bluuebunny/crossref_metadata_2025 huggingface dataset:
X-Gal Staining of the Central Nervous System in Adult Drosophila
Authors: Sweeney Sean T. , Hidalgo Alicia , de Belle J. Steven , Keshishian Haig
Published: February 2012

The Drosophila nervous system provides a valuable model for studying various aspects of brain development and function. The postembryonic Drosophila brain is especially useful, because specific neuron types derive from specific progenitors at specific times. Elucidating the means by which diverse neuron types derive from a limited number of progenitors can contribute significantly to our understanding of the genetic and molecular mechanisms involved in developmental neurobiology. β-Galactosidase, the product of the E. coli lacZ gene, has been used extensively as a reporter in Drosophila research. Staining for β-galactosidase activity can be performed using the substrate X-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside), which produces a blue precipitate visible by light microscopy. This detection method is highly sensitive and has the advantage that the results can be observed without the need for specialized microscopy equipment. This protocol describes general procedures for X-gal labeling of neural tissue from Drosophila.
Generation of 2A-Linked Multicistronic Cassettes by Recombinant PCR
Authors: Szymczak-Workman Andrea L. , Vignali Kate M. , Vignali Dario A.A.
Published: February 2012

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel “cleavage” event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18–22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector. This protocol describes the use of recombinant polymerase chain reaction (PCR) to connect multiple 2A-linked protein sequences. The final construct is subcloned into an expression vector.
How to Cultivate Ectocarpus: Figure 1.
Authors: Coelho Susana M. , Scornet Delphine , Rousvoal Sylvie , Peters Nick T. , Dartevelle Laurence , Peters Akira F. , Cock J. Mark
Published: February 2012

This article describes the standard procedure for growing Ectocarpus in the laboratory. The culture is started with partheno-sporophyte (or sporophyte) filaments because this is the stage that is usually maintained in strain collections. The standard medium is Provasoli-enriched natural seawater (PES), but Ectocarpus can also be grown in artificial seawater, which allows more precise control over the culture conditions. The algae can be cultivated either in plastic Petri dishes or in 10-L bottles with bubbling, if large amounts of biomass are required. Standard growth conditions are 13°C with a 12h/12h d/night cycle and 20 µmol photons m−2 s−1 irradiance using daylight-type fluorescent tubes. All manipulations of Ectocarpus cultures should be performed in a clean environment (if possible, under a laminar flow hood). Forceps should be dipped in ethanol and allowed to dry under the hood.
Colocalization of Fluorescent Probes: Accurate and Precise Registration with Nanometer Resolution
Authors: Churchman L. Stirling , Spudich James A.
Published: February 2012

Colocalization of fluorescent probes is commonly used in cell biology to discern the proximity of two proteins in the cell. Considering that the resolution limit of optical microscopy is on the order of 250 nm, there has not been a need for high-resolution colocalization techniques. However, with the advent of higher resolution techniques for cell biology and single-molecule biophysics, colocalization must also improve. For diffraction-limited applications, a geometric transformation (i.e., translation, scaling, and rotation) is typically applied to one color channel to align it with the other; however, to achieve high-resolution colocalization, this is not sufficient. Single-molecule high-resolution colocalization (SHREC) of single probes uses the local weighted mean transformation to achieve a colocalization resolution of at least 10 nm. This article describes the process of collecting a calibration data set of fiducials and the appropriate analysis to determine the transformation for colocalization.
PoppyAPETALA1/FRUITFULLOrthologs Control Flowering Time, Branching, Perianth Identity, and Fruit Development
Authors: Pabón-Mora Natalia , Ambrose Barbara A. , Litt Amy
Published: January 2012

Several MADS box gene lineages involved in flower development have undergone duplications that correlate with the diversification of large groups of flowering plants. In the APETALA1 gene lineage, a major duplication coincides with the origin of the core eudicots, resulting in the euFUL and the euAP1 clades. Arabidopsis FRUITFULL (FUL) and APETALA1 (AP1) function redundantly in specifying floral meristem identity but function independently in sepal and petal identity (AP1) and in proper fruit development and determinacy (FUL). Many of these functions are largely conserved in other core eudicot euAP1 and euFUL genes, but notably, the role of APETALA1 as an “A-function” (sepal and petal identity) gene is thought to be Brassicaceae specific. Understanding how functional divergence of the core eudicot duplicates occurred requires a careful examination of the function of preduplication (FUL-like) genes. Using virus-induced gene silencing, we show that FUL-like genes in opium poppy (Papaver somniferum) and California poppy (Eschscholzia californica) function in axillary meristem growth and in floral meristem and sepal identity and that they also play a key role in fruit development. Interestingly, in opium poppy, these genes also control flowering time and petal identity, suggesting that AP1/FUL homologs might have been independently recruited in petal identity. Because the FUL-like gene functional repertoire encompasses all roles previously described for the core eudicot euAP1 and euFUL genes, we postulate subfunctionalization as the functional outcome after the major AP1/FUL gene lineage duplication event.
The Influence of Light on Microtubule Dynamics and Alignment in the Arabidopsis Hypocotyl
Authors: Sambade Adrian , Pratap Amitesh , Buschmann Henrik , Morris Richard J. , Lloyd Clive
Published: February 2012

