bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA
Authors: Papenfort Kai , Bouvier Marie , Mika Franziska , Sharma Cynthia M. , Vogel Jörg
Published: November 2010

The abundant class of bacterial Hfq-associated small regulatory RNAs (sRNAs) parallels animal microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast to the universal length and seed pairing mechanism of microRNAs, the sRNAs are heterogeneous in size and structure, and how they regulate multiple targets is not well understood. This paper provides evidence that a 5′ located sRNA domain is a critical element for the control of a large posttranscriptional regulon. We show that the conserved 5′ end of RybB sRNA recognizes multiple mRNAs of
Salmonella
outer membrane proteins by ≥7-bp Watson–Crick pairing. When fused to an unrelated sRNA, the 5′ domain is sufficient to guide target mRNA degradation and maintain σ
E
-dependent envelope homeostasis. RybB sites in mRNAs are often conserved and flanked by 3′ adenosine. They are found in a wide sequence window ranging from the upstream untranslated region to the deep coding sequence, indicating that some targets might be repressed at the level of translation, whereas others are repressed primarily by mRNA destabilization. Autonomous 5′ domains seem more common in sRNAs than appreciated and might improve the design of synthetic RNA regulators.
Stimulated Raman photoacoustic imaging
Authors: Yakovlev Vladislav V. , Zhang Hao F. , Noojin Gary D. , Denton Michael L. , Thomas Robert J. , Scully Marlan O.
Published: November 2010

Achieving label-free, molecular-specific imaging with high spatial resolution in deep tissue is often considered the grand challenge of optical imaging. To accomplish this goal, significant optical scattering in tissues has to be overcome while achieving molecular specificity without resorting to extrinsic labeling. We demonstrate the feasibility of developing such an optical imaging modality by combining the molecularly specific stimulated Raman excitation with the photoacoustic detection. By employing two ultrashort excitation laser pulses, separated in frequency by the vibrational frequency of a targeted molecule, only the specific vibrational level of the target molecules in the illuminated tissue volume is excited. This targeted optical absorption generates ultrasonic waves (referred to as stimulated Raman photoacoustic waves) which are detected using a traditional ultrasonic transducer to form an image following the design of the established photoacoustic microscopy.
Robust crop resistance to broadleaf and grass herbicides provided by aryloxyalkanoate dioxygenase transgenes
Authors: Wright Terry R. , Shan Guomin , Walsh Terence A. , Lira Justin M. , Cui Cory , Song Ping , Zhuang Meibao , Arnold Nicole L. , Lin Gaofeng , Yau Kerrm , Russell Sean M. , Cicchillo Robert M. , Peterson Mark A. , Simpson David M. , Zhou Ning , Ponsamuel Jayakumar , Zhang Zhanyuan
Published: November 2010

Engineered glyphosate resistance is the most widely adopted genetically modified trait in agriculture, gaining widespread acceptance by providing a simple robust weed control system. However, extensive and sustained use of glyphosate as a sole weed control mechanism has led to field selection for glyphosate-resistant weeds and has induced significant population shifts to weeds with inherent tolerance to glyphosate. Additional weed control mechanisms that can complement glyphosate-resistant crops are, therefore, urgently needed. 2,4-dichlorophenoxyacetic acid (2,4-D) is an effective low-cost, broad-spectrum herbicide that controls many of the weeds developing resistance to glyphosate. We investigated the substrate preferences of bacterial aryloxyalkanoate dioxygenase enzymes (AADs) that can effectively degrade 2,4-D and have found that some members of this class can act on other widely used herbicides in addition to their activity on 2,4-D. AAD-1 cleaves the aryloxyphenoxypropionate family of grass-active herbicides, and AAD-12 acts on pyridyloxyacetate auxin herbicides such as triclopyr and fluroxypyr. Maize plants transformed with an AAD-1 gene showed robust crop resistance to aryloxyphenoxypropionate herbicides over four generations and were also not injured by 2,4-D applications at any growth stage. Arabidopsis plants expressing AAD-12 were resistant to 2,4-D as well as triclopyr and fluroxypyr, and transgenic soybean plants expressing AAD-12 maintained field resistance to 2,4-D over five generations. These results show that single AAD transgenes can provide simultaneous resistance to a broad repertoire of agronomically important classes of herbicides, including 2,4-D, with utility in both monocot and dicot crops. These transgenes can help preserve the productivity and environmental benefits of herbicide-resistant crops.
Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries
Authors: Chica Roberto A. , Moore Matthew M. , Allen Benjamin D. , Mayo Stephen L.
Published: November 2010

The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an
in silico
prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a π-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20–26 nm. Moreover, our approach required the experimental screening of a total of ∼5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts.
Political grammar
Authors: Adiel Yair
Published: November 2010

