bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing Climate Change: Temperatures, Solar Radiation and Heat Balance
Authors: Geller Marvin
Published: August 2008

The science of climate change is being investigated by thousands of scientists, is constantly in the news, and is discussed in the political arena worldwide. My Internet search on the words “climate change” produced about 40,600,000 hits. The 2007 Nobel Peace Prize was awarded to former U.S. vice president Al Gore and the United Nations' Intergovernmental Panel on Climate Change (IPCC). Of course, the subject goes beyond the science. The debate on what, if anything, should be done about humankind's influence on climate is the subject of U.S. and international political debate.
Hotspotting: Principles and properties of a plate tectonic Hough transform
Authors: Wessel Paul
Published: August 2008

“Hotspotting” is a geometric technique used to assess the self‐consistency of absolute plate motion models under the assumption of fixed hot spots. Geometric data constraints (typically seamount locations) and the plate motion model are used to determine the optimal locations of hot spots; in a self‐consistent model these should match the assigned hot spot locations. While self‐consistency is a desirable model attribute, it is not sufficient by itself to guarantee a geologically meaningful model. Hotspotting is the study of seafloor flow lines and may be considered a pattern recognition algorithm similar to the Hough transform. Flow line analysis can yield insight into the importance of particular geometric constraints and yield age predictions for undated features. Hotspotting cannot easily be used to derive improved rotation parameters but instead is used in concert with methods that determine plate motions to ensure the aforementioned self‐consistency.
Channeling at the base of the lithosphere during the lateral flow of plume material beneath flow line hot spots
Authors: Sleep Norman H.
Published: August 2008

Chains of volcanic edifices lie along flow lines between plume‐fed hot spots and the thin lithosphere at ridge axes. Discovery and Euterpe/Musicians Seamounts are two examples. An attractive hypothesis is that buoyant plume material flows along the base of the lithosphere perpendicular to isochrons. The plume material may conceivably flow in a broad front or flow within channels convectively eroded into the base to the lithosphere. A necessary but not sufficient condition for convective channeling is that the expected stagnant‐lid heat flow for the maximum temperature of the plume material is comparable to the half‐space surface heat flow of the oceanic lithosphere. Two‐dimensional and three‐dimensional numerical calculations confirm this inference. A second criterion for significant convective erosion is that it needs to occur before the plume material thins by lateral spreading. Scaling relationships indicate spreading and convection are closely related. Mathematically, the Nusselt number (ratio of convective to conductive heat flow in the plume material) scales with the flux (volume per time per length of flow front) of the plume material. A blob of unconfined plume material thus spreads before the lithosphere thins much and evolves to a slowly spreading and slowly convecting warm region in equilibrium with conduction into the base of the overlying lithosphere. Three‐dimensional calculations illustrate this long‐lasting (and hence observable) state of plume material away from its plume source. A different flow domain occurs around a stationary hot plume that continuously supplies hot material. The plume convectively erodes the overlying lithosphere, trapping the plume material near its orifice. The region of lithosphere underlain by plume material grows toward the ridge axis and laterally by convective thinning of the lithosphere at its edges. The hottest plume material channels along flow lines. Geologically, the regions of lithosphere underlain by either warm or hot plume material are likely to extend laterally away from the volcanic edifices whether or not channeling occurs.
North Atlantic weather regimes response to Indian‐western Pacific Ocean warming: A multi‐model study
Authors: SanchezGomez E. , Cassou C. , Hodson D. L. R. , Keenlyside N. , Okumura Y. , Zhou T.
Published: August 2008

The extratropical large‐scale atmospheric circulation is often described in terms of a few preferred and recurrent patterns referred to as weather regimes. Here, we investigate the influence of the observed Indian and western Pacific Ocean (IP) warming over the last decades, on the frequency of occurrence of North Atlantic weather regimes. A multi‐model approach is adopted in which five different atmospheric general circulation models are forced with idealized sea surface temperature patterns mimicking the IP warming. Despite some discrepancies, three models suggest a stronger occurrence of the Zonal regime when IP is warm, compensated by less frequent Greenland Anticyclone regimes, consistently with the observed positive trend of the North Atlantic Oscillation. The other two models simulate instead an increase in the frequency of occurrence of the Atlantic Ridge regime. Variance decomposition into stationary and transient waves suggest two mechanisms at work in the individual models. The AR regime favoured occurrence is associated with a strong transient wave activity along the wave guide in the North Pacific and downstream in the North Atlantic. The Zonal favoured excitation is interpreted as an indirect response to changes in the Tropical Atlantic associated with a global alteration of the Walker cell.
Long‐term trends in sunshine duration over Yunnan‐Guizhou Plateau in Southwest China for 1961–2005
Authors: Zheng Xiaobo , Kang Weimin , Zhao Tianliang , Luo Yuxiang , Duan Changchun , Chen Juan
Published: August 2008

