bluuebunny/crossref_metadata_2025 huggingface dataset:
Origin and evolution of the genetic code: The universal enigma
Authors: Koonin Eugene V. , Novozhilov Artem S.
Published: January 2009

The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly nonrandom. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physicochemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code's evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, that is, the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system. © 2008 IUBMB IUBMB Life, 61(2): 99–111, 2009
Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field
Authors: Kim Seonah , Orendt Anita M. , Ferraro Marta B. , Facelli Julio C.
Published: January 2009

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
The effects of land‐use change on plant–soil–erosion relations, Nyereg Hill, Hungary
Authors: Centeri Csaba , Herczeg Edina , Vona Márton , Balázs Katalin , Penksza Károly
Published: January 2009

Vegetation of the Tihany Peninsula in Hungary has undergone serious changes caused by heavy trampling and overgrazing during the last century. In Tihany, the vegetation started to change towards anthropogenic associations. After grazing ceased, vegetation started to rearrange. There were no significant changes in species composition on trampled areas (on the ridge of the hill) between the examinations in 1994 and 2002. As a result of ceased grazing, the proportion of natural species was high in the grasslands of the S Nyereg Hill in 1994, while during the 2002 investigations, forest and scrub expanded at a rate that did not leave space for grassland on shallow soils and slope steppe (closing dry grasslands on hilly areas). The coverage of Elymus repens decreased, while Festuca species increased. The possible effects of plant‐cover change on soil loss were examined with the USLE (Universal Soil Loss Equation) model on the sloping areas. Eliminating harmful effects can decrease soil degradation, but the original state of soils can be restored only after a long period (hundreds of years). Further degradation of soils assists the expansion of drought‐resistant species and weeds in the associations. In 2007, soil‐thickness measurements and on‐site examinations were carried out to check the results of the former surveys and modeling.
Morphology Controlled Growth of Chitosan‐Bound Microtubes and a Study of their Biocompatibility and Antibacterial Activity
Authors: Henricus Marsiyana M. , Fath Karl R. , Menzenski Monica Z. , Banerjee Ipsita A.
Published: January 2009

Self‐assembled peptide microtubes are fabricated with the biopolymer chitosan. The microtubes are covalently attached to chitosan and the morphology of the chitosan assembled on the surface of the microtubes can be tuned by altering the pH of the growth solution. Cytotoxicity studies in the presence of mouse embryonic fibroblasts indicate that the chitosan‐bound microtubes are highly biocompatible and the cells are able to survive and proliferate at a similar rate to the control. Antibacterial studies in the presence of E. coli prove that the chitosan‐bound microtubes are bactericidal. This simple method for the development of biocompatible microstructures will facilitate cell targeting, fabrication of efficient carrier devices, and the preparation of highly efficient antibacterial materials.

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Fabrication of Large‐Area, Transferable Colloidal Monolayers Utilizing Self‐Assembly at the Air/Water Interface
Authors: Retsch Markus , Zhou Zuocheng , Rivera Sergio , Kappl Michael , Zhao Xiu Song , Jonas Ulrich , Li Qin
Published: January 2009

A versatile and simple method is presented for the rapid fabrication of close‐packed colloidal 2D crystals with large domain sizes by floating and redeposition of colloidal monolayers at the air/water interface. A detailed analysis of the particle surface transformation and packing during the individual steps of the monolayer fabrication process has been conducted. It was found that the quality of the monolayer depends on parameters like colloidal particle distribution on the initial substrate, subphase pH, and addition of surfactants. The floating monolayers could be transferred and stacked onto many substrate types, regardless of surface polarity, roughness, or curvature.

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Myoclonus‐dystonia: An update
Authors: Kinugawa Kiyoka , Vidailhet Marie , Clot Fabienne , Apartis Emmanuelle , Grabli David , Roze Emmanuel
Published: January 2009

Our knowledge of the clinical, neurophysiological, and genetic aspects of myoclonus‐dystonia (M‐D) has improved markedly in the recent years. Basic research has provided new insights into the complex dysfunctions involved in the pathogenesis of M‐D. On the basis of a comprehensive literature search, this review summarizes current knowledge on M‐D, with a focus on recent findings. We also propose modified diagnostic criteria and recommendationsfor clinical management. © 2008 Movement Disorder Society
“Jerky” dystonia in children: Spectrum of phenotypes and genetic testing
Authors: Asmus Friedrich , Langseth Annette , Doherty Elaine , Nestor Therese , Munz Marita , Gasser Thomas , Lynch Tim , King Mary D.
Published: January 2009