Light and dark have antagonistic effects on shoot elongation, but little is known about how these effects are translated into changes of shape. Here we provide genetic evidence that the light/gibberellin–signaling pathway affects the properties of microtubules required to reorient growth. To follow microtubule dynamics for hours without triggering photomorphogenic inhibition of growth, we used Arabidopsis  thaliana light mutants in the gibberellic acid/DELLA pathway. Particle velocimetry was used to map the mass movement of microtubule plus ends, providing new insight into the way that microtubules switch between orthogonal axes upon the onset of growth. Longitudinal microtubules are known to signal growth cessation, but we observed that cells also self-organize a strikingly bipolarized longitudinal array before bursts of growth. This gives way to a radial microtubule star that, far from being a random array, seems to be a key transitional step to the transverse array, forecasting the faster elongation that follows. Computational modeling provides mechanistic insight into these transitions. In the faster-growing mutants, the microtubules were found to have faster polymerization rates and to undergo faster reorientations. This suggests a mechanism in which the light-signaling pathway modifies the dynamics of microtubules and their ability to switch between orthogonal axes.
Skeletal development and abnormalities of the vertebral column and of the fins in hatchery‐reared turbot Scophthalmus maximus
Authors: Tong X. H. , Liu Q. H. , Xu S. H. , Ma D. Y. , Xiao Z. Z. , Xiao Y. S. , Li J.
Published: February 2012

To describe the skeletal development and abnormalities in turbot Scophthalmus maximus, samples were collected every day from hatching to 60 days after hatching (DAH). A whole‐mount cartilage and bone‐staining technique was used. Vertebral ontogeny started with the formation of anterior haemal arches at 5·1 mm standard length (LS) c. 11 DAH, and was completed by the full attainment of parapophyses at 16·9 mm LS c. 31 DAH. Vertebral centra started to develop at 6·3 mm LS c. 16 DAH and ossification in all centra was visible at 11·0 mm LS c. 25 DAH. The caudal fin appeared at 5·1 mm LS c. 11 DAH and ossification was visible at 20·6 mm LS c. 37 DAH. The onset of dorsal and anal fin elements appeared at 5·8 mm LS c. 15 DAH and 6·3 mm LS c. 16 DAH, respectively. Ossifications of both dorsal fin and anal fin were visible at 20·6 mm LS c. 37 DAH. The pectorals were the only fins present before first feeding, their ossifications were completed at 23·5 mm LS c. 48 DAH. Pelvic fins began forming at 7·2 mm LS c. 19 DAH and calcification of the whole structure was visible at 19·8 mm LS c. 36 DAH. In the present study, 24 types of skeletal abnormalities were observed. About 51% of individuals presented skeletal abnormalities, and the highest occurrence was found in the haemal region of the vertebral column. As for each developmental stage, the most common abnormalities were in the dorsal fin during early metamorphic period (stage 2), vertebral fusion during climax metamorphosis (stage 3) and caudal fin abnormality during both late‐metamorphic period (stage 4) and post‐metamorphic period (stage 5). Such research will be useful for early detection of skeletal malformations during different growth periods of reared S. maximus.
Effects of angiotensin receptor blockers on endothelial nitric oxide release: the role of eNOS variants
Authors: Mason R. Preston , Jacob Robert F. , Kubant Ruslan , Jacoby Adam , Louka Febee , Corbalan J. Jose , Malinski Tadeusz
Published: January 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Angiotensin II receptor blockers improve endothelial cell‐dependent vasodilation in patients with hypertension through suppression of angiotensin II type 1 receptors but may have additional and differential effects on endothelial nitric oxide synthase (eNOS) function.

WHAT THIS STUDY ADDS

• The key finding from this study is that angiotensin II receptor blockers (ARBs) differentially enhanced nitric oxide (NO) release in a manner influenced by certain genetic variants of eNOS. This finding provides new insights into the effects of ARBs on endothelial cell‐dependent vasodilation and eNOS function that are of high importance in vascular medicine and clinical pharmacology.

AIM Angiotensin II receptor blockers (ARBs) improve endothelial cell (EC)‐dependent vasodilation in patients with hypertension through suppression of angiotensin II type 1 receptors but may have additional and differential effects on endothelial nitric oxide (NO) synthase (eNOS) function. To investigate this question, we tested the effects of various ARBs on NO release in ECs from multiple donors, including those with eNOS genetic variants linked to higher cardiovascular risk.

METHODS The effects of ARBs (losartan, olmesartan, telmisartan, valsartan), at 1 µm, on NO release were measured with nanosensors in human umbilical vein ECs obtained from 18 donors. NO release was stimulated with calcium ionophore (1 µm) and its maximal concentration was correlated with eNOS variants. The eNOS variants were determined by a single nucleotide polymorphism in the promoter region (T‐786C) and in the exon 7 (G894T), linked to changes in NO metabolism.

RESULTS All of the ARBs caused an increase in NO release as compared with untreated samples (P < 0.01, n= 4–5 in all eNOS variants). However, maximal NO production was differentially influenced by eNOS genotype. Olmesartan increased maximal NO release by 30%, which was significantly greater (P < 0.01, n= 4–5 in all eNOS variants) than increases observed with other ARBs.