Yunnan‐Guizhou Plateau (YGP), a low latitude highland region, covers the two provinces of Yunnan and Guizhou in Southwest China, where a cooling trend in the annual mean surface air temperature since the mid‐20th century was reported as a notable phenomenon of regional climate against the global warming. In this study on the regional climate, we applied the data of sunshine duration and cloud amount from 184 stations across the YGP from year 1961 to 2005. It was found that, over this 45 year period, annual sunshine duration decreased mostly north of 24°N on the YGP with the negative trends reaching −11.8% per decade, while during the same period it increased with the positive trends reaching +3.5% per decade at the stations concentrated on the southwestern YGP. An overall decline in annual sunshine duration over the northern YGP dramatically accelerated from the 1970s to 80s with its maximum rate in the 1980s, but has remarkably decelerated since the 1990s so that going into the 21st century the annual sunshine duration has ceased or even reversed its downward tendency. The evolution of annual mean cloud amount on the YGP was shown to be insignificant and even in decline over the 45 years, exerting less of an influence on the decreasing trends in the annual sunshine duration. The consistent patterns of sunshine duration trends and surface temperature changes on the YGP support the hypothesis that aerosol loading in the atmosphere could be involved in the surface cooling trend.
Intra‐seasonal atmospheric variability and extreme precipitation events in the European‐Mediterranean region
Authors: Sanchez‐Gomez E. , Terray L. , Joly B.
Published: August 2008

The low frequency atmospheric variability over the European‐Mediterranean region is described by the weather regimes, obtained by using a clustering algorithm applied on the September‐December geopotential height at 500 hPa. Links between the European‐Mediterranean weather regimes and extremes of precipitation over Europe are examined. We focus on the autumn season, when heavy precipitation episodes are likely to occur over the Mediterranean coasts. In the second part of this paper, we study whether the European‐Mediterranean weather regimes can be related to the phases of some intra‐seasonal atmospheric oscillation. By using the Multi‐Channel Singular Spectrum Analysis (MSSA), we identify a 50‐day oscillation over the European‐Mediterranean region. The phases of this oscillation are found to be consistent with the preferred weather regimes transitions. This could influence intra‐seasonal predictability and suggests that links between the episodic (weather regimes) and oscillatory (intra‐seasonal oscillations) approaches may also apply to the regional scale.
Foliar uptake of atmospheric organic nitrates
Authors: Lockwood Amanda L. , Filley Timothy R. , Rhodes David , Shepson Paul B.
Published: August 2008

Increasing nitrogen deposition to forests can impact the balance between the carbon and nitrogen cycles. This nitrogen source, if taken up and used by forests, can increase growth and carbon storage. While previous findings have suggested that nitrogen deposition is not an important source of nitrogen for a forest ecosystem, the possibility of canopy uptake was not considered. Foliar uptake and utilization of inorganic nitrogen, such as NO2 and NH3, has been shown to occur, but utilization of organic nitrogen has not been demonstrated directly. Here we show for the first time that atmospheric organic nitrates (RONO2), one form of organic nitrogen, can be taken up by foliage and incorporated into the leaf amino acids, and we discuss possible uptake mechanisms.
A 6‐year AMSU‐based climatology of upper‐level troughs and associated precipitation distribution in the Mediterranean region
Authors: Funatsu B. M. , Claud C. , Chaboureau J.‐P.
Published: August 2008

We present a novel climatology of upper‐tropospheric troughs and associated precipitation in the Mediterranean region, using 6 years (2001–2006) of Advanced Microwave Sounding Unit data. Troughs are more frequent or persistent during November through March in the whole of the Mediterranean basin, with up to 25% of days in the northwestern part of the basin. The interannual variability of number of intrusions is stronger from September through June. During summer, the variability is reduced, except in the NW region, and no troughs were observed in the SE region. Moderate precipitation occurs in at least 60% of the cases when an upper‐level trough is present with weak seasonal dependency. In the southern Mediterranean moderate precipitation is an ubiquitous feature and presents small year‐to‐year fluctuations. The occurrence of deep convective rain associated with trough is lower, around 50%, and reduces to 20% in the northern part of the basin during winter. This occurrence varies a lot with individual years, especially in the southern Mediterranean. Upper‐level troughs have more often a N–S orientation but, while no particular dependency of frequency of precipitation (whether moderate or convective) on their inclination was found, the location of precipitation is generally favored downstream. The North Atlantic Oscillation and Scandinavia patterns were found to be the most important large‐scale circulation modes influencing the variability of number of intrusions, but the East Atlantic/West Russia and East Atlantic patterns are also important in the southeast region.
Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation
Authors: Kolev Nikolay G , Yario Therese A , Benson Eleni , Steitz Joan A
Published: August 2008