Hyperkinetic dystonia is characterized by phasic, tremulous, and “jerky” movements in addition to twisting postures. We studied longitudinally 23 index patients with hyperkinetic dystonia from a quaternary pediatric movement disorder clinic in Ireland. Four clinical categories emerged: (1) Eight patients were diagnosed with myoclonus‐dystonia, of whom seven carried heterozygous epsilon sarcoglycan (SGCE) mutations, including a novel deletion of exon 10. Gait disorder, unsteadiness, or frequent falls before 18 months were detected in all SGCE mutation carriers, whereas the typical neck‐predominant presentation developed only years later. (2) One patient classified as benign hereditary chorea, because jerks were choreiform and continuous rather than action‐induced, carried a heterozygous stop mutation of the TITF‐1 gene (Y114X, exon 2). (3) Three mutation‐negative patients were grouped as “myoclonic dystonia” with jerks only in the body regions affected by dystonia. (4) Eleven patients presented with a novel combination of dystonia and low amplitude poly‐mini myoclonus of the upper limbs and pectoral muscles (D‐PMM). In early childhood up to 3 years of age, an initial presentation with predominant gait impairment with only subtle jerks should prompt consideration of SGCE mutation analysis in addition to testing for DYT1 mutations. A causative gene for D‐PMM remains to be identified. © 2008 Movement Disorder Society
Neuroprotection trials in Parkinson's disease: Systematic review
Authors: Hart Robert G. , Pearce Lesly A. , Ravina Bernard M. , Yaltho Toby C. , Marler John R.
Published: January 2009

Treatments to slow the progression are a major unmet need in Parkinson's disease. Detailed assessment of randomized trials testing putative neuroprotective drugs was undertaken to inform the design, reporting, and interpretation of future studies. This study is a systematic review of trials testing neuroprotective drugs. Data were extracted independently by two coauthors. Fifteen completed, published trials involving 4,087 participants tested 13 different drugs in 18 double‐blind comparisons with placebo. Seven comparisons involving 2,000 subjects assessed MAO‐B inhibitors. The primary outcome was change in the Unified Parkinson's Disease Rating Scale score in eight trials and time to need for dopaminergic therapy in seven. Mean participant age was 62 years, 35% were women, the interval from diagnosis to entry averaged 11 months, and the number of participants averaged 272 (largest = 806). Follow‐up averaged <16 months in all but two trials. Detailed randomization methods and success of double‐blinding were reported in 20% and 13%, respectively. Based on the investigators' conclusions, six trials were interpreted as consistent with a neuroprotective effect, three as negative, and five as either confounded or not meeting criteria for futility. Neuroprotection trials have involved relatively uniform groups of participants early in the clinical disease course, with outcomes weighted heavily toward motor deterioration. Future trials should include participants with wider ranges of disease stages and assess broader neurological outcomes. © 2008 Movement Disorder Society
Diffusion‐weighted imaging in multiple system atrophy: A comparison between clinical subtypes
Authors: Pellecchia Maria Teresa , Barone Paolo , Mollica Carmine , Salvatore Elena , Ianniciello Marta , Longo Katia , Varrone Andrea , Vicidomini Caterina , Picillo Marina , De Michele Giuseppe , Filla Alessandro , Salvatore Marco , Pappatà Sabina
Published: January 2009

Multiple system atrophy can be classified into two main types, a Parkinsonian (MSA‐P) and a cerebellar (MSA‐C) variant based on clinical presentation. We obtained diffusion‐weighted magnetic resonance imaging (DWI) in 9 MSA‐P and 12 MSA‐C patients and 11 controls, and correlated DWI changes with disease duration and severity. We found that Trace (D) values in the entire and anterior putamen were significantly higher in MSA‐P than in MSA‐C patients and controls, whereas Trace (D) values in the cerebellum and middle cerebellar peduncle (MCP) were significantly higher in MSA‐C than in MSA‐P patients and controls. Increased disease duration was significantly correlated with increased Trace (D) values in pons of MSA‐P patients, and in cerebellum and MCP of MSA‐C patients. Both UMSARS and UPDRS motor scores positively correlated with entire and posterior putaminal Trace (D) values in MSA‐P patients. The diffusivity changes parallel phenotypical and pathologic differences between MSA‐P and MSA‐C patients, suggesting that DWI is a feasible tool for in vivo evaluation of neurodegeneration in MSA. Based on our findings, Trace (D) measurements in the putamen and pons in MSA‐P patients and in the cerebellum and MCP in MSA‐C patients could serve as quantitative markers for microstructural damage in the course of disease. © 2008 Movement Disorder Society
Morphology, microhardness, and electrical properties of composites based on polypropylene, montmorillonite, and polypyrrole
Authors: Pandis C. , Logakis E. , Peoglos V. , Pissis P. , Omastová M. , Mravčáková M. , Janke A. , Pionteck J. , Peneva Y. , Minkova L.
Published: January 2009