The Academy of the Hebrew Language is considered the supreme institute for the Hebrew language in Israel, a status which is also expressed legally in Israeli law since 1953. Its members are known and distinguished linguists, poets, writers and translators. In the years 1994–1995 the Academy plenum devoted three meetings to discuss the question of how to pronounce, spell and use the name “Palestine” in Hebrew. The protocols of those discussions are the corpus studied in this article. A close examination of the discussions reveals significant, subtle, and sometimes paradoxical relationships between the political and the linguistic. In addition, the article traces the way in which the inevitable question regarding the possibility of distinguishing between these two facets permeated the debates. The article points out correlations between answers to this question, local political positions, and linguistic theories. It suggests that in addition to critical discourse analysis methodologies, in order to address this question an integration of some notions from the Derridian linguistic critique is indispensable, and by using them renegotiates the nature of the zone between the linguistic and the political. It is within the same blurred, ungraspable zone between the political and the linguistic, the zone from which the very wish to give a name arises and motivates the discussions, that this wish is also, at its peak, exhausted, interrupted, bringing the discussions to their indecisive conclusion.
Gain of MYC underlies recurrent trisomy of the MYC chromosome in acute promyelocytic leukemia
Authors: Jones Letetia , Wei Guangwei , Sevcikova Sabina , Phan Vernon , Jain Sachi , Shieh Angell , Wong Jasmine C. Y. , Li Min , Dubansky Joshua , Maunakea Mei Lin , Ochoa Rachel , Zhu George , Tennant Thelma R. , Shannon Kevin M. , Lowe Scott W. , Le Beau Michelle M. , Kogan Scott C.
Published: November 2010

Gain of chromosome 8 is the most common chromosomal gain in human acute myeloid leukemia (AML). It has been hypothesized that gain of the MYC protooncogene is of central importance in trisomy 8, but the experimental data to support this are limited and controversial. In a mouse model of promyelocytic leukemia in which the MRP8 promoter drives expression of the PML-RARA fusion gene in myeloid cells, a Myc allele is gained in approximately two-thirds of cases as a result of trisomy for mouse chromosome 15. We used this model to test the idea that MYC underlies acquisition of trisomy in AML. We used a retroviral vector to drive expression of wild-type, hypermorphic, or hypomorphic MYC in bone marrow that expressed the PML-RARA transgene. MYC retroviruses cooperated in myeloid leukemogenesis and suppressed gain of chromosome 15. When the PML-RARA transgene was expressed in a Myc haploinsufficient background, we observed selection for increased copies of the wild-type Myc allele concomitant with leukemic transformation. In addition, we found that human myeloid leukemias with trisomy 8 have increased MYC. These data show that gain of MYC can contribute to the pathogenic effect of the most common trisomy of human AML.
Depleted marine fish stocks and ecosystem-based management: on the road to recovery, we need to be precautionary
Authors: Gårdmark Anna , Nielsen Anders , Floeter Jens , Möllmann Christian
Published: November 2010

Gårdmark, A., Nielsen, A., Floeter, J., and Möllmann, C. 2011. Depleted marine fish stocks and ecosystem-based management: on the road to recovery, we need to be precautionary. – ICES Journal of Marine Science, 68: 212–220. Precautionary management for fish stocks in need of recovery requires that likely stock increases can be distinguished from model artefacts and that the uncertainty of stock status can be handled. Yet, ICES stock assessments are predominantly deterministic and many EC management plans are designed for deterministic advice. Using the eastern Baltic cod (Gadus morhua) stock as an example, we show how deterministic scientific advice can lead to illusive certainty of a rapid stock recovery and management decisions taken in unawareness of large uncertainties in stock status. By (i) performing sensitivity analyses of key assessment model assumptions, (ii) quantifying the uncertainty of the estimates due to data uncertainty, and (iii) developing alternative stock and ecosystem indicators, we demonstrate that estimates of recent fishing mortality and recruitment of this stock were highly uncertain and show that these uncertainties are crucial when combined with management plans based on fixed reference points of fishing mortality. We therefore call for fisheries management that does not neglect uncertainty. To this end, we outline a four-step approach to handle uncertainty of stock status in advice and management. We argue that it is time to use these four steps towards an ecosystem-based approach to fisheries management.
Genetic Analysis and Molecular Mapping of Quantitative Trait Loci in Common Bean AgainstPythium ultimum
Authors: Campa Ana , Pérez-Vega Elena , Pascual Aida , Ferreira Juan José
Published: November 2010

Pythium ultimum is a soil pathogen that can cause seed decay and damage to roots in common bean. In this study, the response of a set of 40 common bean genotypes to P. ultimum and inheritance of the resistance in the 92 F7recombinant inbred lines (RIL) developed from a cross between Xana and Cornell 49242 was investigated by using emergence rate and seedling vigor. Emergence of the 40 genotypes showed a significant association between white seed coat and response to this pathogen. Among these, 11 common bean genotypes, all with colored seeds, exhibited a high percentage of emergence and seedling vigor not significantly different (P > 0.05) to noninoculated plants. Response of the RIL population revealed both qualitative and quantitative modes of inheritance. A major gene (Py-1) controlling the emergence rate was mapped in the region of the gene P, a basic color gene involved in control of seed coat color, located on LG 7. Using the RIL subpopulation with colored seeds, a significant quantitative trait loci (QTL) associated with the emergence rate (ER3XC) and another with seedling vigor (SV6XC) were identified on the LG 3 and 6, respectively. QTL SV6XCwas mapped in the region of the gene V, another gene involved the genetic control of color. QTLs associated with seed traits were mapped in the same relative position as regions involved in responses to P. ultimum suggesting the possible implication of avoidance mechanisms in the response to this pathogen.
Monitoring of human papillomavirus vaccination
Authors: Dillner J , Arbyn M , Unger E , Dillner L
Published: November 2010