In eukaryotes, the process of messenger RNA 3′‐end formation involves endonucleolytic cleavage of the transcript followed by synthesis of the poly(A) tail. The complex machinery involved in this maturation process contains two proteins of the metallo‐β‐lactamase (MBL) superfamily, the 73 and 100 kDa subunits of the cleavage and polyadenylation specificity factor (CPSF). By using anin vitrosystem to assess point mutations in these two mammalian proteins, we found that conserved residues from the MBL motifs of both polypeptides are required for assembly of the endonuclease activity that cleaves histone pre‐mRNAs. This indicates that CPSF73 and CPSF100 act together in the process of maturation of eukaryotic pre‐messenger RNAs, similar to other members of the MBL family, RNases Z and J, which function as homodimers.
AMP hydrolysis in soluble and microsomal rat cardiac cell fractions: kinetic characterization and molecular identification of 5′-nucleotidase
Authors: Pochmann Daniela , Innocente Adrine M. , Cotomacci Guilherme , Barreto-Chaves Maria Luiza M. , Sarkis João J. F.
Published: August 2008

The present study describes the enzymatic properties and molecular identification of 5′-nucleotidase in soluble and microsomal fractions from rat cardiac ventricles. Using AMP as a substrate, the results showed that the cation and the concentration required for maximal activity in the two fractions was magnesium at a final concentration of 1 mM. The pH optimum for both fractions was 9.5. The apparent Km (Michaelis constant) values calculated from the Eadie–Hofstee plot were 59.7±10.4 μM and 134.8±32.1 μM, with Vmax values of 6.7±0.4 and 143.8±23.8 nmol Pi/min/mg of protein (means±S.D., n=4) from soluble and microsomal fractions respectively. Western blotting analysis of ecto-5′-nucleotidase revealed a 70 kDa protein in both fractions, with the major proportion present in the microsomal fraction. The presence of these enzymes in the heart probably has a physiological function in adenosine signalling. Furthermore, the presence of ecto-5′-nucleotidase in the microsomal fraction could have a role in the modulation of the excitation–contraction-coupling process through involvement of the Ca2+ influx into the sarcoplasmic reticulum. The measurement of maximal enzyme activities in the two fractions highlights the potential capacity of the different pathways of purine metabolism in the heart.
Yeast linker histone Hho1p is required for efficient RNA polymerase I processivity and transcriptional silencing at the ribosomal DNA
Authors: Levy Anat , Eyal Miri , Hershkovits Gitit , Salmon-Divon Mali , Klutstein Michael , Katcoff Don Jay
Published: August 2008

Nucleosome core particles in eukaryotes are linked by a stretch of DNA that is usually associated with a linker histone. Here, we show in yeast, that the presence of yeast linker histone Hho1p represses expression of a pol II transcribed gene (
MET15
) embedded in the rDNA.
In vivo
deletions of Hho1p sequences showed that the second globular domain is sufficient for that repression, whereas the presence of the N terminus is required for its derepression. In contrast, a run-on assay confirmed by a ChIP experiment showed that Hho1p is required for maximal pol I processivity during rDNA transcription. Psoralen accessibility experiments indicated that Hho1p is necessary for normal rDNA compaction. DNA array expression analysis comparing RNA transcripts in wild-type and
hho1
strains before and after a heat-shock showed that Hho1p is necessary to achieve wild-type mRNA levels of transcripts that encode ribosomal components. Taken together, our results suggest that Hho1p is involved in rDNA compaction, and like core histones, is required for efficient rDNA transcription by pol I.
Probing the resonance potential in the F atom reaction with hydrogen deuteride with spectroscopic accuracy
Authors: Ren Zefeng , Che Li , Qiu Minghui , Wang Xingan , Dong Wenrui , Dai Dongxu , Wang Xiuyan , Yang Xueming , Sun Zhigang , Fu Bina , Lee Soo-Y. , Xu Xin , Zhang Dong H.
Published: August 2008

Reaction resonances are transiently trapped quantum states along the reaction coordinate in the transition state region of a chemical reaction that could have profound effects on the dynamics of the reaction. Obtaining an accurate reaction potential that holds these reaction resonance states and eventually modeling quantitatively the reaction resonance dynamics is still a great challenge. Up to now, the only viable way to obtain a resonance potential is through high-level
ab initio
calculations. Through highly accurate crossed-beam reactive scattering studies on isotope-substituted reactions, the accuracy of the resonance potential could be rigorously tested. Here we report a combined experimental and theoretical study on the resonance-mediated F + HD → HF + D reaction at the full quantum state resolved level, to probe the resonance potential in this benchmark system. The experimental result shows that isotope substitution has a dramatic effect on the resonance picture of this important system. Theoretical analyses suggest that the full-dimensional FH
2
ground potential surface, which was believed to be accurate in describing the resonance picture of the F + H
2
reaction, is found to be insufficiently accurate in predicting quantitatively the resonance picture for the F + HD → HF + D reaction. We constructed a global potential energy surface by using the CCSD(T) method that could predict the correct resonance peak positions as well as the dynamics for both F + H
2
→ HF + H and F + HD → HF + D, providing an accurate resonance potential for this benchmark system with spectroscopic accuracy.
Nanocalorimetry in mass spectrometry: A route to understanding ion and electron solvation
Authors: Donald William A. , Leib Ryan D. , O'Brien Jeremy T. , Holm Anne I. S. , Williams Evan R.
Published: August 2008