The morphology, microhardness, and electrical properties of composites consisting of conductive polypyrrole (PPy) dispersed into a nonconductive polypropylene matrix (PP) as pure component or in form of a sodium montmorillonite/PPy (MMT/PPy) composite have been studied. For comparison, also PP/MMT composites were studied. All types of composites were processed by compression molding or by melt mixing followed by compression molding into plates, which were used for characterization. Scanning electron microscopy and transmission electron microscopy was used to examine the morphology of the prepared materials. The investigation of electrical and dielectric properties was done by dielectric relaxation spectroscopy in a wide frequency range and was related to the composite composition and processing method. The analysis of the conductivity as a function of temperature indicated that the charge transfer mechanism could be described by the variable range hopping model in three dimensions. The microhardness of PP/MMT/PPy composites with different content of MMT or PPy was determined and the creep rate has been estimated. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 407–423, 2009
Dielectric relaxation processes in epoxy resin—ZnO composites
Authors: Soulintzis A. , Kontos G. , Karahaliou P. , Psarras G. C. , Georga S. N. , Krontiras C. A.
Published: January 2009

Polymer matrix‐ZnO microcomposites were prepared in different filler concentrations. The electrical relaxation dynamics of all samples was examined by means of broadband dielectric spectroscopy (BDS) over a wide temperature range. Two relaxation modes (namely β and γ), observed in the low temperature region, are attributed to the reorientation of small polar groups of the polymer matrix. Glass‐rubber transition (α‐mode) of the polymeric matrix and interfacial polarization phenomena are considered as responsible for the recorded relaxation processes in the high temperature region. An additional relaxation mode, named intermediate dipolar effect (IDE), is recorded at temperatures higher than −30 °C in all composites. Its occurrence and dynamics are related to the presence and concentration of the filler. IDE and α‐relaxation are observed in the same frequency and temperature range, leading to a mutual superposition. The two processes were distinguished following a simulation procedure employing the simultaneous fitting of two Havrilliak‐Negami terms and a third term describing the contribution of DC conductivity to dielectric losses. The temperature dependence of relaxation times for α‐mode follows the Vogel‐Tamann‐Fulcher equation, whereas IDE relaxation times follow unusual temperature dependence. The latter is discussed under the assumption of intrinsic interfacial polarization phenomena within ZnO crystal domains. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 445–454, 2009
A randomized control trial of a supervised versus a self‐directed exercise program for allogeneic stem cell transplant patients
Authors: Shelton Margarette L. , Lee Jeannette Q. , Morris G. Stephen , Massey Pamela R. , Kendall Deborah G. , Munsell Mark F. , Anderson Karen O. , Simmonds Maureen J. , Giralt Sergio A.
Published: January 2009

Objectives: To determine if therapist supervision of an exercise program produced better functional outcomes in allogeneic stem cell transplant patients than a patient‐directed exercise program.

Methods: Sixty‐one patients who were less than 6 months post allogeneic stem cell transplant were randomly assigned to either a therapist supervised training group (supervised) or a patient‐directed training group (Self‐directed). Training consisted of aerobic exercises (treadmill, bicycle ergometer versus walking) and resistance exercises (free weights, weight machines versus resistive band activities). Subjects completed physical performance tests (50‐foot fast walk, 6‐min walk, forward reach, repeated sit‐to‐stand, uniped stance) and the Brief Fatigue Inventory (BFI) before and after 4 weeks of training. Pre‐ and post‐training outcomes and group differences were analyzed by a Student t‐test.

Results: Patients in both groups were similarly deconditioned at baseline. Training increased the 6‐min walk distance and 50‐foot walk in the supervised group by 12 and 14%, respectively, and increased the 6‐min walk distance by 10% in the Self‐directed group (p<0.05). BFI score for worst level of fatigue declined in both groups but not significantly.

Conclusions: These results demonstrate that allogeneic transplant patients derive functional benefits from short‐term exercise training regardless of how the training program is supervised. Determining (1) the reasons for the low participation rate (28%), (2) the patient‐preferred characteristics of each exercise supervision style and (3) how best to match patient preference to exercise supervision style remain significant issues in this area of patient delivery services. Copyright © 2008 John Wiley & Sons, Ltd.
The report of coping strategies and psychosocial adjustment in Korean mothers of children with cancer
Authors: Han Hae‐Ra , Cho Eun Joo , Kim Daehee , Kim Jiyun
Published: January 2009

Objective: Parents of children with cancer must cope with multiple challenges over time. As most research on parental coping has been conducted in Western countries, little information is available on the parental experience of coping in non‐Western countries. Using a new cultural sample of Korean mothers, this study describes their coping strategies. In addition, the association of particular coping patterns with mothers' report of psychosocial adjustment is investigated.

Methods: A total of 200 Korean mothers of children with cancer participated in the study. Coping strategies were measured by the Coping Health Inventory for Parents in the following three categories: Maintaining Family Integration and an Optimistic Outlook for the Situation, Seeking Social Support, and Seeking Information. Maternal psychosocial adjustment was measured by psychological distress, family relationship, and social relationship subscales from the Psychosocial Adjustment to Illness Scale.