Persistent infection with oncogenic human papillomavirus (HPV) is a necessary causal factor in the development of cervical cancer. Moreover, HPV, predominately type 16 and to a lesser degree type 18, is linked causally to varying proportions of other anogenital cancers (vulva, vagina, penis, anus) as well as cancers elsewhere in the body (oropharynx, larynx, conjunctiva). HPV types 6 and 11 cause most of genital warts and recurrent respiratory papillomatosis. Effective prophylactic vaccines have been developed. In this review, we address briefly the immunological aspects of HPV infection and the results of HPV vaccination trials. Internationally standardized monitoring and evaluation of prophylactic HPV vaccination programmes will be essential for arriving at the most cost-effective strategies for cancer control.
Effect of an individualised education programme on asthma control, inhaler use skill, asthma knowledge and health‐related quality of life among poorly compliant Korean adult patients with asthma
Authors: Choi Ja Yun , Cho Chung Hyang‐In
Published: November 2010

Aims and objectives.  This study assessed the effect of an individualised education programme on asthma control, inhaler use, asthma knowledge and health‐related quality of life among poorly compliant adult Korean patients with asthma.

Background.  Previous studies show that proper educational strategies are necessary to increase asthma knowledge and skills to improve patients’ self‐management and health‐related quality of life.

Design.  A one‐group quasi‐experimental design with repeated measurements.

Methods.  Adult patients with asthma (n = 101) were recruited from University hospital located in K City, Korea. Three interventions consisting of 30‐minute sessions of individualised education were provided by an education team. Peak expiratory flow rate (PEFR), daily record card (DRC) scores, skill scores for use of metered dose inhaler, level of asthma knowledge and health‐related quality of life scores were obtained before the intervention and 2–4 and 4–8 weeks after the intervention. One‐way repeated measures analysis of variance was used to identify the effect of the education programme on the dependent variables.

Results.  Peak expiratory flow rate, DRC scores, inhaler using skill scores and health‐related quality of life scores benefitted from intervention, whereas knowledge score did not. The effect on the PEFR and DRC score was sustained, with that of inhaler use skill increased over time from 4–8 weeks. However, the health‐related quality of life effect was not sustained for 4–8 weeks after the intervention.

Conclusions.  Repetitive education and innovative education methods may be needed to improve and to maintain pulmonary function, symptom control, asthma knowledge and health‐related quality of life of poorly compliant adult Korean patients with asthma.

Relevance to clinical practice.  This study confirmed the importance of education for patients suffering from asthma in managing their symptoms and promoting their quality of life.
The effect of hormones and peptides involved in water balance on rat colonic motility in vitro
Authors: VODERHOLZER W. A. , ALLESCHER H.‐D. , MÜLLER‐LISSNER S. A.
Published: November 2010

Abstract We have previously shown that restriction of water intake decreased stool frequency and stool weight in volunteers. The aim of this study was to investigate whether these effects of thirst could be mediated by an action of systematically released hormones on colonic smooth muscle. Using isolated colonic smooth muscle strips the effect of arginine‐vasopressin (AVP), angiotensin II (ANG II) and aldosterone on rat colonic motility in vitro was investigated. AVP (10−12‐10−10 mol/***1) and aldosterone (3 times 10−10‐3 times 10−8 mol/1) and physiological hormonal concentrations of ANG II (10−13‐10−10 mol/***1) had no effect on either basal activity, direct stimulation of colonic smooth muscle or neurally stimulated contractions using carbachol 10−7‐3 times 10−5 mol/***1 or neurally stimulated contractions using electrical field stimulation at various stimulation frequencies (1–10 pps, 1 ms, 40 V). ANG II in higher concentrations (10−7‐10−6 mol/***1) increased basal activity and neurally mediated contractions. Accordingly, ANG II (10−6 mol/***1) caused a prestimulation but did not increase the maximum contractile effect of carbachol. The response to ANG II was not affected by atropine (10−6 mol/1). TTX (10−6 mol/1) and N‐nitro‐L8‐arginine (L‐NNA) (3 times 10−4 mol/1) stimulated basal muscular activity but did not affect the maximum contractile effect of ANG II. Systemic serum concentrations of AVP, aldosterone and ANG II are presumably not involved in thirst‐induced colonic motility changes. The ANG II effect in higher concentrations is mediated by a direct stimulatory smooth muscle effect and/or by facilitating neuronal liberation of acetylcholine. These higher concentrations of ANG II could be reached when ANG II is acting as a neurotransmitter or through a local renin‐angiotensin system.
Autonomic dysfunction in patients with achalasia
Authors: ECKARDT V. F. , STENNER F. , LIEWEN H. , RÖDER R. , KOOP H. , BERNHARD G.
Published: November 2010

