bluuebunny/crossref_metadata_2025 huggingface dataset:
Atomic radiative and radiationless yields for K and L shells
Authors: Krause M. O.
Published: April 2010

The available body of information on (a) fluorescence, Auger, and Coster-Kronig yields, (b) radiative and radiationless transition rates, (c) level widths, (d) x-ray and Auger line widths, (e) x-ray and Auger spectra, and (f) Coster-Kronig energies has been used to generate an internally consistent set of values of atomic radiative and radiationless yields for the K shell (5 ?Z?110) and the L subshells (12 ?Z?110). Values of fluorescence yields ωk, ω1, ω2, ω3, Coster-Kronig yields ℱ1, ℱ1.2, ℱ1.3, ℱ1.3, ℱ2.3. Auger yields ak, a1, a2, a3, and effective fluorescence yields ν1 and ν2 are presented in tables and graphs. Estimates of uncertainties are given. Updated and expanded graphs of partial and total widths of K, L1, L2, and L3 levels are presented as well as a reference list of papers published since about 1972.
Natural widths of atomic K and L levels, Kα X-ray lines and several K
L
L Auger lines
Authors: Krause M. O. , Oliver J. H.
Published: April 2010

Semi-empirical values of the natural widths of K, L1, L2, and L3 levels, Kα1 and Kα2 x-ray lines, and KL1L1, KL1L2 and KL2L3 Auger lines for the elements 10?Z?110 are presented in tables and grapahs. Level width Γi (i=K, L1,L2, L3) is obtained from the relation Γi=ΓR,i/ωi, using the theoretical radiative rate ΓR,i from Scofield’s relativistic, relaxed Hartree-Fock calculation and the fluorescence yield ωi from Krause’s evaluation. X-ray and Auger lines widths are calculated as the sums of pertinent level widths. This tabulation of natural level and line widths is internally consistent, and is compatible with all relevant experimental and theoretical information. Present semi-empirical widths, especially those of Kα1 and Kα2 x-rays, are compared with measured widths. Uncertainties of semi-empirical values are estimated.
A correlation of the viscosity and thermal conductivity data of gaseous and liquid propane
Authors: Holland P. M. , Hanley H. J. M. , Gubbins K. E. , Haile J. M.
Published: April 2010

Data for the viscosity and thermal conductivity of gaseous and liquid propane have been evaluated and represented by empirical functions developed in previous work. Tables of values are presented for the range 140–500 K for pressures to 50 MPa (? 500 atm). The viscosities are estimated to have uncertainties of about ±5%, with corresponding uncertainties of the thermal conductivities of about ±8%. It is stressed that the data base should be improved. As in our work with other fluids, the anomalous contribution to the thermal conductivity in the vicinity of the critical point is included.
Electrical resistivity of alkali elements
Authors: Chi T. C.
Published: April 2010

This paper presents and discusses the available data and information on the electrical resistivity of alkali elements (lithium, sodium, potassium, rubidium, cesium, and francium) and contains recommended reference values (or provisional or typical values). The compiled data include all the experimental data available from the literature and cover the temperature dependence, pressure dependence, and magnetic flux density dependence. The temperature range covered by the compiled data is from cryogenic temperatures to above the critical temperature of the elements. The recommended values are generated from critical evaluation, analysis, and synthesis of the available data and information and are given for both the total electrical resistivity and the intrinsic electrical resistivity. For most of the elements, the recommended values cover the temperature range from 1 K to 2000 K.
Electrical resistivity of alkaline earth elements
Authors: Chi T. C.
Published: April 2010

This paper presents and discusses the available data and information on the electrical resistivity of alkaline earth elements (beryllium, magnesium, calcium, strontium, barium, and radium) and contains recommended or provisional reference values. The compiled data include all the experimental data available from the literature. The temperature range covered by the compiled data is from cryogenic temperatures to above the melting temperature of the elements. The recommended values are generated from critical evaluation, analysis, and synthesis of the available data and information and are given for both the total electrical resistivity and the intrinsic electrical resistivity. For most of the elements, the recommended values cover the temperature range from 1 K to 1000 K.
Vapor pressures and boiling points of selected halomethanes
Authors: Kudchadker A. P. , Kudchadker S. A. , Shukla R. P. , Patnaik P. R.
Published: April 2010