Results: Korean mothers reported coping strategies related to Maintaining Family Integration and an Optimistic Outlook for the Situation as being most helpful. More frequent use of coping pattern, Maintaining Family Integration and an Optimistic Outlook for the Situation, and less frequent use of coping pattern, Information‐Seeking were significantly associated with lower psychological distress and better family relationship after children's medical and maternal characteristics were controlled for. Coping pattern, Seeking Social Support was only predictive of social relationships.

Conclusions: This study suggests that culture may play a significant role in the report of coping among Korean mothers. Future studies should consider culturally preferred coping methods and available resources as they relate to different adjustment outcomes. Copyright © 2008 John Wiley & Sons, Ltd.
Effect of dimethylhydrazine on p‐type conductivity of as‐grown Mg‐doped GaN
Authors: Kim Dong Hyuk , Lee Go Eun , Yoon Euijoon , Park Do‐Young , Cheong Hyeonsik , Choi Woo Seok , Noh Tae Won , Cho Jin‐Hyoung , Park Joong‐Seo
Published: January 2009

Mg dopants in GaN need post‐growth thermal activation to be activated. However, it was observed that GaN grown with dimethylhydrazine (DMHy) resulted in p‐type conductivity without activation. The reduction of NH3 flow by adding DMHy resulted in a very low hydrogen concentration of 2.8 × 1017 cm–3 in Mg‐doped GaN, which was even lower than the hole concentration. The low‐temperature infrared transmittance spectra also showed that many hydrogen atoms were captured by incorporated carbon impurities. The combined effect of low concentration of hydrogen and the preferred trapping of hydrogen at carbon impurities is attributed to the p‐type conductivity of as‐grown Mg‐doped GaN when a mixture of DMHy and NH3 was used for group V sources. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Boundary maintenance in living systems theory and social entropy theory
Authors: Bailey Kenneth D.
Published: January 2009

Past analyses of social systems have too often relied upon obsolete dualities such as open system/closed system. The purpose of this paper is to provide a more comprehensive analysis of the full range of boundary‐maintenance operations that are at work in the modern complex social system. I first analyse the role of the boundary in Living Systems Theory (LST), and then turn to the analysis and comparison of boundary maintenance in Social Entropy Theory (SET). Among the topics discussed are boundary control for matter‐energy (M‐E) flows, boundary control for information flows, types of information inflows across social‐system boundaries, types of information outflows across social‐systems boundaries and types of M‐E inflows and outflows across social systems boundaries. Among the types of information inflows discussed are neutral, fatal, catalytic and cancelling. Among the types of information outflows discussed are obligatory, routine and formatted. Finally, some of the M‐E inflows and outflows discussed are obligatory, optional and routine. Copyright © 2009 John Wiley & Sons, Ltd.
Influence of Commercial Dietary Oils on Lipid Composition and Testosterone Production in Interstitial Cells Isolated from Rat Testis
Authors: de Catalfo Graciela E. Hurtado , de Alaniz María J. T. , Marra Carlos Alberto
Published: January 2009

The aim of this study was to examine the influence of dietary fat on lipid composition, as well as on the steroidogenic function of interstitial cells isolated from Wistar rats that had been fed semi‐synthetic diets containing four different commercial oils (S soybean, O olive, C coconut, and G grape seed). Steroidogenic enzyme activities, lipid composition, and androgen production were measured in testicular interstitial cells. Lipid analysis included measurement of the contents of major lipid subclasses (neutral lipids, polar lipids, free and esterified cholesterol), as well as principal polar and neutral lipid fatty acyl compositions. Significant differences in lipid composition were observed among the groups, most of them reflecting the specific fatty acyl composition of the diet tested. Testosterone concentration was higher in O and C groups compared with S or G. In agreement with this observation, the activity of both key enzymes involved in testosterone biosynthesis (3‐β‐HSD and 17‐β‐HSD) was higher in O and C groups with significant differences between them (O > C). A significant negative correlation was found between cellular testosterone production and cellular cholesterol ester content. Additionally, testosterone concentration directly correlated with cholesterol levels. We conclude that dietary oils qualitatively and quantitatively modified the lipid composition of interstitial cells, producing either a direct or indirect regulatory effect on testicular steroidogenic function.
Goal frustration, coping and well‐being in the context of adolescent headache: A self‐regulation approach
Authors: Massey Emma K. , Garnefski Nadia , Gebhardt Winifred A.
Published: January 2009