Abstract It has been previously shown that patients with achalasia may have motor abnormalities of the stomach, small bowel and biliary system. This study investigates whether a disturbance of extraintestinal autonomic function occurs. Autonomic function studies were performed in 15 patients with achalasia and 15 age‐ and sex‐matched healthy controls. Pupillo‐grams were obtained during darkness, light exposure and after pilocarpine administration. Cardiovascular function studies included determinations of heart rate variation during deep breathing and orthostasis. In addition, we determined blood pressure changes in response to sustained handgrip, cold exposure and orthostasis. Neurohormonal function was investigated by measuring serum pancreatic polypeptide (PP) levels prior to and following sham feeding. Pupillary function did not differ in patients as compared with controls. However, 9 of 15 patients (95% CI: 32–84%) and none of the controls showed at least one abnormal autonomic cardiovascular response. A significant difference between the two groups was observed in sympathetic function (P = 0.023). More patients than controls did not respond to sharn feeding with a PP increase. It is concluded that some patients with achalasia exhibit an abnormality of the autonomic nervous system that extends beyond the gastrointestinal tract. These abnormalities mainly concern cardiovascular function but may also involve neurohormonal responses.
Sham feeding disrupts phase III of the duodenal migrating motor complex in humans
Authors: POUDEROUX P. , VEYRAC M. , MICHEL H.
Published: November 2010

The role of the vagus nerve in the control of the intestinal migrating motor complex (MMC) is unclear. This study aimed to evaluate the effect of physiological vagal stimulation with sham feeding on phase III of the MMC. Antroduodenal motility was recorded in six healthy volunteers. The first phase III was used as a control, and sham feeding was performed during the second phase III. The MMC was disrupted within 1.5 ± 0.4 min of sham feeding and its duration was shorter than the control phase III. Phase III propagation was inhibited in all subjects, most of them exhibiting no propagation beyond the third duodenal recording site. During sham feeding, the antrum exhibited transient phasic contractions in five out of six subjects. The duodenal motility index recorded for up to 30 min after the onset of the sham feeding was unchanged in five out of six subjects. We conclude that sham feeding consistently interrupted phase III of the duodenal MMC and induced antral contractions, but failed to provoke significant motor events in the duodenum.
Photoperiodism in Higher Plants: An Interaction of Phytochrome and Circadian Rhythms
Authors: HEIDE OLA M.
Published: November 2010

A theoretical model for photoperiodic time measurement in higher plants is presented. It is based on the concept that the diurnal change in responsiveness to the phytochrome pigment system is dependent upon a circadian rhythm in membrane functioning and configuration, which is reflected in a parallel rhythm in membrane binding capacity for phytochrome Pfr. Phytochrome in turn, being an integrated part of the membrane clock, is acting as a “Zeitgeber” by mediating the external light stimuli in phase‐controlling of the membrane oscillation. Phytochrome and the circadian clock is thus integrated into one structural and functional unity.

Applied to the field of photoperiodic control of flowering the model is shown to account for most of the conflicting experimental results in both short‐day and long‐day plants.
The Structure of Pea Alcohol Dehydrogenase Using Inactivation by Iodoacetate
Authors: LAPKA ROMAN , LEBLOVÁ SYLVA
Published: November 2010

Alcohol dehydrogenase (E.C. 1.1.1.1, abbreviated ADH) isolated from germinating pea seeds (Pisum arvense L.) is inactivated by iodoacetate. The inactivation rate is decreased by ATP, ADP, AMP, NAD, chloride ions and o‐phenanthroline. The nucleotides studied are bound in the area of the coenzyme binding site, similar to iodoacetate. On the other hand, o‐phenanthroline binds zinc ions in a chelate which is apparently bound in the close vicinity of the coenzyme binding site.
Prognostic significance of replication protein A (RPA) expression levels in bladder urothelial carcinoma
Authors: Levidou Georgia , Gakiopoulou Hariklia , Kavantzas Nikolaos , Saetta Angelica A. , Karlou Maria , Pavlopoulos Petros , Thymara Irene , Diamantopoulou Kalliopi , Patsouris Efstratios , Korkolopoulou Penelope
Published: November 2010

What’s known on the subject? and What does the study add?

The prognostic utility of cyclin D1 in non‐muscle and muscle‐invasive urothelial bladder carcinomas has already been examined by our group and our investigators previously. Moreover, recent investigations have shown that RPA protein expression may be implicated in the pathogenesis of various malignant tumours. In this study, RPA1 and RPA2 overexpression seems to be more important during early T‐categories of bladder carcinogenesis, showing similar kinetics with cyclin D1, whereas RPA2 expression emerges as a valuable marker of favourable prognosis in the entire cohort and in non‐muscle‐invasive tumours, supplementing the information obtained by standard clinicopathological prognosticators.

OBJECTIVE

• To elucidate the role of replication protein A (RPA) in both superficial (Ta–T1) and muscle‐invasive (T2–T4) urothelial carcinomas (UCs), investigating its potential prognostic usefulness.

