95% confidence interval (CI): 0.52–0.99] and HRQoL improved (standardized mean difference: −0.63, 95% CI: −0.80 to −0.37) with exercise therapy. Any effect of cardiac exercise training on total mortality and HRQoL was independent of degree of left ventricular dysfunction, type of cardiac rehabilitation, dose of exercise intervention, length of follow‐up, trial quality, and trial publication date.

Conclusion

Compared with usual care, in selected heart failure patients, exercise training reduces heart failure‐related hospitalizations and results in clinically important improvements in HRQoL. High‐quality RCT and cost‐effectiveness evidence is needed for the effect of exercise training in community‐based settings and in more severe heart failure patients, elderly people, and women.
Cardiac resynchronization therapy for low‐flow, low‐gradient aortic stenosis
Authors: Konstantino Yuval , Zimetbaum Peter J. , Hsing Jeff , Kramer Daniel B. , Chang James D.
Published: May 2010

Low‐flow, low‐gradient aortic stenosis is a heterogeneous entity that encompasses truly severe aortic stenosis as well as mild‐to‐moderate aortic stenosis in which aortic valve orifice area is severely reduced primarily due to left ventricular (LV) contractile dysfunction. Under such circumstances the capacity of the LV to generate stroke‐work is severely compromised. In this case report, we describe a patient with severe LV dysfunction and ventricular dyssynchrony due to right ventricular pacing who presented with decompensated heart failure in the setting of low‐flow, low‐gradient aortic stenosis. We discuss the management of this high‐operative‐risk patient, who ultimately underwent upgrading of his dual chamber pacemaker to a biventricular pacemaker with significant echocardiographic, haemodynamic, and clinical improvement.
Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats
Authors: Cadrin Steven X. , Bernreuther Matthias , Daníelsdóttir Anna Kristín , Hjörleifsson Einar , Johansen Torild , Kerr Lisa , Kristinsson Kristjan , Mariani Stefano , Nedreaas Kjell , Pampoulie Christophe , Planque Benjamin , Reinert Jákup , Saborido-Rey Fran , Sigurðsson Thorsteinn , Stransky Christoph
Published: May 2010

Cadrin, S. X., Bernreuther, M., Daníelsdóttir, A. K., Hjörleifsson, E., Johansen, T., Kerr, L., Kristinsson, K., Mariani, S., Nedreaas, K., Pampoulie, C., Planque, B., Reinert, J., Saborido-Rey, F., Sigurðsson, T., and Stransky, C. 2010. Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats. – ICES Journal of Marine Science, 67: 1617–1630. Throughout their range, Sebastes spp. are adapted to a diversity of ecological niches, with overlapping spatial distributions of different species that have little or no morphological differences. Divergence of behavioural groups into depth-defined adult habitats has led to reproductive isolation, adaptive radiation, and speciation in the genus Sebastes. Recent genetic research, supported by life-history information, indicates four biological stocks of Sebastes mentella in the Irminger Sea and adjacent waters: a western stock, a deep-pelagic stock, a shallow-pelagic stock, and an Iceland slope stock. Congruent differences in fatty acids and parasites suggest that these genetically distinct populations are adapted to disparate trophic habitats in pelagic waters (shallower and deeper than the deep-scattering layer) and in demersal habitats on the continental slope. Morphology of pelagic forms is also more streamlined than demersal forms. Although genetic differences and evidence for reproductive isolation are clear, these populations appear to share common nursery habitats on the Greenland shelf. We propose a redefinition of practical management units near the Irminger Sea based on geographic proxies for biological stocks and minimizing mixed-stock catches according to the spatial patterns of the recent fishery.
Lactobacillus kimchicus sp. nov., a β-glucosidase-producing bacterium isolated from kimchi
Authors: Liang Zhi-Qi , Srinivasan Sathiyaraj , Kim Yeon-Ju , Kim Ho-Bin , Wang Hong-Tao , Yang Deok-Chun
Published: May 2010