The aim of this study was to investigate the relationships between goal frustration, coping and well‐being in the context of adolescent headache. Firstly, we investigated whether adolescents with weekly, monthly or no headache complaints differed with regard to the importance assigned to their personal goals, experience of goal frustration, coping with goal frustration and well‐being. Secondly, the extent to which goal and coping factors contributed to well‐being and whether this relationship differed according to the frequency of headache complaints was examined. For this purpose, 1202 adolescents aged 12–18 completed self‐report questionnaires in schools. Adolescents were divided into three groups based on their experience of headache: no headache reported (38%); monthly headache (40%); weekly headache (18%). Results show that these groups did not differ with respect to the importance they attach to goals. They did, however, differ according to experience of goal frustration, use of strategies to cope with goal frustration and well‐being, although effect sizes were small. After controlling for individual and headache characteristics, frustration of self acceptance and health goals, and the use of self blame, rumination and other blame were consistently related to lower well‐being. Moreover, interactions with headache group indicated that for adolescents with weekly headache, greater frustration of school and self acceptance goals and a lower importance assigned to health goals was more detrimental to well‐being than for those with no headache complaints. We conclude that frustration to goal pursuit and strategies for coping with this frustration are important factors in adolescent well‐being and may offer important targets for intervention.
Categories of congruence between inpatient self‐reported pain and nurses evaluation
Authors: Melotti Rita Maria , Dekel Boaz Gedaliahu Samolsky , Carosi Francesca , Ricchi Ennio , Chiari Paolo , D'Andrea Rocco , Di Nino GianFranco
Published: January 2009

Objective: To enhance the awareness that biased pain estimation may undermine its treatment, we sought to determine the congruence categories (CCs) between inpatient self‐reported pain (PSRP) and nurse pain‐evaluation (NEP) and to look for associations between CCs and inpatient and situational moderators.

Design: A point cross‐sectional survey.

Subjects: The inpatient population [(n=869), ≥6years old and hospitalised for at least 24h] and n=115 nurses of the University of Bologna's teaching hospital, Italy.

Measures: Using numerical rating scale, inpatients self‐reported their pain while nurses indirectly rated these patients’ pain using information acquired during their professional activity prior to the study and by reviewing patients’ medical charts.

Outcome measures: Congruence moderator data were: gender, age, marital status, clinical area and length of hospital stay. The study was set to assess: PSRP–NEP mean of absolute difference (MAD), agreement and correlation; and to analyse the CCs dependence upon the PSRP and the congruence moderator variables.

Results: PSRP–NEP agreement and correlation were mild and moderate, respectively, while their MAD=2.0 (95% CI 1.8–2.2). Congruence was found in 50% of the cases. Under‐estimation (21%) was directly proportional to the PSRP severity, while congruence and over‐estimation (29%) were inversely proportional to it. The ‘PSRP effect’ on the CCs detected was further modulated by the moderators studied.

Conclusions: PSRP–NEP congruence was limited while CCs were associated with PSRP, inpatient and situational moderators. Further prospective studies are needed to verify generalization and whether the studied moderators operate through patient stereotyping mechanisms. Awareness of the influence of such mechanisms on pain evaluation may ameliorate pain assessment.
ApoC‐III gene expression is sharply increased during adipogenesis and is augmented by retinoid X receptor (RXR) agonists
Authors: Takahashi Yu , Inoue Jun , Kagechika Hiroyuki , Sato Ryuichiro
Published: January 2009

ApoC‐III, a lipoprotein lipase inhibitor and a key regulator of the metabolism of triglyceride‐rich lipoproteins, is mainly synthesized in liver and intestine, but little is known about its expression in adipocytes. We here show that apoC‐III mRNA levels are dramatically induced during adipocyte differentiation. Among many transcriptional factors involved in adipocyte differentiation, RXRα, acting alone and not as a heterodimer partner of other nuclear receptors, solely regulates apoC‐III gene expression. These results suggest that apoC‐III may play a specific role in lipid storage and mobilization in adipocytes, non‐lipoprotein‐secreting cells, and indicate the functional role of RXRα during adipocyte differentiation.
Gibberellin biosynthesis in bacteria: Separate ent‐copalyl diphosphate and ent‐kaurene synthases in Bradyrhizobium japonicum
Authors: Morrone Dana , Chambers Jacob , Lowry Luke , Kim Gunjune , Anterola Aldwin , Bender Kelly , Peters Reuben J.
Published: January 2009

Gibberellins are ent‐kaurene‐derived diterpenoid phytohormones produced by plants, fungi, and bacteria. The distinct gibberellin biosynthetic pathways in plants and fungi are known, but not that in bacteria. Plants typically use two diterpene synthases to form ent‐kaurene, while fungi use only a single bifunctional diterpene synthase. We demonstrate here that Bradyrhizobium japonicum encodes separate ent‐copalyl diphosphate and ent‐kaurene synthases. These are found in an operon whose enzymatic composition indicates that gibberellin biosynthesis in bacteria represents a third independently assembled pathway relative to plants and fungi. Nevertheless, sequence comparisons also suggest potential homology between diterpene synthases from bacteria, plants, and fungi.
Normograde, minimally invasive technique for oesophagostomy in cats
Authors: Formaggini Luca
Published: January 2009