This critical review is a study of the vapor pressure–boiling point data from the triple point to the critical point for CH4–a Xa (X=Br, I) and CH4−(a+b+c+d) FaClbBrcId halomethanes. The available data are carefully analyzed and the ’’best’’ data selected. The selection procedure is discussed. Uncertainties in the selected temperatures and pressures are reported. The selected data were fitted to the Antoine equation for data up to 1500 mm Hg pressure and the Wagner equation for data up to the critical point. Antoine constants for nineteen compounds and the Wagner constants for five compounds are reported. The enthalpy of vaporization at 298.15 K and at the normal boiling point have been computed.
Ideal gas thermodynamic properties of selected bromoethanes and iodoethane
Authors: Kudchadker S. A. , Kudchadker A. P.
Published: April 2010

The available molecular parameters, fundamental frequencies, potential barrier heights, torsional frequencies, and standard enthalpies of formation at 298.15 K for selected bromoethanes and iodoethane containing one symmetric-top group have been critically evaluated and recommended values selected. The chemical thermodynamic properties in the ideal gas state at one atmosphere pressure using the rigid-rotor harmonic-oscillator approximation have been calculated for CH3CH2Br, CH3CHBr2, CH3CBr3 C2Br6, and CH3CH2I. The internal rotational contributions have been obtained from the partition function formed by the summation of internal rotation energy levels.
Microwave spectra of molecules of astrophysical interest XV. Propyne
Authors: Bauer A. , Boucher D. , Burie J. , Demaison J. , Dubrulle A.
Published: April 2010

The microwave spectrum of propyne is critically reviewed for information applicable to radio-astronomy. Molecular data such as the derived rotational constants, centrifugal distortion parameters, hyperfine coupling constants, electric dipole moment, and molecular structure are tabulated. The observed rotational transitions are presented for the astronomically interesting isotopic forms and the lowest lying vibrational state of propyne. Calculated rotational transitions are presented for the ground vibrational state of 12CH3 12C≡ 12CH, 13CH3 12C≡ 12CH, 12CH313C≡ 12CH and 12CH3 12C≡ 13CH, and for the vibrationally excited state ν10 of 12CH3 12C≡ 12CH.
Simulated atmospheric processing of iron oxyhydroxide minerals at low pH: Roles of particle size and acid anion in iron dissolution
Authors: Rubasinghege Gayan , Lentz Robert W. , Scherer Michelle M. , Grassian Vicki H.
Published: April 2010

A number of recent studies have shown that iron dissolution in Fe-containing dust aerosol can be linked to source material (mineral or anthropogenic), mineralogy, and iron speciation. All of these factors need to be incorporated into atmospheric chemistry models if these models are to accurately predict the impact of Fe-containing dusts into open ocean waters. In this report, we combine dissolution measurements along with spectroscopy and microscopy to focus on nanoscale size effects in the dissolution of Fe-containing minerals in low-pH environments and the importance of acid type, including HNO
3
, H
2
SO
4
, and HCl, on dissolution. All of these acids are present in the atmosphere, and dust particles have been shown to be associated with nitrate, sulfate, and/or chloride. These measurements are done under light and dark conditions so as to simulate and distinguish between daytime and nighttime atmospheric chemical processing. Both size (nano- versus micron-sized particles) and anion (nitrate, sulfate, and chloride) are found to play significant roles in the dissolution of α-FeOOH under both light and dark conditions. The current study highlights these important, yet unconsidered, factors in the atmospheric processing of iron-containing mineral dust aerosol.
Inhibitor-induced structural change in the HCV IRES domain IIa RNA
Authors: Paulsen Ryan B. , Seth Punit P. , Swayze Eric E. , Griffey Richard H. , Skalicky Jack J. , Cheatham Thomas E. , Davis Darrell R.
Published: April 2010

Translation of the hepatitis C virus (HCV) RNA is initiated from a highly structured internal ribosomal entry site (IRES) in the 5′ untranslated region (5′ UTR) of the RNA genome. An important structural feature of the native RNA is an approximately 90° helical bend localized to domain IIa that positions the apical loop of domain IIb of the IRES near the 40S ribosomal E-site to promote eIF2-GDP release, facilitating 80S ribosome assembly. We report here the NMR structure of a domain IIa construct in complex with a potent small-molecule inhibitor of HCV replication. Molecular dynamics refinement in explicit solvent and subsequent energetic analysis indicated that each inhibitor stereoisomer bound with comparable affinity and in an equivalent binding mode. The in silico analysis was substantiated by fluorescence-based assays showing that the relative binding free energies differed by only 0.7 kcal/mol. Binding of the inhibitor displaces key nucleotide residues within the bulge region, effecting a major conformational change that eliminates the bent RNA helical trajectory, providing a mechanism for the antiviral activity of this inhibitor class.
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases
Authors: Huang Haiyan , Liu Chun-Chi , Zhou Xianghong Jasmine
Published: April 2010