A Gram-reaction-positive, non-spore-forming, rod-shaped, non-motile, β-glucosidase-producing bacterium, designated DCY51T, was isolated from kimchi, a Korean fermented vegetable food. 16S rRNA gene sequence analysis revealed that strain DCY51T belonged to the genus Lactobacillus and exhibited highest 16S rRNA gene sequence similarity with Lactobacillus paracollinoides AB 74 (96.9 %), L. similis JCM 2765T (96.9 %), L. collinoides JCM 1123T (96.7 %) and L. hilgardii DSM 20176T (95.5 %). Subsequently, pheS sequence analysis confirmed that strain DCY51T formed a distinct lineage within the Lactobacillus plantarum group. The major polar lipid of strain DCY51T was phosphatidylethanolamine and minor amounts of phosphatidylglycerol and diphosphatidylglycerol were found. Phenotypic characteristics and DNA–DNA relatedness indicated that strain DCY51T was clearly distinguished from other type strains of species of the genus Lactobacillus. A novel species, Lactobacillus kimchicus sp. nov., is proposed, with type strain DCY51T ( = KCTC 12976T  = JCM 15530T).
Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium
Authors: Inoue Kentaro , Itoh Takashi , Ohkuma Moriya , Kogure Kazuhiro
Published: May 2010

A novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0–8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11T in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11T ( = JCM 16495T  = KCTC 4074T).
Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method
Authors: Nagai Aya , Khan Shams Tabrez , Tamura Tomohiko , Takagi Motoki , Shin-ya Kazuo
Published: May 2010

A Gram-positive actinobacterium, designated M24DS4T, was isolated from a soil sample collected from Aomi, Tokyo, Japan, using the membrane-filter method. Strain M24DS4T exhibited low 16S rRNA gene sequence similarity (96.1 %) with Streptomyces scabrisporus NBRC 100760T. Cell hydrolysates contained the ll-isomer of diaminopimelic acid and the predominant quinones were MK-9(H8) and MK-9(H6). The genomic DNA G+C content was 75 mol%. Comparison of the characteristics of strain M24DS4T and related members of the genus Streptomyces with validly published names showed that the strain represents a novel species of the genus, for which the name Streptomyces aomiensis sp. nov. is proposed. The type strain is M24DS4T ( = NBRC 106164T  = KACC 14925T).
Corynebacterium humireducens sp. nov., an alkaliphilic, humic acid-reducing bacterium isolated from a microbial fuel cell
Authors: Wu Chun-Yuan , Zhuang Li , Zhou Shun-Gui , Li Fang-Bai , He Jian
Published: May 2010

A novel halotolerant, alkaliphilic, humic acid-reducing bacterium, designated MFC-5T, was isolated from a microbial fuel cell that was fed continuously with artificial wastewater (pH 10.0). Cells were Gram-positive-staining, facultatively anaerobic, non-fermentative, non-motile rods and had a G+C content of 59.0 mol%. Microbial growth was observed with <13 % (w/v) NaCl (optimum 10 %), at pH 7.0–11.0 (optimum pH 9.0) and at 25–45 °C (optimum 37 °C). Strain MFC-5T was active in the anaerobic reduction of a humic acid analogue, anthraquinone-2,6-disulphonate, with lactate, formate, acetate, ethanol or sucrose as the electron donor. The major cellular fatty acids were C18 : 1ω9c (42.68 %), C16 : 0 (33.69 %), C18 : 0 (7.56 %), C17 : 1ω8c (5.14 %) and C17 : 0 (3.39 %). Phylogenetic analysis demonstrated that strain MFC-5T displayed >3 % 16S rRNA gene sequence divergence from its closest relatives. Based on phenotypic, genetic and phylogenetic analysis, a novel species, Corynebacterium humireducens sp. nov., is proposed. The type strain is MFC-5T ( = NBRC 106098T  = CGMCC 2452T  = DSM 45392T).
Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort
Authors: Schauer S. , Kämpfer P. , Wellner S. , Spröer C. , Kutschera U.
Published: May 2010

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1T, was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27T, Methylobacterium fujisawaense DSM 5686T, Methylobacterium radiotolerans JCM 2831T and Methylobacterium jeotgali S2R03-9T, with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA–DNA relatedness between strain JT1T and these and the type strains of other closely related species were lower than 70 %. Cells of JT1T stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm−2). Major fatty acids were C18 : 1ω7c and C16 : 0. Based on the morphological, physiological and biochemical data presented, strain JT1T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1T ( = DSM 21328T  = CCUG 56108T).