A percutaneous technique to place oesophageal feeding tubes in cats is described. Nineteen traumatised cats underwent different surgical procedures for facial and/or oral trauma and subsequent oesophagostomy. The tube placement was easy to perform, requiring a 14 G over-the-needle vascular catheter, a curved forceps and a 1.2 mm feeding tube. During insertion, the tube was directed aborally (normograde direction) to its definitive position in a one-step procedure. The tube was removed when the patient started to eat voluntarily. A major limit of this technique was represented by the small diameter of the feeding tube, requiring the use of a liquid diet. However, considering the absence of complications, the rapidity of the procedure and its cost efficacy, it was considered as an effective alternative to more complicated and invasive techniques, in particular if a short period of starvation is predictable.
Diathermy power settings as a risk factor for hemorrhage after tonsillectomy
Authors: Lowe David , Cromwell David A. , Lewsey James D. , Copley Lynn P. , Brown Peter , Yung Matthew , van der Meulen Jan H.
Published: January 2009

OBJECTIVE

To investigate bipolar diathermy power settings as a risk factor for postoperative hemorrhage following tonsillectomy.

STUDY DESIGN AND SETTING

A prospective cohort study was undertaken between July 2003 and September 2004 in National Health Service (NHS) and independent hospitals in England and Northern Ireland. Data were collected on patient characteristics, tonsillectomy technique, and postoperative hemorrhage within 28 days of surgery.

RESULTS

Among the 9572 patients who had a tonsillectomy performed with bipolar diathermy dissection and hemostasis, the overall rate of hemorrhage was 4.6 percent and the risk of hemorrhage was not associated with the diathermy power setting. Among the 8465 patients who had tonsillectomy with cold steel dissection and bipolar diathermy hemostasis, the rate of hemorrhage increased from 1.8% in patients with the lowest power settings (6 to 8 watts) to 3.7% in those with settings above 18 watts (P value for trend = 0.005).

CONCLUSION

In tonsillectomies using cold steel dissection and bipolar diathermy for hemostasis, the risk of postoperative hemorrhage becomes greater as diathermy power increases.
Influence of Cochlear Implantation on Sacculus Function
Authors: Krause Eike , Wechtenbruch Juliane , Rader Tobias , Gürkov Robert
Published: January 2009

OBJECTIVES

To examine the influence of cochlear implantation (CI) on the sacculus function and to analyze a possible correlation with resulting vertigo symptoms.

METHODS

In a prospective study including 25 patients undergoing CI, preoperative and postoperative assessment of vestibular evoked myogenic potentials (VEMP), caloric horizontal semicircular canal (hSCC) response, and subjective vertigo symptoms were assessed. The patients with postoperative vertigo were compared to the patients without postoperative vertigo with regard to the findings of VEMP responses and caloric testing.

RESULTS

Nine patients reported postoperative vertigo. Before surgery, eight of 23 patients (35%) had regular VEMP responses. Two months after CI, four patients had a new loss of sacculus function on VEMP testing. The CI represents a significant risk factor for sacculus impairment. In seven of 12 patients with preoperatively preserved caloric response, this decreased after the operation. The impaired vestibular function did not correlate with vertigo symptoms. When comparing the patient group with vertigo and the group without vertigo after CI, there is a significant difference in the patients' age.

CONCLUSIONS

Although CI can cause damage to sacculus and hSCC function, this is probably not the only cause for postoperative vertigo. Advanced age is a significant risk factor for vertigo after CI.
Practical guide to efficient analysis and diagramming articles
Authors: Gail Neely J. , Karni Ron J. , Wang Eric W. , Rich Jason T. , Paniello Randal C. , Voelker Courtney C. J. , Nussenbaum Brian
Published: January 2009

OBJECTIVE

In a busy practice, time is a commodity in rare supply, and keeping abreast of the relevant medical literature is a daunting task. Even after reading an article carefully, important information may be lost because of undue attention to the methodological minutia.

METHOD

Fundamental to reducing a complex article into a well‐organized and consistent format is the technique of quantitatively diagramming the principal components in the design and findings of the study. This approach allows a coherent brief summary statement of the article, and a platform for a focused scientific discussion and analysis of the clinical applicability of the findings.