The rapid accumulation of gene expression data has offered unprecedented opportunities to study human diseases. The National Center for Biotechnology Information Gene Expression Omnibus is currently the largest database that systematically documents the genome-wide molecular basis of diseases. However, thus far, this resource has been far from fully utilized. This paper describes the first study to transform public gene expression repositories into an automated disease diagnosis database. Particularly, we have developed a systematic framework, including a two-stage Bayesian learning approach, to achieve the diagnosis of one or multiple diseases for a query expression profile along a hierarchical disease taxonomy. Our approach, including standardizing cross-platform gene expression data and heterogeneous disease annotations, allows analyzing both sources of information in a unified probabilistic system. A high level of overall diagnostic accuracy was shown by cross validation. It was also demonstrated that the power of our method can increase significantly with the continued growth of public gene expression repositories. Finally, we showed how our disease diagnosis system can be used to characterize complex phenotypes and to construct a disease-drug connectivity map.
Salmonella
-mediated delivery of RNase P-based ribozymes for inhibition of viral gene expression and replication in human cells
Authors: Bai Yong , Li Hongjian , Vu Gia-Phong , Gong Hao , Umamoto Sean , Zhou Tianhong , Lu Sangwei , Liu Fenyong
Published: April 2010

A fundamental challenge in gene therapy is to develop approaches for delivering nucleic acid-based gene interfering agents, such as small interfering RNAs and ribozymes, to the appropriate cells in a way that is tissue/cell specific, efficient, and safe. Using human cytomegalovirus (HCMV) infection of differentiated macrophages as the model, we showed that
Salmonella
can efficiently deliver RNase P-based ribozyme sequence in specific human cells, leading to substantial ribozyme expression and effective inhibition of viral infection. We constructed a functional RNase P ribozyme (M1GS RNA) that targets the overlapping mRNA region of two HCMV capsid proteins, the capsid scaffolding protein (CSP) and assemblin, which are essential for viral capsid formation. Substantial expression of ribozymes was observed in human differentiated macrophages that were treated with attenuated
Salmonella
strains carrying the ribozyme sequence constructs. A reduction of 87–90% in viral CSP expression and a reduction of about 5,000-fold in viral growth were observed in cells that were treated with
Salmonella
carrying the sequence of the functional ribozyme but not with those carrying the sequence of a control ribozyme that contained mutations abolishing the catalytic activity. To our knowledge, this study showed for the first time that ribozymes expressed following targeted gene transfer with
Salmonella
-based vectors are highly active and specific in blocking viral infection. Moreover, these results demonstrate the feasibility to develop
Salmonella
-mediated gene transfer of RNase P ribozymes as an effective approach for gene-targeting applications.
X-ray emission processes in stars and their immediate environment
Authors: Testa Paola
Published: April 2010

A decade of X-ray stellar observations with
Chandra
and
XMM-Newton
has led to significant advances in our understanding of the physical processes at work in hot (magnetized) plasmas in stars and their immediate environment, providing new perspectives and challenges, and in turn the need for improved models. The wealth of high-quality stellar spectra has allowed us to investigate, in detail, the characteristics of the X-ray emission across the Hertzsprung-Russell (HR) diagram. Progress has been made in addressing issues ranging from classical stellar activity in stars with solar-like dynamos (such as flares, activity cycles, spatial and thermal structuring of the X-ray emitting plasma, and evolution of X-ray activity with age), to X-ray generating processes (e.g., accretion, jets, magnetically confined winds) that were poorly understood in the pre
Chandra
/
XMM-Newton
era. I will discuss the progress made in the study of high energy stellar physics and its impact in a wider astrophysical context, focusing on the role of spectral diagnostics now accessible.
Indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis
Authors: Obata Takashi , Goto Yoshiyuki , Kunisawa Jun , Sato Shintaro , Sakamoto Mitsuo , Setoyama Hiromi , Matsuki Takahiro , Nonaka Kazuhiko , Shibata Naoko , Gohda Masashi , Kagiyama Yuki , Nochi Tomonori , Yuki Yoshikazu , Fukuyama Yoshiko , Mukai Akira , Shinzaki Shinichiro , Fujihashi Kohtaro , Sasakawa Chihiro , Iijima Hideki , Goto Masatoshi , Umesaki Yoshinori , Benno Yoshimi , Kiyono Hiroshi
Published: April 2010