PATIENTS AND METHODS

• Paraffin‐embedded tissue from 156 patients with bladder UC was immunostained for RPA1 and RPA2.

RESULTS

• RPA1 and RPA2 labelling indexes (LIs) decreased with increasing histological grade (both P < 0.001) and T‐category in the entire cohort (P= 0.008 and P < 0.001, respectively) and in muscle‐invasive carcinomas (P= 0.014 and P= 0.012, respectively).

• RPA1 expression was positively correlated with RPA2 (Spearman’s correlation coefficient ρ= 0.309, P < 0.001). Both RPA1 and RPA2 LIs were positively correlated with cyclin D1 expression (ρ= 0.354, P < 0.001 and ρ= 0.934, P < 0.001).

• In survival analysis of the entire cohort decreased RPA2 and RPA1 correlated with a lesser probability of survival (P < 0.001 and P= 0.018). In non‐muscle‐invasive tumours (Ta–T1) only lower RPA2 (P < 0.001) was correlated with shortened survival, whereas in muscle‐invasive tumours (T2–T4) decreased RPA2 and RPA1 expression levels were associated with adverse prognosis (P= 0.035 and P= 0.042, respectively).

• In multivariate survival analysis of the entire cohort and in non‐muscle‐invasive cases RPA2 expression remained significant, even when adjustment for cyclin D1 expression was applied.

CONCLUSIONS

• RPA1 and RPA2 overexpression seems to be more important during early T‐categories of bladder carcinogenesis. Showing similar kinetics with cyclin D1.

• RPA2 expression emerges as a valuable marker of favourable prognosis in the entire cohort and in non‐muscle‐invasive tumours, supplementing the information obtained by standard clinicopathological prognosticators.
Global agriculture R&D and the changing aid architecture
Authors: Pingali Prabhu
Published: November 2010

Agriculture research knowledge and technology that transcends national borders has played a crucial role in enhancing developing country productivity growth over the past 50 years. The demand for international agriculture research (IAR) continues to be strong today even while becoming increasingly differentiated by the stage of development that a particular country or region is in. The supply of IAR to developing country research programs is, however, becoming increasingly constrained by: variable donor support; a push toward downstream product adaptation and dissemination activities relative to innovation and product development; and a lack of clear links between international public good research and national agriculture development priorities. Country‐level donor coordination and alignment mechanisms, specified in the Paris Declaration on Aid Effectiveness, do not explicitly account for the role of IAR in the development process. While the movement toward national ownership of its development agenda and donor alignment around it is unquestionably good, an unintended consequence could be a break in the R&D pipeline that supplies public good research and technologies for enhancing developing country agriculture productivity growth. The article presents options for rebuilding synergies between international public good research and national agriculture development priorities.
Genetic regulation of human brain development: lessons from Mendelian diseases
Authors: Dixon‐Salazar Tracy J. , Gleeson Joseph G.
Published: November 2010

One of the fundamental goals in human genetics is to link gene function to phenotype, yet the function of the majority of the genes in the human body is still poorly understood. This is especially true for the developing human brain. The study of human phenotypes that result from inherited, mutated alleles is the most direct evidence for the requirement of a gene in human physiology. Thus, the study of Mendelian central nervous system (CNS) diseases can be an extremely powerful approach to elucidate such phenotypic/genotypic links and to increase our understanding of the key components required for development of the human brain. In this review, we highlight examples of how the study of inherited neurodevelopmental disorders contributes to our knowledge of both the “normal” and diseased human brain, as well as elaborate on the future of this type of research. Mendelian disease research has been, and will continue to be, key to understanding the molecular mechanisms that underlie human brain function, and will ultimately form a basis for the design of intelligent, mechanism‐specific treatments for nervous system disorders.
Generalized, severe, chronic periodontitis is associated with anemia of chronic disease: a pilot study in urban, Indian males
Authors: Naik Vidya , Acharya Aneesha , Deshmukh Vijay L. , Shetty Sharath , Shirhatti Ravi
Published: November 2010

Aim:  Anemia of chronic disease, a cytokine‐mediated anemia, is a frequent complication of many chronic inflammatory conditions. The present case‐control study was aimed to evaluate levels of systemic hematological markers indicative of anemia in patients with generalized, severe, chronic periodontitis.

Methods:  A convenience quota sample of 30 systemically‐healthy, urban, male patients comprised two groups, based on full mouth periodontal examination: group A patients (n = 15) were diagnosed with generalized, severe, chronic periodontitis, and group B patients comprised the control group (n = 15), which included patients with a clinically‐healthy periodontium. Laboratory blood investigations included hemoglobin (g%), total number of erythrocytes (red blood cells), hematocrit/packed cell volume, erythrocyte sedimentation rate, mean corpuscular volume of erythrocytes, and mean corpuscular hemoglobin concentration. An analysis of covariance using age as a covariate was done to compare the mean values of hematological parameters within groups.