CONCLUSIONS The ARBs differentially enhanced NO release in ECs in a manner influenced by eNOS single nucleotide polymorphisms. These findings provide new insights into the effects of ARBs on EC‐dependent vasodilation and eNOS function.
Non‐steroidal anti‐inflammatory drugs and the risk of Clostridium difficile‐associated disease
Authors: Suissa Daniel , Delaney Joseph A. C. , Dial Sandra , Brassard Paul
Published: January 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Increasing age, length of hospital stay and previous antibiotic use have been established as important risk factors in the development of Clostridium difficile associated disease (CDAD). Several case reports over the past 30 years have linked diclofenac, a non‐steroidal anti‐inflammatory drug (NSAID) with CDAD. We assessed whether NSAID use in general, and diclofenac use in particular, is associated with an increased risk of CDAD.

WHAT THIS STUDY ADDS

• In this population based study, the use of diclofenac was associated with a 35% increase in the risk of developing CDAD. This association persisted when we limited the analysis to non‐hospitalized patients. No association was found between the use of any other NSAIDs and the risk of CDAD.

AIM Several case reports have linked diclofenac, a non‐steroidal anti‐inflammatory drug (NSAID), with Clostridium difficile associated disease (CDAD). We assessed whether NSAID use in general, and diclofenac use in particular, is associated with an increased risk of CDAD.

METHODS We used the United Kingdom's General Practice Research Database (GPRD) to conduct a population‐based case–control study. All cases of CDAD occurring between 1994 and 2005 were identified and were matched to 10 controls each. Conditional logistic regression was used to estimate the odds ratio of CDAD associated with current NSAID use, adjusting for covariates.

RESULTS We identified 1360 CDAD cases and 13 072 controls. We found an increased risk of CDAD associated with diclofenac (adjusted odds ratio (RR) 1.35, 95% confidence interval (CI) 1.10, 1.67). We did not observe an increased risk of CDAD with use of any other NSAID. No dose–response for diclofenac exposure was found. When we analyzed only patients who were not hospitalized in the year before the index date, we found diclofenac to have a similar effect on CDAD risk (adjusted RR 1.43, 95% CI 1.11, 1.84).

CONCLUSION Diclofenac use is associated with a modest increase in the risk of CDAD. In patients at risk of CDAD, other NSAIDs could be prescribed.
Effects of genetic variation in the P2RX7 gene on pharmacodynamics of a P2X7 receptor antagonist: a prospective genotyping approach
Authors: McHugh Simon M. , Roman Shilina , Davis Bill , Koch Annelize , Pickett Alison M. , Richardson Jill C. , Miller Sam R. , Wetten Sally , Cox Charles J. , Karpe Fredrik , Todd John A. , Bullmore Edward T.
Published: February 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Analysis of allelic variation in large populations has identified numerous single nucleotide polymorphisms (SNPs) in the P2RX7 gene. In vitro transfection has demonstrated SNP‐dependent alterations (gain or loss) of P2X7 receptor function, as measured by ATP‐induced ethidium uptake and interleukin‐1β production.

WHAT THIS STUDY ADDS

• We provide definitive evidence of SNP‐dependent alteration in P2X7 receptor pharmacodynamics to a specific antagonist (GSK1370319A) in a small sample of prospectively genotyped subjects. These effects on drug response underline the importance of genetic stratification in drug development of P2X7 receptor antagonists.

AIMS To investigate the effects of two single nucleotide polymorphisms (SNPs) in the human P2X7 receptor gene (P2RX7) – 1068G>A (A348T) and 1513A>C (E496A) – on P2X7 receptor function, using a specific receptor antagonist (GSK1370319A) and prospective genetic stratification.

METHODS Lipopolysaccharide‐ and ATP‐stimulated interleukin‐1β production was determined in the presence or absence of GSK1370319A in blood culture from 32 prospectively genotyped subjects.

RESULTS There was approximately 6.7‐fold difference (P < 0.0001) in IC50 for inhibition of ATP‐stimulated interleukin‐1β release by GSK1370319A between individuals with the homozygous gain‐ (1068A) and loss‐of‐function (1513C) genotypes (expressing the 348T, 496E and 348A, 496A alleles, respectively).

CONCLUSIONS Leukocyte P2X7 receptors had significantly altered pharmacodynamic responses to a specific antagonist (GSK1370319A), directly related to SNP genotype.
Seasonal bryophyte productivity in the sub‐Arctic: a comparison with vascular plants
Authors: Street Lorna E. , Stoy Paul C. , Sommerkorn Martin , Fletcher Benjamin J. , Sloan Victoria L. , Hill Timothy C. , Williams Mathew
Published: February 2012

1. Arctic ecosystems are experiencing rapid climate change, which could result in positive feedbacks on climate warming if ecosystem carbon (C) loss exceeds C uptake through plant growth. Bryophytes (mosses, liverworts and hornworts) are important components of Arctic vegetation, but are currently not well represented in terrestrial C models; in particular, seasonal patterns in bryophyte C metabolism compared to vascular plant vegetation are poorly understood.