The indigenous bacteria create natural cohabitation niches together with mucosal Abs in the gastrointestinal (GI) tract. Here we report that opportunistic bacteria, largely
Alcaligenes
species, specifically inhabit host Peyer's patches (PPs) and isolated lymphoid follicles, with the associated preferential induction of antigen-specific mucosal IgA Abs in the GI tract.
Alcaligenes
were identified as the dominant bacteria on the interior of PPs from naïve, specific-pathogen-free but not from germ-free mice. Oral transfer of intratissue uncultured
Alcaligenes
into germ-free mice resulted in the presence of
Alcaligenes
inside the PPs of recipients. This result was further supported by the induction of antigen-specific Ab-producing cells in the mucosal (e.g., PPs) but not systemic compartment (e.g., spleen). The preferential presence of
Alcaligenes
inside PPs and the associated induction of intestinal secretory IgA Abs were also observed in both monkeys and humans. Localized mucosal Ab-mediated symbiotic immune responses were supported by
Alcaligenes
-stimulated CD11c
+
dendritic cells (DCs) producing the Ab-enhancing cytokines TGF-β, B-cell-activating factor belonging to the TNF family, and IL-6 in PPs. These CD11c
+
DCs did not migrate beyond the draining mesenteric lymph nodes. In the absence of antigen-specific mucosal Abs, the presence of
Alcaligenes
in PPs was greatly diminished. Thus, indigenous opportunistic bacteria uniquely inhabit PPs, leading to PP-DCs-initiated, local antigen-specific Ab production; this may involve the creation of an optimal symbiotic environment on the interior of the PPs.
Concerted O atom–proton transfer in the O—O bond forming step in water oxidation
Authors: Chen Zuofeng , Concepcion Javier J. , Hu Xiangqian , Yang Weitao , Hoertz Paul G. , Meyer Thomas J.
Published: April 2010

As the terminal step in photosystem II, and a potential half-reaction for artificial photosynthesis, water oxidation (2H2O → O2 + 4e- + 4H+) is key, but it imposes a significant mechanistic challenge with requirements for both 4e-/4H+loss and O—O bond formation. Significant progress in water oxidation catalysis has been achieved recently by use of single-site Ru metal complex catalysts such as [Ru(Mebimpy)(bpy)(OH2)]2+[Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine; bpy = 2,2′-bipyridine]. When oxidized fromto RuV = O3+, these complexes undergo O—O bond formation by O-atom attack on a H2O molecule, which is often the rate-limiting step. Microscopic details of O—O bond formation have been explored by quantum mechanical/molecular mechanical (QM/MM) simulations the results of which provide detailed insight into mechanism and a strategy for enhancing catalytic rates. It utilizes added bases as proton acceptors and concerted atom–proton transfer (APT) with O-atom transfer to the O atom of a water molecule in concert with proton transfer to the base (B). Base catalyzed APT reactivity in water oxidation is observed both in solution and on the surfaces of oxide electrodes derivatized by attached phosphonated metal complex catalysts. These results have important implications for catalytic, electrocatalytic, and photoelectrocatalytic water oxidation.
Boronic acid-based inhibitor of autotaxin reveals rapid turnover of LPA in the circulation
Authors: Albers Harald M. H. G. , Dong Anping , van Meeteren Laurens A. , Egan David A. , Sunkara Manjula , van Tilburg Erica W. , Schuurman Karianne , van Tellingen Olaf , Morris Andrew J. , Smyth Susan S. , Moolenaar Wouter H. , Ovaa Huib
Published: April 2010

Autotaxin (ATX) is a secreted nucleotide pyrophosphatase/phosphodiesterase that functions as a lysophospholipase D to produce the lipid mediator lysophosphatidic acid (LPA), a mitogen, chemoattractant, and survival factor for many cell types. The ATX-LPA signaling axis has been implicated in angiogenesis, chronic inflammation, fibrotic diseases and tumor progression, making this system an attractive target for therapy. However, potent and selective nonlipid inhibitors of ATX are currently not available. By screening a chemical library, we have identified thiazolidinediones that selectively inhibit ATX-mediated LPA production both in vitro and in vivo. Inhibitor potency was approximately 100-fold increased (IC
50
 ∼ 30 nM) after the incorporation of a boronic acid moiety, designed to target the active-site threonine (T210) in ATX. Intravenous injection of this inhibitor into mice resulted in a surprisingly rapid decrease in plasma LPA levels, indicating that turnover of LPA in the circulation is much more dynamic than previously appreciated. Thus, boronic acid-based small molecules hold promise as candidate drugs to target ATX.
Synaptic dynamics and decision making
Authors: Deco Gustavo , Rolls Edmund T. , Romo Ranulfo
Published: April 2010