A gaseous nanocalorimetry approach is used to investigate effects of hydration and ion identity on the energy resulting from ion–electron recombination. Capture of a thermally generated electron by a hydrated multivalent ion results in either loss of a H atom accompanied by water loss or exclusively loss of water. The energy resulting from electron capture by the precursor is obtained from the extent of water loss. Results for large-size-selected clusters of Co(NH
3
)
6
(H
2
O)

n
3

+
and Cu(H
2
O)

n
2

+
indicate that the ion in the cluster is reduced on electron capture. The trend in the data for Co(NH
3
)
6
(H
2
O)

n
3

+
over the largest sizes (
n
≥ 50) can be fit to that predicted by the Born solvation model. This agreement indicates that the decrease in water loss for these larger clusters is predominantly due to ion solvation that can be accounted for by using a model with bulk properties. In contrast, results for Ca(H
2
O)

n
2

+
indicate that an ion–electron pair is formed when clusters with more than ≈20 water molecules are reduced. For clusters with
n
= ≈20–47, these results suggest that the electron is located near the surface, but a structural transition to a more highly solvated electron is indicated for
n
= 47–62 by the constant recombination energy. These results suggest that an estimate of the adiabatic electron affinity of water could be obtained from measurements of even larger clusters in which an electron is fully solvated.
Laser mass spectrometric detection of extraterrestrial aromatic molecules: Mini-review and examination of pulsed heating effects
Authors: Spencer Maegan K. , Hammond Matthew R. , Zare Richard N.
Published: August 2008

Laser mass spectrometry is a powerful tool for the sensitive, selective, and spatially resolved analysis of organic compounds in extraterrestrial materials. Using microprobe two-step laser mass spectrometry (μL
2
MS), we have explored the organic composition of many different exogenous materials, including meteorites, interplanetary dust particles, and interstellar ice analogs, gaining significant insight into the nature of extraterrestrial materials. Recently, we applied μL
2
MS to analyze the effect of heating caused by hypervelocity particle capture in aerogel, which was used on the NASA Stardust Mission to capture comet particles. We show that this material exhibits complex organic molecules upon sudden heating. Similar pulsed heating of carbonaceous materials is shown to produce an artifactual fullerene signal. We review the use of μL
2
MS to investigate extraterrestrial materials, and we discuss its recent application to characterize the effect of pulsed heating on samples of interest.
Loss of PINK1 causes mitochondrial functional defects and increased sensitivity to oxidative stress
Authors: Gautier Clement A. , Kitada Tohru , Shen Jie
Published: August 2008

Parkinson's disease (PD) is a common neurodegenerative disorder thought to be associated with mitochondrial dysfunction. Loss of function mutations in the putative mitochondrial protein PINK1 (PTEN-induced kinase 1) have been linked to familial forms of PD, but the relation of PINK1 to mammalian mitochondrial function remains unclear. Here, we report that germline deletion of the
PINK1
gene in mice significantly impairs mitochondrial functions. Quantitative electron microscopic studies of the striatum in
PINK1
−/−
mice at 3–4 and 24 months revealed no gross changes in the ultrastructure or the total number of mitochondria, although the number of larger mitochondria is selectively increased. Functional assays showed impaired mitochondrial respiration in the striatum but not in the cerebral cortex at 3–4 months of age, suggesting specificity of this defect for dopaminergic circuitry. Aconitase activity associated with the Krebs cycle is also reduced in the striatum of
PINK1
−/−
mice. Interestingly, mitochondrial respiration activities in the cerebral cortex are decreased in
PINK1
−/−
mice at 2 years compared with control mice, indicating that aging can exacerbate mitochondrial dysfunction in these mice. Furthermore, mitochondrial respiration defects can be induced in the cerebral cortex of
PINK1
−/−
mice by cellular stress, such as exposure to H
2
O
2
or mild heat shock. Together, our findings demonstrate that mammalian PINK1 is important for mitochondrial function and provides critical protection against both intrinsic and environmental stress, suggesting a pathogenic mechanism by which loss of PINK1 may lead to nigrostriatal degeneration in PD.
Roaming is the dominant mechanism for molecular products in acetaldehyde photodissociation
Authors: Heazlewood Brianna R. , Jordan Meredith J. T. , Kable Scott H. , Selby Talitha M. , Osborn David L. , Shepler Benjamin C. , Braams Bastiaan J. , Bowman Joel M.
Published: August 2008