2. Our objective was to quantify land‐surface CO2 fluxes for common sub‐Arctic bryophyte patches (dominated by Polytrichum piliferum and Sphagnum fuscum) in spring (March–May) and during the summer growing season (June–August) and to develop a simple model of bryophyte gross primary productivity fluxes (PB). We use the model to explore the key environmental controls over PB for P. piliferum and S. fuscum and compare seasonal patterns of productivity with those of typical vascular plant communities at the same site.

3. The modelled total gross primary productivity (ΣPB) over 1 year (March – November) for P. piliferum was c. 360 g C m−2 ground and for S. fuscum c. 112 g C m−2 ground, c. 90% and 30% of total gross primary productivity for typical vascular plant communities (ΣPV) over the same year. In spring (March–May), when vascular plant leaves are not fully developed, ΣPB for P. piliferum was 3 × ΣPV.

4. Model sensitivity analysis indicated that bryophyte turf water content does not significantly affect (March–November) ΣPB for P. piliferum and S. fuscum, at least for periods without sustained lack of precipitation. However, we find that seasonal changes in bryophyte photosynthetic capacity are important in determining ΣPB for both bryophyte species.

5. Our study implies that models of C dynamics in the Arctic must include a bryophyte component if they are intended to predict the effects of changes in the timing of the growing season, or of changes in vegetation composition, on Arctic C balance.
Expression of Inhibin/Activin Proteins and Receptors in the Human Hypothalamus and Basal Forebrain
Authors: Miller M. C. , Lambert‐Messerlian G. M. , Eklund E. E. , Heath N. L. , Donahue J. E. , Stopa E. G.
Published: February 2012

The inhibin/activin family of proteins is known to have a broad distribution of synthesis and expression in many species, as well as a variety of functions in reproductive and other physiological systems. Yet, our knowledge regarding the production and function of inhibin and activin in the central nervous system is relatively limited, especially in humans. The present study aimed to explore the distribution of inhibin/activin protein subunits and receptors in the adult human brain. The human hypothalamus and surrounding basal forebrain was examined using post‐mortem tissues from 29 adults. Immunocytochemical studies were conducted with antibodies directed against the inhibin/activin α, βA, and βB subunits, betaglycan and the activin type IIA and IIB receptors. An immunoassay was also utilised to measure dimeric inhibin A and B levels in tissue homogenates of the infundibulum of the hypothalamus. Robust βA subunit immunoreactivity was present in the paraventricular, supraoptic, lateral hypothalamic, infundibular, dorsomedial and suprachiasmatic nuclei of the hypothalamus, in the basal ganglia, and in the nucleus basalis of Meynert. A similar staining distribution was noted for the βB subunit, betaglycan and the type II receptor antibodies, whereas α subunit staining was not detected in any of the major anatomical regions of the human brain. Inhibin B immunoreactivity was present in all tissues, whereas inhibin A levels were below detectable limits. These studies show for the first time that the inhibin/activin protein subunits and receptors can be co‐localised in the human brain, implicating potential, diverse neural functions.
An exploration of the experience of mental health service users when they decide they would like to change or withdraw from prescribed medications
Authors: GALE C. , BALDWIN L. , STAPLES V. , MONTAGUE J. , WALDRAM D.
Published: February 2012

Accessible summary

This study reports on a small collaborative research project started by service users, and on a subject chosen by them, and then carried out with staff from a local NHS Trust and University.

It looks at the choices people make in changing or stopping mental health medications, and their experiences of how professional staffs were either helpful or unhelpful in advising and helping them with these choices. Some of the themes generated in the focus groups are examined in detail and recommendations made for practice including the need for better information giving to support choice.

The themes examined include ‘the two faces of service provision’ which looks at positive and less positive experiences of service provision, the general practice/mental health divide which points out differences and difficulties between general practice and specialist practice, and ‘becoming an informed service user’ which examines the many sources of information available to service users and how they use these.

This paper reports on a collaborative research project initiated by service user representatives and led by clinicians from the mental health service in Derbyshire. The study explored the experiences of mental health service users when they either changed or terminated their use of mental health‐related medications. Three focus groups were conducted with mental health service users from across the county. An inductive thematic analysis identified six key themes, three of which are reported here: the ‘two faces’ of service provision, describing the positive and negative experiences of services; the general practice/mental health divide, relating to the lack of continuity between the two services; and becoming an informed service user, where participants discussed the importance of seeking information. It is important that mental health professionals always consider presenting their ‘best face’ to service users, and facilitate the prescribing process with general practitioners. The findings also highlight the potential for supporting service users in using different sources of information to become more informed about medication.
Psychosocial and cultural correlates of depression among Hispanic men with HIV infection: a pilot study
Authors: DE SANTIS J.P. , GONZALEZ‐GUARDA R. M. , VASQUEZ E. P.
Published: February 2012

Accessible summary

Depression is a common mental health condition among people living with HIV infection.

About one third of the study's participants were depressed.

A history of substance abuse and child/adult violence was common among the participants.

Healthcare providers need awareness of the intersection of HIV, substance abuse, and violence among Hispanic men with HIV infection.