CONCLUSIONS

The technique of diagramming an article is a tool that the senior author has used for years and has found it valuable in capturing the scientific fundamentals of a manuscript. Once prepared, the diagram has proven to be useful in clarifying presentations during journal club, preparing the background and significance sections of grant applications, reviewing articles as a journal editor and as a journal reviewer, and easily retrieving documents to support evidence‐based practice efforts.
Mutational, inhibitory and microcalorimetric analyses of Plasmodium falciparum TMP kinase. Implications for drug discovery
Authors: KANDEEL M. , ANDO T. , KITAMURA Y. , ABDEL-AZIZ M. , KITADE Y.
Published: January 2009

Plasmodium falciparum thymidylate kinase (PfTMK) can tolerate a range of substrates, which distinguishes it from other thymidylate kinases. The enzyme not only phosphorylates TMP and dUMP but can also tolerate bulkier purines, namely, dGMP, GMP, and dIMP. In order to probe the flexibility of PfTMK in accommodating ligands of various sizes, we developed 6 mutant enzymes and subjected these to thermodynamic, inhibitory and catalytic evaluation. Kinase activity was markedly affected by introducing a larger lysine residue instead of A111. The lack of the hydroxyl group after inducing mutation of Y107F affected enzyme activity, and had a more severe impact on dGMP kinase activity. PfTMK can be inhibited by both purine and pyrimidine nucleosides, raising the possibility of developing highly selective drugs. Thermodynamic analysis revealed that enthalpic forces govern both purine and pyrimidine nucleoside monophosphate binding, and the binding affinity of both substrates was highly comparable. The heat produced due to dGMP binding is lower than that attributable to TMP. This indicates that additional interactions occur with TMP, which may be lost with larger dGMP. Targeting PfTMK not only affects thymidine nucleotide synthesis but may also affect purine nucleotides, and thus the enzyme represents an attractive antimicrobial target.
Estimating specific yield and storage change in an unconfined aquifer using temporal gravity surveys
Authors: Gehman Carter L. , Harry Dennis L. , Sanford William E. , Stednick John D. , Beckman Nathaniel A.
Published: January 2009

Two high‐precision gravity surveys were conducted to determine groundwater mass changes at a managed groundwater recharge site in northeastern Colorado. Gravity data were collected during pumping and two months after pumping ceased. During pumping, gravity was lower by as much as 46 μGal near the pumping wells and higher by as much as 90 μGal near the recharge ponds in comparison to data collected after pumping had ceased. These differences are attributed to changes in groundwater mass associated with drawdown and infiltration. Inverse modeling of the gravity data indicates a 5.1 × 105 m3 decrease in storage beneath the recharge ponds between the two surveys, which we attribute to dissipation of the groundwater mound created by recharge during pumping. This estimate of the change in groundwater storage is made independently of assumptions of physical properties of the aquifer. Dividing the change in water volume per unit area determined from the gravity modeling by the change in water level measured in wells provides an estimate of specific yield (Sy) of 0.21 ± 0.03, which is within the range of specific yield estimates derived from aquifer tests at the site. Water level changes predicted from the gravity data agree on average to within ±0.45 m of those measured, which we take to be an estimate of the uncertainty in water table depth predictions that can be obtained from gravimetric data in unconfined aquifers. The study covers a 3.2 km2 area, providing a prototype for similar studies at larger scales.
Impact of initialization strategies and observations on seasonal forecast skill
Authors: Balmaseda M. , Anderson D.
Published: January 2009

Seasonal forecasting is a rapidly developing field with considerable effort devoted to developing comprehensive coupled general circulation models. Initialising these models is also important, as the forecast skill depends strongly on the way the coupled model is initialised. Three commonly used strategies are evaluated using the ECMWF System3, a state of the art coupled model. The most skillful scheme is that which makes most use of atmospheric and oceanic data even though this may generate initial imbalances in the coupled state. At seasonal time scales, increasing the balance at the cost of being further from the observations can degrade the forecasts. The relative importance of different components of the ocean observing system, equatorial moorings, altimetery and Argo floats, on forecast skill is assessed.
Relative occurrence rates and connection of discrete frequency oscillations in the solar wind density and dayside magnetosphere
Authors: Viall N. M. , Kepko L. , Spence H. E.
Published: January 2009

We present an analysis of the occurrence distributions of statistically significant apparent frequencies of periodic solar wind number density structures and dayside magnetospheric oscillations in the f = 0.5–5.0 mHz range. Using 11 years (1995–2005) of solar wind data, we identified all spectral peaks that passed both an amplitude test and a harmonic F test at the 95% confidence level in 6‐hour data segments. We find that certain discrete frequencies, specifically f = 0.7, 1.4, 2.0, and 4.8 mHz, occur more often than do other frequencies over those 11 years. We repeat the analysis on discrete oscillations observed in 10 years (1996–2005) of dayside magnetospheric data. We find that certain frequencies, specifically f = 1.0, 1.5, 1.9, 2.8, 3.3, and 4.4 mHz, occur more often than do other frequencies over those 10 years. Many of the enhancements found in the magnetospheric occurrence distributions are similar to those found in the solar wind. Lastly, we counted the number of times the same discrete frequencies were identified as statistically significant using our two spectral tests on corresponding solar wind and magnetospheric 6‐hour time series. We find that in 54% of the solar wind data segments in which we identified a spectral peak, at least one of the same discrete frequencies was statistically significant in the corresponding magnetospheric data segment. Our results argue for the existence of inherent apparent frequencies in the solar wind number density that directly drive global magnetospheric oscillations at the same discrete frequencies, although the magnetosphere also oscillates through other physical mechanisms.
Solar zenith and viewing geometry‐dependent errors in satellite retrieved cloud optical thickness: Marine stratocumulus case
Authors: Kato Seiji , Marshak Alexander
Published: January 2009