Reaction pathways that bypass the conventional saddle-point transition state (TS) are of considerable interest and importance. An example of such a pathway, termed “roaming,” has been described in the photodissociation of H
2
CO. In a combined experimental and theoretical study, we show that roaming pathways are important in the 308-nm photodissociation of CH
3
CHO to CH
4
+ CO. The CH
4
product is found to have extreme vibrational excitation, with the vibrational distribution peaked at ≈95% of the total available energy. Quasiclassical trajectory calculations on full-dimensional potential energy surfaces reproduce these results and are used to infer that the major route to CH
4
+ CO products is via a roaming pathway where a CH
3
fragment abstracts an H from HCO. The conventional saddle-point TS pathway to CH
4
+ CO formation plays only a minor role. H-atom roaming is also observed, but this is also a minor pathway. The dominance of the CH
3
roaming mechanism is attributed to the fact that the CH
3
+ HCO radical asymptote and the TS saddle-point barrier to CH
4
+ CO are nearly isoenergetic. Roaming dynamics are therefore not restricted to small molecules such as H
2
CO, nor are they limited to H atoms being the roaming fragment. The observed dominance of the roaming mechanism over the conventional TS mechanism presents a significant challenge to current reaction rate theory.
The kinase domain of mitochondrial PINK1 faces the cytoplasm
Authors: Zhou Chun , Huang Yong , Shao Yufang , May Jessica , Prou Delphine , Perier Celine , Dauer William , Schon Eric A. , Przedborski Serge
Published: August 2008

Mutations in PTEN-induced putative kinase 1 (PINK1) are a cause of autosomal recessive familial Parkinson's disease (PD). Efforts in deducing the PINK1 signaling pathway have been hindered by controversy around its subcellular and submitochondrial localization and the authenticity of its reported substrates. We show here that this mitochondrial protein exhibits a topology in which the kinase domain faces the cytoplasm and the N-terminal tail is inside the mitochondria. Although deletion of the transmembrane domain disrupts this topology, common PD-linked PINK1 mutations do not. These results are critical in rectifying the location and orientation of PINK1 in mitochondria, and they should help decipher its normal physiological function and potential pathogenic role in PD.
Direct analysis of cooperativity in multisubunit allosteric proteins
Authors: Zandany Nitzan , Ovadia Maya , Orr Irit , Yifrach Ofer
Published: August 2008

Allosteric regulation of protein function is a fundamental phenomenon of major importance in many cellular processes. Such regulation is often achieved by ligand-induced conformational changes in multimeric proteins that may give rise to cooperativity in protein function. At the heart of allosteric mechanisms offered to account for such phenomenon, involving either concerted or sequential conformational transitions, lie changes in intersubunit interactions along the ligation pathway of the protein. However, structure–function analysis of such homooligomeric proteins by means of mutagenesis, although it provides valuable indirect information regarding (allosteric) mechanisms of action, it does not define the contribution of individual subunits nor interactions thereof to cooperativity in protein function, because any point mutation introduced into homooligomeric proteins will be present in all subunits. Here, we present a general strategy for the direct analysis of cooperativity in multisubunit proteins that combines measurement of the effects on protein function of all possible combinations of mutated subunits with analysis of the hierarchy of intersubunit interactions, assessed by using high-order double-mutant cycle-coupling analysis. We show that the pattern of high-order intersubunit coupling can serve as a discriminative criterion for defining concerted versus sequential conformational transitions underlying protein function. This strategy was applied to the particular case of the voltage-activated potassium channel protein (Kv) to provide compelling evidence for a concerted all-or-none activation gate opening of the Kv channel pore domain. An direct and detailed analysis of the contribution of high-order intersubunit interactions to cooperativity in the function of an allosteric protein has not previously been presented.
Spinocerebellar ataxia type 6 knockin mice develop a progressive neuronal dysfunction with age-dependent accumulation of mutant Ca
V
2.1 channels
Authors: Watase Kei , Barrett Curtis F. , Miyazaki Taisuke , Ishiguro Taro , Ishikawa Kinya , Hu Yuanxin , Unno Toshinori , Sun Yaling , Kasai Sayumi , Watanabe Masahiko , Gomez Christopher M. , Mizusawa Hidehiro , Tsien Richard W. , Zoghbi Huda Y.
Published: August 2008

Spinocerebellar ataxia type 6 (SCA6) is a neurodegenerative disorder caused by CAG repeat expansions within the voltage-gated calcium (Ca
V
) 2.1 channel gene. It remains controversial whether the mutation exerts neurotoxicity by changing the function of Ca
V
2.1 channel or through a gain-of-function mechanism associated with accumulation of the expanded polyglutamine protein. We generated three strains of knockin (KI) mice carrying normal, expanded, or hyperexpanded CAG repeat tracts in the
Cacna1a
locus. The mice expressing hyperexpanded polyglutamine (

Sca6
84Q

) developed progressive motor impairment and aggregation of mutant Ca
V
2.1 channels. Electrophysiological analysis of cerebellar Purkinje cells revealed similar Ca
2+
channel current density among the three KI models. Neither voltage sensitivity of activation nor inactivation was altered in the

Sca6
84Q

neurons, suggesting that expanded CAG repeat
per se
does not affect the intrinsic electrophysiological properties of the channels. The pathogenesis of SCA6 is apparently linked to an age-dependent process accompanied by accumulation of mutant Ca
V
2.1 channels.
A photoactive carotenoid protein acting as light intensity sensor
Authors: Wilson Adjélé , Punginelli Claire , Gall Andrew , Bonetti Cosimo , Alexandre Maxime , Routaboul Jean-Marc , Kerfeld Cheryl A. , van Grondelle Rienk , Robert Bruno , Kennis John T. M. , Kirilovsky Diana
Published: August 2008