Depression is a common mental health condition among persons with human immunodeficiency virus (HIV) infection. Depression influences quality of life, social relationships and adherence to medication therapy. Little is known about depression among Hispanic men with HIV infection. The purpose of this pilot study was to describe the relationships of depression to other psychosocial factors (self‐esteem, Hispanic stress, substance abuse and violence) and cultural factors (familism and Hispanic stress) among a sample of Hispanic men with HIV infection. Using a cross‐sectional, descriptive research design a convenience sample of 46 Hispanic men with HIV infection was recruited and surveyed from the South Florida area of the USA. The majority of the participants (65%; n = 30) were depressed. In addition, the majority of participants reported high familism and self‐esteem and low Hispanic stress. A history of substance abuse and childhood and adult violence were common. Significant relationships were noted between depression, and self‐esteem, Hispanic stress, substance abuse, and adult physical violence. Healthcare providers need to be aware of the high rates of depression, substance abuse and violence that may occur among Hispanic men with HIV infection. More research is needed to further explore the relationship of these factors, as well as to determine the impact that these variables have on adherence to medication therapy among Hispanic men with HIV infection.
An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR
Authors: Yin Wen‐Bing , Amaike Saori , Wohlbach Dana J. , Gasch Audrey P. , Chiang Yi‐Ming , Wang Clay C. C. , Bok Jin Woo , Rohlfs Marko , Keller Nancy P.
Published: January 2012

The eukaryotic bZIP transcription factors are critical players in organismal response to environmental challenges. In fungi, the production of secondary metabolites (SMs) is hypothesized as one of the responses to environmental insults, e.g. attack by fungivorous insects, yet little data to support this hypothesis exists. Here we establish a mechanism of bZIP regulation of SMs through RsmA, a recently discovered YAP‐like bZIP protein. RsmA greatly increases SM production by binding to two sites in the Aspergillus nidulans AflR promoter region, a C6 transcription factor known for activating production of the carcinogenic and anti‐predation SM, sterigmatocystin. Deletion of aflR in an overexpression rsmA (OE:rsmA) background not only eliminates sterigmatocystin production but also significantly reduces asperthecin synthesis. Furthermore, the fungivore, Folsomia candida, exhibited a distinct preference for feeding on wild type rather than an OE:rsmA strain. RsmA may thus have a critical function in mediating direct chemical resistance against predation. Taken together, these results suggest RsmA represents a bZIP pathway hardwired for defensive SM production.
Comparative analysis of phase III migrating motor complexes in stomach and small bowel using wireless motility capsule and antroduodenal manometry
Authors: Brun R. , Michalek W. , Surjanhata B. C. , Parkman H. P. , Semler J. R. , Kuo B.
Published: February 2012

Background  Assessment of phase III MMC is often not performed due to the invasive nature of antroduodenal manometry used to detect it. The aim of the study was to evaluate the ability of wireless motility capsule (WMC) to detect phase III MMC and correlate it with the simultaneous measurements by antroduodenal manometry (ADM).

Methods  Eighteen patients underwent simultaneous ADM and WMC. MMCs were identified first on ADM and then correlated with WMC events occurring simultaneously. Frequency of contractions per min, AUC, MI, and criteria for amplitude thresholds of contractions representing MCCs on WMC tracings were defined.

Key Results  In 18 patients, a total of 29 MMCs were recorded by ADM. WMC detected 86% of MMC events measured by ADM. Hundred percent (10/10) of MMCs in stomach were detected by WMC, whereas 79% (15/19) of MMCs were detected in SB. The sensitivity and specificity of WMC high amplitude contractions to represent phase III MMC were 90% and 71.8% in the stomach; 73.7% and 84.7% in SB, respectively, and negative predictive value was 99.9% in both regions.

Conclusions & Inferences  Wireless motility capsule was able to detect the phase III MMCs as the high amplitude contractions with good fidelity. WMC does not detect the propagation of MMC. Using the pressure thresholds, WMC can detect high amplitude contraction representing phase III MMC with favorable sensitivity/specificity profile and 99.9% negative predictive value. This observation may have clinical significance, as the absence of high amplitude contractions recorded by WMC during fasting state suggests absence of MMCs.
Short‐term electrical stimulation of the lower esophageal sphincter increases sphincter pressure in patients with gastroesophageal reflux disease
Authors: Rodríguez L. , Rodríguez P. , Neto M. G. , Ayala J. C. , Saba J. , Berel D. , Conklin J. , Soffer E.
Published: February 2012

Background  Electrical stimulation (ES) of the lower esophageal sphincter (LES) increases resting LES pressure (LESP) in animal models. Our aims were to evaluate the safety of such stimulation in humans, and test the hypothesis that ES increases resting LESP in patients with gastroesophageal reflux disease (GERD).

Methods  A total of 10 subjects (nine female patients, mean age 52.6 years), with symptoms of GERD responsive to PPIs, low resting LES pressure, and abnormal 24‐h intraesophageal pH test were enrolled. Those with hiatal hernia >2 cm and/or esophagitis >Los Angeles Grade B were excluded. Bipolar stitch electrodes were placed longitudinally in the LES during an elective laparoscopic cholecystectomy, secured by a clip and exteriorized through the abdominal wall. Following recovery, an external pulse generator delivered two types of stimulation for periods of 30 min: (i) low energy stimulation; pulse width of 200 μs, frequency of 20 Hz and current of 5–15 mA (current was increased up to 15 mA if LESP was less than 15 mmHg), and (ii) high energy stimulation; pulse width of 375 ms, frequency of 6 cpm, and current 5 mA. Resting LESP, amplitude of esophageal contractions and residual LESP in response to swallows were assessed before and after stimulation. Symptoms of chest pain, abdominal pain, and dysphagia were recorded before, during, and after stimulation and 7‐days after stimulation. Continuous cardiac monitoring was performed during and after stimulation.