The error in the domain‐averaged cloud optical thickness retrieved from satellite‐based imagers is investigated using a cloud field generated by a cloud model and a 3D radiative transfer model. The objective of this study is to identify the optimal geometry for the optical thickness retrieval and quantify the error. The cloud field used in the simulation is a relatively uniform (retrieved shape parameter of a gamma distribution averaged over all simulated viewing and solar zenith angles is 18) and nearly isotropic stratocumulus field. The retrieved cloud cover with a 1‐km pixel resolution is 100%. The domain‐averaged optical thickness error is separated into two terms, the error caused by an assumption of a horizontally uniform cloud over a 1‐km pixel (internal variability) and error caused by neglecting the horizontal flux through the boundary of subpixels (external variability). For the cloud field used in this study, the external variability term increases with solar zenith angle and the sign changes from negative to positive while the internal variability term is generally negative and becomes more negative as the solar zenith angle increases. At a small solar zenith angle, therefore, both terms are negative, but the error partially cancels at a large solar zenith angle. When the solar zenith angle is less than 30°, both terms are small; the error in the viewing zenith angle and domain‐averaged cloud optical thickness derived from the relative azimuth angle smaller than 150 is less than 10%. However, if the optical thickness is derived from nadir view only for overhead sun, the domain‐averaged optical thickness is underestimated by more than 10%. When the solar zenith angle increases to 60°, the internal variability term exceeds 10%, especially viewed from the forward direction, but the domain and viewing zenith angle averaged optical thickness error can be less than 10% in the backward direction. When the solar zenith angle is 70°, both terms are greater than 10%. The shape parameter of a gamma distribution derived from retrieved optical thicknesses increases with the viewing zenith angle but decreases with solar zenith angle. On the basis of this simulation and Terra Moderate Resolution Imaging Spectroradiometer (MODIS) viewing geometry and solar zenith angle at the sampling time over the northeastern Pacific, the error in the domain‐averaged retrieved optical thickness of uniform stratocumulus over northeastern Pacific is less than 10% in March and September.
Angiotensin II Modulates BBB Permeability via Activation of the AT1Receptor in Brain Endothelial Cells
Authors: Fleegal-DeMotta Melissa A , Doghu Shinya , Banks William A
Published: January 2009

Hypertensive encephalopathy occurs when acute changes in blood pressure cause breakdown of the blood—brain barrier (BBB). Angiotensin II (Ang II) plays a role in this pathophysiology. We determined whether Ang II directly regulates endothelial cell function at the BBB. In BBB microvessel endothelial cells (MECs), the Ang II (100 nmol/L; 0 to 6 h) effects on permeability to125I-albumin and transendothelial electrical resistance (TEER) were assessed. Angiotensin II (100 nmol/L) caused significant time-dependent changes in both125I-albumin permeability (25%) at 2 h and TEER (−8.87 Ω·cm2) at 6 h. Next, MECs were pretreated with the Ang II type 1 (AT1) receptor blocker telmisartan (1 μmol/L) or the Ang II type 2 (AT2) receptor blocker PD123,319 (1 μmol/L) followed by treatment with Ang II (100 nm). Telmisartan completely inhibited the Ang II-induced increase in125I-albumin permeability in MECs whereas PD123,319 had no effect. Using western blot analysis, we showed that MECs express AT1receptors but not AT2receptors. Treatment with Ang II (100 nmol/L; 0 to 6 h) also increased total protein kinase C activity. In contrast, Ang II had no effect on the expression of occludin, claudin 5, or actin. These results show that Ang II directly modulates transcytotic and paracellular permeability in BBB endothelial cells and could contribute to the pathophysiology of hypertensive encephalopathy.
Expression profile of genes involved in hydrogen sulphide liberation by Saccharomyces cerevisiae grown under different nitrogen concentrations
Authors: Mendes-Ferreira Ana , Barbosa Catarina , del Olmo Marcel.lí , Mendes-Faia Arlete , Leão Cecília
Published: January 2009

The present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in S. cerevisiae associated to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were downregulated when yeast stopped growing which could associate MET gene expression levels with cell growth. The over expression of MET genes after nitrogen addition was confirmed by a new release of H2S during the new set of fermentation experiments. In addition, to confirm gene expression profiles observed from macroarray results, real time RT-PCR was performed on 6 genes using additional sets of biological replicates. These genes were selected based on the assumption that differences in sulphide production observed among strains are due to genetic variations of the expression of genes involved in the Sulphate Reduction Pathway. An integration of expression data of genes involved in sulphur assimilation and sulphur amino acid biosynthesis with hydrogen sulphide production is presented.