Intense sunlight is dangerous for photosynthetic organisms. Cyanobacteria, like plants, protect themselves from light-induced stress by dissipating excess absorbed energy as heat. Recently, it was discovered that a soluble orange carotenoid protein, the OCP, is essential for this photoprotective mechanism. Here we show that the OCP is also a member of the family of photoactive proteins; it is a unique example of a photoactive protein containing a carotenoid as the photoresponsive chromophore. Upon illumination with blue-green light, the OCP undergoes a reversible transformation from its dark stable orange form to a red “active” form. The red form is essential for the induction of the photoprotective mechanism. The illumination induces structural changes affecting both the carotenoid and the protein. Thus, the OCP is a photoactive protein that senses light intensity and triggers photoprotection.
Incidence Density and Relative Risk of Nosocomial Infection in Taiwan's Only Children's Hospital, 1999-2003
Authors: Maa Suh-Hwa , Lee Hsin-Lun , Huang Yhu-Chering , Wu June Hsieh , Tsou Tsung-Shan , MacDonald Karen , Abraham Ivo
Published: August 2008

We report on 2,688 nosocomial infection episodes involving 3,238 pathogens in Taiwan's only children's hospital. The mean annual incidence density was 4.06 cases per 1,000 patient-days. The relative risk was highest in intensive care units, oncology wards, and neonatal observation wards. Very young, low-birth-weight, critically ill, and oncology patients were most at risk.
Surveillance of Healthcare-Acquired Infections in Queensland, Australia: Data and Lessons From the First 5 Years
Authors: Morton Anthony P. , Clements Archie C. A. , Doidge Shane R. , Stackelroth Jenny , Curtis Merrilyn , Whitby Michael
Published: August 2008

Objective.

To present healthcare-acquired infection surveillance data for 2001-2005 in Queensland, Australia.

Design.

Observational prospective cohort study.

Setting.

Twenty-three public hospitals in Queensland.

Methods.

We used computer-assisted surveillance to identify episodes of surgical site infection (SSI) in surgical patients. The risk-adjusted incidence of SSI was calculated by means of a risk-adjustment score modified from that of the US National Nosocomial Infections Surveillance System, and the incidence of inpatient bloodstream infection (BSI) was adjusted for risk on the basis of hospital level (level 1, tertiary referral center; level 2, large general hospital; level 3, small general hospital). Funnel and Bayesian shrinkage plots were used for between-hospital comparisons.

Patients.

A total of 49,804 surgical patients and 4,663 patients who experienced healthcare-associated BSI.

Results.

The overall cumulative incidence of in-hospital SSI ranged from 0.28% (95% confidence interval [CI], 0%–1.54%) for radical mastectomies to 6.15% (95% CI, 3.22%–10.50%) for femoropopliteal bypass procedures. The incidence of inpatient BSI was 0.80,0.28, and 0.22 episodes per 1,000 occupied bed-days in level 1, 2, and 3 hospitals, respectively.Staphylococcus aureuswas the most commonly isolated microorganism for SSI and BSI. Funnel and shrinkage plots showed at least 1 hospital with a signal indicating a possible higher-than-expected rate of S. aureus-associated BSI.

Conclusions.

Comparisons between hospitals should be viewed with caution because of imperfect risk adjustment. It is our view that the data should be used to improve healthcare-acquired infection control practices using evidence-based systems rather than to judge institutions.
Development of Al and Al/Cu (composite/alloy) formulations with enhanced properties through microwave power variations during hybrid sintering
Authors: Kotecha R D , Nai S M L , Gupta M
Published: August 2008

In this study, the microwave power level during sintering was used as a processing variable to develop a metastable Al–Cu composite and an Al–Cu alloy from a common starting Al/Cu formulation. Both materials exhibited a superior combination of properties when compared with conventional Al-based composites. The results clearly revealed that microwaves provide a viable option to sinter pure aluminium and aluminium–copper formulation which is otherwise difficult due to the presence of an adherent and defect free aluminium oxide layer on aluminium powder particles.
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
Authors: Huang Zhibin , Wu Yong , Robertson Joseph , Feng Liang , Malmberg Russell L. , Cai Liming
Published: August 2008

Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph.

Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high specificity, and in a reasonable amount of time.

Availability: The source code in C++ for RNATOPS is available at www.uga.edu/RNA-Informatics/software/rnatops/

Contact:  cai@cs.uga.edu

Supplementary information: The online Supplementary Material contains all illustrative figures and tables referenced by this article.
Peptide Finder: mapping measured molecular masses to peptides and proteins
Authors: Alexandridou Anastasia , Tsangaris George Th. , Vougas Konstantinos , Nikita Konstantina , Spyrou George
Published: August 2008

Summary: The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF.

Availability: Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.