Key Results  All patients were successfully implanted nine subjects received high frequency, low energy, and four subjects received low frequency, high energy stimulation. Both types of stimulation significantly increased resting LESP: from 8.6 mmHg (95% CI 4.1–13.1) to 16.6 mmHg (95% CI 10.8–19.2), P < 0.001 with low energy stimulation and from 9.2 mmHg (95% CI 2.0–16.3) to 16.5 mmHg (95% CI 2.7–30.1), P = 0.03 with high energy stimulation. Neither type of stimulation affected the amplitude of esophageal peristalsis or residual LESP. No subject complained of dysphagia. One subject had retrosternal discomfort with stimulation at15 mA that was not experienced with stimulation at 13 mA. There were no adverse events or any cardiac rhythm abnormalities with either type of stimulation.

Conclusions & Inferences  Short‐term stimulation of the LES in patients with GERD significantly increases resting LESP without affecting esophageal peristalsis or LES relaxation. Electrical stimulation of the LES may offer a novel therapy for patients with GERD.
Low mortality risk but high loss to follow‐up among patients in the Tanzanian national HIV care and treatment programme
Authors: Somi G. , Keogh S. C. , Todd J. , Kilama B. , Wringe A. , van den Hombergh J. , Malima K. , Josiah R. , Urassa M. , Swai R. , Zaba B.
Published: February 2012

Objective  To analyse survival and retention rates of the Tanzanian care and treatment programme.

Methods  Routine patient‐level data were available from 101 of 909 clinics. Kaplan–Meier probabilities of mortality and attrition after ART initiation were calculated. Mortality risks were corrected for biases from loss to follow‐up using Egger’s nomogram. Smoothed hazard rates showed mortality and attrition peaks. Cox regression identified factors associated with death and attrition. Median CD4 counts were calculated at 6 month intervals.

Results  In 88,875 adults, 18% were lost to follow up 12 months after treatment initiation, and 36% after 36 months. Cumulative mortality reached 10% by 12 months (15% after correcting for loss to follow‐up) and 14% by 36 months. Mortality and attrition rates both peaked within the first six months, and were higher among males, those under 45 kg and those with CD4 counts below 50 cells/μl at ART initiation. In the first year on ART, median CD4 count increased by 126 cells/μl, with similar changes in both sexes.

Conclusion  Earlier diagnoses through expanded HIV testing may reduce high mortality and attrition rates if combined with better patient tracing systems. Further research is needed to explore reasons for attrition.
Integrating genomic and epigenomic information: a promising strategy for identifying functional DNA variants of human disease
Authors: Zaina S , Lund G
Published: February 2012

Zaina S, Lund G. Integrating genomic and epigenomic information: a promising strategy for identifying functional DNA variants of human disease.

In a clinical setting diagnosis, heritability, risk and outcome of human disease rely heavily on the use of markers present in specific tissues. In the past decade, the development of genome‐wide, non‐hypothesis driven methods to identify molecular markers associated with disease have led to the discovery of numerous genetic variations associated with specific human diseases, the majority of which map within non‐coding regions of the genome. In parallel, whole‐genome studies focused on the role of gene regulatory epigenetic modifications such as DNA methylation and histone modifications are providing a conceptual framework for understanding the functional significance of sequence variation in human disease. This review highlights selected recent development in epigenetics and discusses their implications with respect to the identification of functional or novel single nucleotide polymorphisms.
Rapid evolution of body fluid regulation following independent invasions into freshwater habitats
Authors: LEE CAROL EUNMI , POSAVI MARIJAN , CHARMANTIER GUY
Published: February 2012

Colonizations from marine to freshwater environments constitute among the most dramatic evolutionary transitions in the history of life. Colonizing dilute environments poses great challenges for acquiring essential ions against steep concentration gradients. This study explored the evolution of body fluid regulation following freshwater invasions by the copepod Eurytemora affinis. The goals of this study were to determine (1) whether invasions from saline to freshwater habitats were accompanied by evolutionary shifts in body fluid regulation (hemolymph osmolality) and (2) whether parallel shifts occurred during independent invasions. We measured hemolymph osmolality for ancestral saline and freshwater invading populations reared across a range of common‐garden salinities (0.2–25 PSU). Our results revealed the evolution of increased hemolymph osmolality (by 16–31%) at lower salinities in freshwater populations of E. affinis relative to their saline ancestors. Moreover, we observed the same evolutionary shifts across two independent freshwater invasions. Such increases in hemolymph osmolality are consistent with evidence of increased ion uptake in freshwater populations at low salinity, found in a previous study, and are likely to entail increased energetic costs upon invading freshwater habitats. Our findings are consistent with the evolution of increased physiological regulation accompanying transitions into stressful environments.
Shoot Proliferation and Leaf Malformation of Celosia argentea and Celosia spicata Caused by a Phytoplasma of the 16SrIII‐J Group
Authors: Eckstein Bárbara , Gonçalves Da Silva Eliane , Paulo Bedendo Ivan
Published: February 2012