Results:  The mean values of hemoglobin, red blood cells, packed cell volume, and mean corpuscular hemoglobin concentration were significantly lower, while the mean corpuscular volume of erythrocytes and erythrocyte sedimentation rate were significantly higher in group A patients compared to those in group B, indicating mild anemia.

Conclusions:  Severe periodontal disease can be linked with anemic status.
An 8‐week, randomized, controlled, clinical study of the use of a 0.1% chlorhexidine mouthwash by chronic periodontitis patients
Authors: Tenenbaum Henri , Luc Jöelle , Schaaf Jean‐François , Federlin‐Ducani Marie , Cotton Christine , Elkaim René , Cuisinier Frédéric J.G. , Roques Christine
Published: November 2010

Aim:  To evaluate the efficacy of a 2‐week administration of a 0.1% chlorhexidine mouthwash in the short‐term treatment of chronic periodontitis patients and the impact of this product when administered twice by pocket irrigation.

Methods:  Sixty patients were enrolled in a single‐centre, placebo‐controlled, randomized study with the blind allocation of product to two parallel groups. Clinical assessments were performed, and samples from six selected subgingival sites were collected for microbial analysis by culture at baseline, D15 and D56. Three of the six sites were randomly selected and were treated by subgingival irrigation with the same 0.1% chlorhexidine product at D0 and D7. A subsequent statistical analysis was performed using the paired Student’s t‐test and Wilcoxon rank sum test for within‐group analyses; analysis of variance and the Kruskall–Wallis test were used for between‐group analyses.

Results:  Two‐week treatment with a 0.1% chlorhexidine mouthwash slightly reduced the gingival inflammation associated with periodontitis. We observed a significant decrease in Gram‐negative, facultative anaerobes and micro‐aerophiles, and a significant increase in Gram‐positive cocci. No increase in the treatment effect was demonstrated by irrigation of the periodontal pockets.

Conclusion:  The 0.1% chlorhexidine mouthwash showed limited beneficial effects in the treatment of periodontitis patients.
Genetic dissection of ion currents underlying all‐or‐none action potentials in C. elegans body‐wall muscle cells
Authors: Liu Ping , Ge Qian , Chen Bojun , Salkoff Lawrence , Kotlikoff Michael I. , Wang Zhao‐Wen
Published: November 2010

Non‐technical summary

Mammalian skeletal muscle contractions are initiated by all‐or‐none action potentials (APs) triggered by motoneurons. In C. elegans locomotory muscle, however, the characteristics of APs, the underlying ion channels, and their role in Ca2+ release are poorly understood. Here we show that C. elegans locomotory muscle fires spontaneous, all‐or‐none APs, which appear to be modulated by motoneuron activity. The upstroke of muscle APs requires Ca2+ entry through a voltage‐gated Ca2+ channel (EGL‐19), whereas the downstroke of the APs relies on a voltage‐gated potassium channel as well as a Ca2+‐ and Cl−‐activated potassium channel. AP‐elicited elevations of intracellular Ca2+ concentration require both EGL‐19 in the plasma membrane and the ryanodine receptor in the sarcoplasmic reticulum membrane. The discovery of all‐or‐none action potentials in C. elegans body‐wall muscle brings the physiology of C. elegans much closer to that of other metazoans, and strengthens its utility as a model organism.
Resonant coupling to a dipole absorber inside a metamaterial: Anticrossing of the negative index response
Authors: Smolev Svyatoslav , Ku Zahyun , Brueck S. R. J , Brener Igal , Sinclair Michael B. , Ten Eyck Gregory A. , Langston W. L. , Basilio Lorena I.
Published: November 2010

The authors experimentally demonstrate a resonant hybridization between the magnetic dipole structural resonance in the permeability of a fishnet metamaterial and an electric dipole material resonance in the permittivity of the dielectric spacer layer. The hybrid resonances in the permeability and the negative index response exhibit an anticrossing behavior. A simple analytic model and numerical simulations using a rigorous coupled-wave analysis are in excellent qualitative agreement with the experiment.
Bitter Medicine
Authors: Foley John F.
Published: November 2010

Agonists of bitter taste receptors in the airways induce bronchodilation in a mouse model of asthma.
Focus Issue: Getting Excited About Glia
Authors: Adler Elizabeth M.
Published: November 2010

Complementing the 5 November
Science
Special Issue, this issue highlights glial cell function, development, and disease.
Use of historical data and a novel metric in the evaluation of the effectiveness of hearing conservation program components
Authors: Heyer Nicholas , Morata Thais C , Pinkerton Lynne E , Brueck Scott E , Stancescu Daniel , Panaccio Mary Prince , Kim Hyoshin , Sinclair J Stephen , Waters Martha A , Estill Cherie F , Franks John R
Published: November 2010

Objectives

To evaluate the effectiveness of hearing conservation programs (HCP) and their specific components in reducing noise-induced hearing loss (NIHL).

Methods

This retrospective cohort study was conducted at one food-processing plant and two automotive plants. Audiometric and work-history databases were combined with historical noise monitoring data to develop a time-dependent exposure matrix for each plant. Historical changes in production and HCP implementation were collected from company records, employee interviews and focus groups. These data were used to develop time-dependent quality assessments for various HCP components. 5478 male (30 427 observations) and 1005 female (5816 observations) subjects were included in the analysis.