Contact:  gspyrou@bioacademy.gr
A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund
Authors: Wiik Anne Caroline , Wade Claire , Biagi Tara , Ropstad Ernst-Otto , Bjerkås Ellen , Lindblad-Toh Kerstin , Lingaas Frode
Published: August 2008

Cone-rod dystrophy is a retinal degenerative disorder occurring naturally in man and dog. Here we identify a novel gene for early-onset cone-rod dystrophy in the wire-haired dachshund. For the first time, we use genome-wide association-based Sibling Transmission Disequilibrium Test (sibTDT) analysis of only 13 discordant sib-pairs to identify a single significantly associated 6.5-Mb region (PrawTDT = 4.8 × 10−5, PgenomeTDT = 6 × 10−4) on canine chromosome 5, containing more than 70 genes. Segregation studies using microsatellites in the candidate region including additional meiosis supported the sibTDT analysis but could not further reduce the area. Candidate gene resequencing identified a 180-bp deletion in exon/intron 5 of NPHP4 (nephronophthisis 4, also known as nephroretinin). RT-PCR analysis of NPHP4 in cases and controls showed exon skipping of exon 5, resulting in a truncated protein that retains the binding domain interacting with nephronophthisis 1 (also known as nephrocystin-1) in the kidney but lacks the domain interacting with RPGRIP1 in retina. We suggest that this deletion in the canine NPHP4 gene is the cause of cone-rod dystrophy in the standard wire-haired dachshund. In humans, mutations in NPHP4 have been associated with simultaneous eye and kidney disease. Here we describe the first naturally occurring mutation in NPHP4 without additional kidney disease. Further studies will permit elucidation of the complex molecular mechanism of this retinopathy and the development of potential therapies.
A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
Authors: Smith Aileen M. , Sanchez Maria-Jose , Follows George A. , Kinston Sarah , Donaldson Ian J. , Green Anthony R. , Göttgens Berthold
Published: August 2008

Altered cis-regulation is thought to underpin much of metazoan evolution, yet the underlying mechanisms remain largely obscure. The stem cell leukemia TAL1 (also known as SCL) transcription factor is essential for the normal development of blood stem cells and we have previously shown that the Tal1 +19 enhancer directs expression to hematopoietic stem cells, hematopoietic progenitors, and to endothelium. Here we demonstrate that an adjacent region 1 kb upstream (+18 element) is in an open chromatin configuration and carries active histone marks but does not function as an enhancer in transgenic mice. Instead, it boosts activity of the +19 enhancer both in stable transfection assays and during differentiation of embryonic stem (ES) cells carrying single-copy reporter constructs targeted to the Hprt locus. The +18 element contains a mammalian interspersed repeat (MIR) which is essential for the +18 function and which was transposed to the Tal1 locus ∼160 million years ago at the time of the mammalian/marsupial branchpoint. Our data demonstrate a previously unrecognized mechanism whereby enhancer activity is modulated by a transposon exerting a “booster” function which would go undetected by conventional transgenic approaches.
Reduced purifying selection prevails over positive selection in human copy number variant evolution
Authors: Nguyen Duc-Quang , Webber Caleb , Hehir-Kwa Jayne , Pfundt Rolph , Veltman Joris , Ponting Chris P.
Published: August 2008

Copy number variation is a dominant contributor to genomic variation and may frequently underlie an individual’s variable susceptibilities to disease. Here we question our previous proposition that copy number variants (CNVs) are often retained in the human population because of their adaptive benefit. We show that genic biases of CNVs are best explained, not by positive selection, but by reduced efficiency of selection in eliminating deleterious changes from the human population. Of four CNV data sets examined, three exhibit significant increases in protein evolutionary rates. These increases appear to be attributable to the frequent coincidence of CNVs with segmental duplications (SDs) that recombine infrequently. Furthermore, human orthologs of mouse genes, which, when disrupted, result in pre- or postnatal lethality, are unusually depleted in CNVs. Together, these findings support a model of reduced purifying selection (Hill–Robertson interference) within copy number variable regions that are enriched in nonessential genes, allowing both the fixation of slightly deleterious substitutions and increased drift of CNV alleles. Additionally, all four CNV sets exhibited increased rates of interspecies chromosomal rearrangement and nucleotide substitution and an increased gene density. We observe that sequences with high G+C contents are most prone to copy number variation. In particular, frequently duplicated human SD sequence, or CNVs that are large and/or observed frequently, tend to be elevated in G+C content. In contrast, SD sequences that appear fixed in the human population lie more frequently within low G+C sequence. These findings provide an overarching view of how CNVs arise and segregate in the human population.
Establishment and molecular profiling of a novel human pancreatic cancer panel for 5‐FU
Authors: Yanagihara Kazuyoshi , Takigahira Misato , Tanaka Hiromi , Arao Tokuzo , Aoyagi Yasuyuki , Oda Tatsuya , Ochiai Atsushi , Nishio Kazuto
Published: August 2008