Ornamental plants of Celosia argentea L. and Celosia spicata L. displaying typical phytoplasma‐induced symptoms were observed in Piracicaba, State of São Paulo, south‐eastern Brazil. Our aim was to identify the possible phytoplasma involved. PCR revealed the association of phytoplasma with diseased plants of both species. Based on actual and virtual RFLP analysis and phylogenetic analysis, the phytoplasma was characterized as a member of the 16SrIII‐J subgroup. Transmission of the pathogen by dodder supported the evidence that the symptoms observed in naturally diseased plants were induced by a phytoplasma. Our results show that C. spicata is a new host for phytoplasma and that this is the first report of a 16SrXIII‐J phytoplasma infecting plants of C. argentea and C. spicata in Brazil.
New look at antiplatelet agent‐related peptic ulcer: An update of prevention and treatment
Authors: Hsu Ping‐I
Published: January 2012

Patients taking antiplatelet agents for the prevention of cardiovascular diseases who develop gastrointestinal bleeding represent a serious challenge in clinical practice. The initial step in reducing gastrointestinal risk of antiplatelet therapy is to assess whether the patient has a continued need for antiplatelet therapy. The next step is to eliminate the risk factors that may place the patient at increased gastrointestinal risk. In the management of bleeding ulcer patients with high‐risk stigmata of recent hemorrhage, resuming antiplatelet agents at 3–5 days after the last dosing is a reasonable strategy. However, patients with low‐risk stigmata can keep taking antiplatelet agents immediately following endoscopy. In the management of aspirin‐related uncomplicated peptic ulcers in patients requiring antiplatelet therapies, continuing aspirin plus a powerful proton pump inhibitor is the choice of treatment. Patients who require antiplatelet agents for the prevention of cardiovascular diseases should be tested and treated for Helicobacter pylori infection before starting antiplatelet therapy. Additionally, those with high risks for upper gastrointestinal bleeding should receive co‐therapy with a gastroprotective drug, preferably a proton pump inhibitor at standard dose. H2‐receptor antagonist can significantly reduce upper gastrointestinal bleeding risk in patients taking low‐dose aspirin but it is ineffective in the prevention of upper gastrointestinal bleeding in clopidogrel users. Although several retrospective studies reported that patients prescribed clopidogrel who also took proton pump inhibitors had significant increases in cardiovascular events, the current evidence from a prospective randomized trial does not justify a conclusion that proton pump inhibitors are associated with cardiovascular events among clopidgrel users.
Increased 25‐hydroxycholesterol concentrations in the lungs of patients with chronic obstructive pulmonary disease
Authors: SUGIURA HISATOSHI , KOARAI AKIRA , ICHIKAWA TOMOHIRO , MINAKATA YOSHIAKI , MATSUNAGA KAZUTO , HIRANO TSUNAHIKO , AKAMATSU KEIICHIRO , YANAGISAWA SATORU , FURUSAWA MAKOTO , UNO YUMIKO , YAMASAKI MASASHI , SATOMI YOSHINORI , ICHINOSE MASAKAZU
Published: February 2012

Background and objective:  25‐Hydroxycholesterol (25‐HC) is produced from cholesterol by the enzyme cholesterol 25‐hydroxylase and is associated with atherosclerosis of vessels. Recently, 25‐HC was reported to cause inflammation in various types of tissues. The aim of this study was to assess the production of 25‐HC in the airways and to elucidate the role of 25‐HC in neutrophil infiltration in the airways of patients with chronic obstructive pulmonary disease (COPD).

Methods:  Eleven control never‐smokers, six control ex‐smokers without COPD and 13 COPD patients participated in the lung tissue study. The expression of cholesterol 25‐hydroxylase in the lung was investigated. Twelve control subjects and 17 patients with COPD also participated in the sputum study. The concentrations of 25‐HC in sputum were quantified by liquid chromatography/mass spectrometry/mass spectrometry analysis. To elucidate the role of 25‐HC in neutrophilic inflammation of the airways, the correlation between 25‐HC levels and neutrophil counts in sputum was investigated.

Results:  The expression of cholesterol 25‐hydroxylase was significantly enhanced in lung tissue from COPD patients compared with that from control subjects. Cholesterol 25‐hydroxylase was localized in alveolar macrophages and pneumocytes of COPD patients. The concentration of 25‐HC in sputum was significantly increased in COPD patients and was inversely correlated with percent of predicted forced vital capacity, forced expiratory volume in 1 s and diffusing capacity of carbon monoxide. The concentrations of 25‐HC in sputum were significantly correlated with sputum interleukin‐8 levels and neutrophil counts.