Results

Analyses were conducted separately for males and females. Females tended to have less NIHL at given exposure levels than males. Duration of noise exposure stratified by intensity (dBA) was a better predictor of NIHL than the standard equivalent continuous noise level (Leq) based upon a 3-dBA exchange. Within this cohort, efficient dBA strata for males were <95 versus ≥95, and for females <90 versus ≥90. The reported enforced use of hearing protection devices (HPDs) significantly reduced NIHL. The data did not have sufficient within-plant variation to determine the effectiveness of noise monitoring or worker training. An association between increased audiometric testing and NIHL was believed to be an artifact of increased participation in screening.

Conclusions

Historical audiometric data combined with noise monitoring data can be used to better understand the effectiveness of HCPs. Regular collection and maintenance of quality data should be encouraged and used to monitor the effectiveness of these interventions.
ANISOTROPIC UNIVERSE WITH HESSENCE DARK ENERGY
Authors: CHAKRABORTY SHUVENDU , DEBNATH UJJAL
Published: November 2010

In this work, we have considered a noncanonical complex scalar field named hessence to play the role of quintom in anisotropic universe (particularly in the Bianchi I model) as a new approach to look into the unknown mysterious world of dark energy. We have solved the field equations by considering the power-law form of scale factors and found the potential function in terms of ϕ with some restrictions. We also show here that hessence can avoid the Q-ball formation in anisotropic universe.
DEPENDABILITY ANALYSIS OF HYBRID REDUNDANCY SYSTEMS USING FUZZY APPROACH
Authors: CHELLAPPAN C. , VIJAYALAKSHMI G.
Published: November 2010

With the increasing demand for high reliability in mission critical systems such as space shuttle, digital flight and real time control to mention a few, reliability analysis of fault tolerant systems continues to be the focus of most researchers. The reliability analysis of triple modular redundancy (TMR) and hybrid redundancy (TMR with spares) systems is in general carried out with the assumption of failure rate being precise. However, in practice failure rate is imprecise due to the uncertainties of system operation. In this paper, the dependability analysis of hybrid redundancy systems (HRS) comprising of N-modular redundancy (NMR) and standby redundancy is presented assuming failure rates and repair rates as fuzzy numbers. Each module of the NMR is assumed to have access to a number of cold spares and a repair facility. A Markov model for the HRS is developed. As the Markov model parameters may not be precisely known due to various reasons, vertex method and α-cut method is applied. These methods allow uncertainty-based parameters that are represented as fuzzy numbers. The dependability measures such as availability and reliability are obtained. A comparative study of the fuzzy results and the conventional results using probability concepts is presented.
User-based evaluation of data-driven haptic rendering
Authors: Höver Raphael , Luca Massimiliano Di , Harders Matthias
Published: November 2010

In this article, the data-driven haptic rendering approach presented in our earlier work is assessed. The approach relies on recordings from real objects from which a data-driven model is derived that captures the haptic properties of the object. We conducted two studies. In the first study, the Just Noticeable Difference (JND) for small forces, as encountered in our set-up, was determined. JNDs were obtained both for active and passive user interaction. A conservative threshold curve was derived that was then used to guide the model generation in the second study. The second study examined the achievable rendering fidelity for two objects with different stiffnesses. Subjects directly compared data-driven virtual feedback with the real objects. Results indicated that it is crucial to include dynamic material effects to achieve haptic feedback that cannot be distinguished from real objects. Results also showed that the fidelity is considerably decreased for stiffer objects due to limits of the display hardware.
Parallelism generics for Ada 2005 and beyond
Authors: Moore Brad J.
Published: November 2010

The Ada programming language is seemingly well-positioned to take advantage of emerging multi-core technologies. While it has always been possible to write parallel algorithms in Ada, there are certain classes of problems however, where the level of effort to write parallel algorithms outweighs the ease and simplicity of a sequential approach. This can result in lost opportunities for parallelism and slower running software programs. Languages such as Cilk++ and OpenMB provide expressive mechanisms to add parallelism to code using a C++ based syntax by adding special syntactic directives where parallelism is desired. This paper explores Ada's concurrency features to see whether it is possible to easily inject similar iterative and recursive parallelism to code written in Ada, without having to resort to special language extensions or non-standard language features. This paper identifies a "work-seeking" technique, which can be viewed as a form of compromise between work-sharing and work-stealing, two other existing strategies. The paper presents performance results to illustrate the benefits of use for the generics and goes on to suggest how parallelism pragmas could possibly be added to the Ada language to further facilitate writing parallel applications.
CYBEX
Authors: Rutkowski Anthony , Kadobayashi Youki , Furey Inette , Rajnovic Damir , Martin Robert , Takahashi Takeshi , Schultz Craig , Reid Gavin , Schudel Gregg , Hird Mike , Adegbite Stephen
Published: November 2010