Ten novel human pancreatic carcinoma cell lines (Sui65 through Sui74) were established from a transplantable pancreatic carcinoma cell line. All the cell lines resembled the original clinical carcinoma in terms of the morphological and biological features, presenting with genetic alterations such as point mutations of K‐ras and p53, attenuation or lack of SMAD4 and p16 and other relevant cellular characteristics. Using this panel, we evaluated the effects of 5‐FU in suppressing the proliferation of pancreatic carcinoma cells. When tested in vitro, although Sui72 was highly susceptible to 5‐FU, the other cell lines were found to be resistant to the drug. When Sui72 and Sui70 were implanted subcutaneously in SCID mice followed by treatment with 5‐FU, the drug was found to be effective against Sui72 but not Sui70, consistent with the results in vitro. In order to identify the molecular determinant for high sensitivity of Sui72 to 5‐FU, we examined the mRNA expression levels of the metabolic enzymes of 5‐FU. Decreased expression of DPYD was observed in Sui72 as compared with other cell lines (0.1 versus 0.6 ± 0.5, 0.1‐fold).

It is believed that the novel cell lines established in the present study will be useful for analyzing the pattern of progression of pancreatic cancer and for evaluating the efficacy of anticancer agents. (Cancer Sci 2008; 99: 1859–1864)
Palmitoylation‐dependent endosomal localization of AATYK1A and its interaction with Src
Authors: Tsutsumi Koji , Tomomura Mineko , Furuichi Teiichi , Hisanaga Shin‐ichi
Published: August 2008

Apoptosis‐associated tyrosine kinase 1 (AATYK1), also named LMTK1, was previously isolated as an apoptosis‐related gene from 32Dcl3 myeloid precursor cells, but its precise function remains unknown. AATYK1A, an isoform without a transmembrane domain, is highly expressed in neurons. We identified palmitoylation of AATYK1A at three N‐terminal cysteine residues in cortical cultured neurons and COS‐7 cells and found that palmitoylation determined localization of AATYK1A to the transferrin receptor‐positive recycling endosomes. Further, we identified the tyrosine kinase Src as a novel AATYK1A‐interacting protein. Src and Fyn phosphorylated AATYK1A at tyrosines 25 and 46 in a palmitoylation‐dependent manner. The association of AATYK1A with Src in endosomes was also found to be palmitoylation‐dependent. These results indicate that palmitoylation is a critical factor not only for the subcellular localization of AATYK1A but also for its interaction with Src.
Physicochemical and sensory optimisation of a low glycemic index ice cream formulation
Authors: Whelan Anthony P. , Vega Cesar , Kerry Joseph P. , Goff H. Douglas
Published: August 2008

The development of a low glycemic index ice cream with as close as possible physicochemical properties and sensory quality compared with a sucrose‐sweetened ice cream was investigated. Three relatively new novel commercial sweeteners – tagatose, erythritol and trehalose – were studied, along with maltitol and polydextrose. Once the freezing curves were matched, other physicochemical properties also were found to match. Sweetness and sweet taste could then be adjusted for sensory optimisation with a combination of these sugars and supplementation with sucralose to boost the sweetness as necessary.
Effect of glutamate and inosinate on sensory and instrumental texture of extruded products
Authors: Cassar Renata , Sardinha Fátima A. , Arêas José A. G.
Published: August 2008

Expanded products have been developed by extrusion of non‐conventional highly nutritious raw materials such as amaranth and chickpea blended with bovine lung. As sensory acceptance of these snacks is restricted, this study aimed at improving their texture, through the addition of monosodium glutamate (MSG) and disodium inosinate (IMP) flavor enhancers to the feeding material, or to the flavor added after the extrusion. Sensory and mechanical analyses showed that both enhancers affected texture, assessed by sensory and instrumental methods. Addition of IMP together with MSG to the chickpea‐based snacks presented the best results. This beneficial effect was not observed in the amaranth‐based snack, suggesting that IMP and MSG can favorably impact texture of extruded products depending on the amount and type of protein present.
Physicochemical and sensory characteristics of cookies containing residue from king palm (Archontophoenix alexandrae) processing
Authors: Vieira Manoela A. , Tramonte Karina C. , Podestá Rossana , Avancini Sandra R. P. , Amboni Renata D. de M. C. , Amante Edna R.
Published: August 2008

The aim of this study was to evaluate the chemical properties of the flours prepared with residues from organic king palm processing, and also to determine the cookie‐making performance of residue blends from organic king palm processing and wheat flour, as well as the effect of the blends on the consumers’ acceptance and purchase intent of high‐fibre cookies. The king palm flours (PFs) contained high contents of total dietary fibre and total ash. Blends containing 0%, 10%, 15%, 20% and 25% of either PF or sieved king‐palm flour (SPF) replacing wheat flour were prepared. The total dietary fibre content of the cookies ranged from 4 to 7 g (100 g)−1on a dry‐matter basis. The level of these components improved with increased amounts of PF and SPF in the blends. All the cookies were acceptable and approved in relation to purchase intent.