Conclusions:  25‐HC production was enhanced in the airways of COPD patients and may play a role in neutrophilic inflammation.
Publishing: art or science? Reflections from an editorial perspective
Authors: Clarkson Peter M.
Published: February 2012

This essay conveys insights into the ‘journal process’ gained through my experiences serving in an editorial capacity. Here, three basic messages emerge. First, if a study is to be successful, it must address an interesting and important topic and then investigate it in a rigorous, scientific and robust manner. Second, the study must be communicated in a sufficiently transparent and accessible fashion so that the gatekeepers can critically evaluate the work, and ultimately so that it influences the readers of the journal. Finally, authors are strongly advised to subject their work to external scrutiny before submitting it for peer review, by exposing it to colleagues and/or by presenting it in public forum such as conferences or workshop seminars.
Transcriptional programs regulating seed dormancy and its release by after‐ripening in common wheat (Triticum aestivum L.)
Authors: Gao Feng , Jordan Mark C. , Ayele Belay T.
Published: February 2012

Seed dormancy is an important agronomic trait in wheat (Trticum aestivum). Seeds can be released from a physiologically dormant state by after‐ripening. To understand the molecular mechanisms underlying the role of after‐ripening in conferring developmental switches from dormancy to germination in wheat seeds, we performed comparative transcriptomic analyses between dormant (D) and after‐ripened (AR) seeds in both dry and imbibed states. Transcriptional activation of genes represented by a core of 22 and 435 probesets was evident in the dry and imbibed states of D seeds, respectively. Furthermore, two‐way ANOVA analysis identified 36 probesets as specifically regulated by dormancy. These data suggest that biological functions associated with these genes are involved in the maintenance of seed dormancy. Expression of genes encoding protein synthesis/activity inhibitors was significantly repressed during after‐ripening, leading to dormancy decay. Imbibing AR seeds led to transcriptional activation of distinct biological processes, including those related to DNA replication, nitrogen metabolism, cytoplasmic membrane‐bound vesicle, jasmonate biosynthesis and cell wall modification. These after‐ripening‐mediated transcriptional programs appear to be regulated by epigenetic mechanisms. Clustering of our microarray data produced 16 gene clusters; dormancy‐specific probesets and abscisic acid (ABA)‐responsive elements were significantly overrepresented in two clusters, indicating the linkage of dormancy in wheat with that of seed sensitivity to ABA. The role of ABA signalling in regulating wheat seed dormancy was further supported by the down‐regulation of ABA response‐related probesets in AR seeds and absence of differential expression of ABA metabolic genes between D and AR seeds.
Models and simulations in material science: two cases without error bars
Authors: Wenmackers Sylvia , Vanpoucke Danny E. P.
Published: February 2012

We discuss two research projects in material science in which the results cannot be stated with an estimation of the error: a spectroscopic ellipsometry study aimed at determining the orientation of DNA molecules on diamond and a scanning tunneling microscopy study of platinum‐induced nanowires on germanium. To investigate the reliability of the results, we apply ideas from the philosophy of models in science. Even if the studies had reported an error value, the trustworthiness of the result would not depend on that value alone.
Model choice using reversible jump Markov chain Monte Carlo
Authors: Hastie David I. , Green Peter J.
Published: February 2012

We review the across‐model simulation approach to computation for Bayesian model determination, based on the reversible jump Markov chain Monte Carlo method. Advantages, difficulties and variations of the methods are discussed. We also discuss some limitations of the ideal Bayesian view of the model determination problem, for which no computational methods can provide a cure.
Estimation and testing of crossing‐points in fixed design regression
Authors: Ferger Dietmar , Klotsche Jens , Lüken Ulrike
Published: February 2012

Many phenomena in the life sciences can be analyzed by using a fixed design regression model with a regression function m that exhibits a crossing‐point in the following sense: the regression function runs below or above its mean level, respectively, according as the input variable lies to the left or to the right of that crossing‐point, or vice versa. We propose a non‐parametric estimator and show weak and strong consistency as long as the crossing‐point is unique. It is defined as maximizing point arg max of a certain marked empirical process. For testing the hypothesis H0 that the regression function m actually is constant (no crossing‐point), a decision rule is designed for the specific alternative H1 that m possesses a crossing‐point. The pertaining test‐statistic is the ratio max/argmax of the maximum value and the maximizing point of the marked empirical process. Under the hypothesis the ratio converges in distribution to the corresponding ratio of a reflected Brownian bridge, for which we derive the distribution function. The test is consistent on the whole alternative and superior to the corresponding Kolmogorov–Smirnov test, which is based only on the maximal value max. Some practical examples of possible applications are given where a certain study about dental phobia is discussed in more detail.
Team creativity: the effects of perceived learning culture, developmental feedback and team cohesion
Authors: Joo Baek‐Kyoo (Brian) , Song Ji Hoon , Lim Doo Hun , Yoon Seung Won
Published: February 2012

This study investigates the influence of perceived learning culture, developmental feedback and team cohesion on team creativity. The results showed that the demographic variables, the three antecedents and their interactions explained 41 per cent of variance in team creativity. Team creativity was positively correlated with a higher level of learning culture, developmental feedback and team cohesion. In addition to the main effects, two interaction effects (developmental feedback and team cohesion; learning culture and team cohesion) were significant. In view of these results, organizations seeking to increase team creativity need an integrated strategy incorporating elements of culture management, effective coaching and team development. Implications, limitations and recommendations for future research are discussed.