The cybersecurity information exchange framework, known as CYBEX, is currently undergoing its first iteration of standardization efforts within ITU-T. The framework describes how cybersecurity information is exchanged between cybersecurity entities on a global scale and how the exchange is assured. The worldwide implementation of the framework will eventually minimize the disparate availability of cybersecurity information. This paper provides a specification overview, use cases, and the current status of CYBEX.
Unsteady Unidirectional Flow of Second‐Grade Fluid through a Microtube with Wall Slip and Different Given Volume Flow Rate
Authors: Chen Cha′o-Kuang , Lai Hsin-Yi , Chen Wei-Fan
Published: November 2010

The second‐grade flows through a microtube with wall slip are solved by Laplace transform technique. The effects of rarefaction and elastic coefficient are considered with an unsteady flow through a microtube for a given but arbitrary inlet volume flow rate with time. Five cases of inlet volume flow rate are as follows: (1) trapezoidal piston motion, (2) constant acceleration, (3) impulsively started flow, (4) impulsively blocked fully developed flow, and (5) oscillatory flow. The results obtained are compared to those solutions under no‐slip and slip condition.
Novel Interaction of MUC4 and Galectin: Potential Pathobiological Implications for Metastasis in Lethal Pancreatic Cancer
Authors: Senapati Shantibhusan , Chaturvedi Pallavi , Chaney William G. , Chakraborty Subhankar , Gnanapragassam Vinayaga S. , Sasson Aaron R. , Batra Surinder K.
Published: November 2010

Purpose: Several studies have reported aberrant expression of MUC4 in pancreatic cancer (PC), which is associated with tumorigenicity and metastasis. Mechanisms through which MUC4 promote metastasis of PC cells to distant organs are poorly defined.

Experimental Design: Identification of MUC4–galectin-3 interaction and its effect on the adhesion of cancer cells to endothelial cells were done by immunoprecipitation and cell–cell adhesion assays, respectively. Serum galectin-3 level for normal and PC patients were evaluated through ELISA.

Results: In the present study, we have provided clinical evidence that the level of galectin-3 is significantly elevated in the sera of PC patients with metastatic disease compared with patients without metastasis (P = 0.04) and healthy controls (P = 0.00001). Importantly, for the first time, we demonstrate that MUC4 present on the surface of circulating PC cells plays a significant role in the transient and reversible attachment (docking) of circulating tumor cells to the surface of endothelial cells. Further, exogenous galectin-3 at concentrations similar to that found in the sera of PC patients interacts with MUC4 via surface glycans such as T antigens, which results in the clustering of MUC4 on the cell surface and a stronger attachment (locking) of circulating tumor cells to the endothelium.

Conclusions: Altogether, these findings suggest that PC cell-associated MUC4 helps in the docking of tumor cells on the endothelial surface. During cancer progression, MUC4–galectin-3 interaction–mediated clustering of MUC4 may expose the surface adhesion molecules, which in turn promotes a stronger attachment (locking) of tumor cells to the endothelial surface. Clin Cancer Res; 17(2); 267–74. ©2010 AACR. Clin Cancer Res; 17(2); 267–74. ©2010 AACR.
Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissues
Authors: Kibriya Muhammad G , Jasmine Farzana , Roy Shantanu , Paul-Brutus Rachelle M , Argos Maria , Ahsan Habibul
Published: November 2010

Background

We evaluated (a) the feasibility of whole genome cDNA-mediated Annealing, Selection, extension and Ligation (DASL) assay on formalin-fixed paraffin-embedded (FFPE) tissue and (b) whether similar conclusions can be drawn by examining FFPE samples as proxies for fresh frozen (FF) tissues. We used a whole genome DASL assay (addressing 18,391 genes) on a total of 72 samples from paired breast tumor and surrounding healthy tissues from both FF and FFPE samples.

Results

Gene detection was very good with comparable success between the FFPE and FF samples. Reproducibility was also high (r2 = 0.98); however, concordance between the two types of samples was low. Only one-third of the differentially expressed genes in tumor tissues (compared to corresponding normal) from FF samples could be detected in FFPE samples and conversely only one-fourth of the differentially expressed genes from FFPE samples could be detected in FF samples. GO-enrichment analysis, gene set enrichment analysis (GSEA) and GO-ANOVA analyses also suggested small overlap between the lead functional groups that were differentially expressed in tumor detectable by examining FFPE and FF samples. In other words, FFPE samples may not be ideal for picking individual target gene(s), but may be used to identify some of the lead functional group(s) of genes that are differentially expressed in tumor. The differentially expressed genes in breast cancer found in our study were biologically meaningful. The "cell cycle" & "cell division" related genes were up-regulated and genes related to "regulation of epithelial cell proliferation" were down-regulated.

Conclusions

Gene expression experiments using the DASL assay can efficiently handle fragmentation issues in the FFPE tissues. However, formalin fixation seems to change RNA and consequently significantly alters gene expression in a number of genes which may not be uniform between tumor and normal tissues. Therefore, considerable caution needs to be taken when interpreting gene expression data from FFPE tissues, especially in relation to specific genes.