During decision making between sequential stimuli, the first stimulus must be held in memory and then compared with the second. Here, we show that in systems that encode the stimuli by their firing rate, neurons can use synaptic facilitation not only to remember the first stimulus during the delay but during the presentation of the second stimulus so that they respond to a combination of the first and second stimuli, as has been found for “partial differential” neurons recorded in the ventral premotor cortex during vibrotactile flutter frequency decision making. Moreover, we show that such partial differential neurons provide important input to a subsequent attractor decision-making network that can then compare this combination of the first and second stimuli with inputs from other neurons that respond only to the second stimulus. Thus, both synaptic facilitation and neuronal attractor dynamics can account for sequential decision making in such systems in the brain.
Effects of precompetition state anxiety interventions on performance time and accuracy among amateur soccer players: Revisiting the matching hypothesis
Authors: Abouzekri Omar A. , Karageorghis Costas I.
Published: April 2010

In this study, we tested the matching hypothesis, which contends that administration of a cognitive or somatic anxiety intervention should be matched to a participant's dominant anxiety response. Sixty‐one male soccer players (mean age 31.6 years, s=6.3) were assigned to one of four groups based on their responses to the Competitive State Anxiety Inventory‐2, which was modified to include a directional scale. Interventions were randomly administered in a counterbalanced order 10 min before each performance trial on a soccer skill test. The dominantly cognitive anxious group (n=17), the dominantly somatic anxious group (n=17), and the non‐anxious control intervention group (n=14) completed a baseline performance trial. The second and third trials were completed with random administration of brief cognitive and somatic interventions. The non‐anxious control group (n=13) completed three trials with no intervention. A mixed‐model, Group×Treatment multivariate analysis of variance indicated significant (P<0.05) changes in cognitive anxiety intensity and somatic anxiety intensity, but not in state anxiety direction (P>0.05), or performance time or accuracy (P>0.05). The present findings do not provide support for the matching hypothesis for state anxiety intensity and direction, or for performance.
Effects of a motivational climate intervention on state anxiety, self‐efficacy, and skill development in physical education
Authors: Barkoukis Vassilis , Koidou Eirini , Tsorbatzoudis Haralambos
Published: April 2010

The objective of the present study was to test the effects of TARGET premises on state anxiety, self‐efficacy, and sport skill development. A total of 317 high school students with a mean age of 13.9 years (s=0.76) were assigned either to an intervention group or a control group. The triple jump and the Baryshnikov shot put techniques were taught to both groups in 10 teaching units. In the intervention group the teachers employed the TARGET structures, while in the control group the command style was used. Students completed pre‐ and post‐intervention measures of state anxiety and self‐efficacy just before execution of the two techniques. Motor skill development was evaluated by both absolute performance (in centimetres) and technical execution of the tasks. The results of repeated‐measures analyses of variance indicated that the intervention group reported higher triple jump self‐efficacy and better technical execution of the shot put than the control group. No intervention effects were observed for the anxiety responses. Our findings provide partial evidence for positive effects of a task‐involving motivational climate on sport skill development and performance‐related states.
Recovery following an Ironman triathlon: A case study
Authors: Nosaka Kazunori , Abbiss Chris R. , Watson Greig , Wall Bradley , Suzuki Katushiko , Laursen Paul
Published: April 2010

Completion of an Ironman triathlon results in muscle damage, indicated by reductions in muscle function and muscle soreness. However, the time course of recovery from this damage has received little attention. The purpose of this case study was to examine the time course of changes in blood markers of muscle damage and inflammation, muscle function, muscle soreness, and economy of motion following an Ironman event. An experienced well‐trained male triathlete aged 35 years completed the Western Australian Ironman triathlon in 11 h 38 min 41 s (winner's time: 8 h 3 min 56 s). Before and on several occasions in the 15 days after the event, the participant performed an incremental cycling test to exhaustion, running economy test at 12 km · h−1 (2% incline), maximal isometric knee flexion and extension at 90° knee flexion, and maximal squat and countermovement jumps. Venous blood samples and muscle soreness were also assessed. Maximal oxygen consumption, efficiency of motion, maximal muscle strength, and jump performance were all markedly reduced (4.5–54%) following the event, but returned to baseline within 15, 8, 2, and 8 days following the event, respectively. Muscle soreness and blood markers peaked 2–24 h after the race but returned to baseline within 8 days. In conclusion, although the Ironman triathlon induces marked muscle damage, a trained triathlete recovered almost completely within approximately one week, without the use of any therapeutic interventions after the event.
Distribution of modern cricket bowling actions in New Zealand
Authors: Ferdinands Rene , Kersting Uwe G. , Marshall Robert N. , Stuelcken Max
Published: April 2010

The classification of bowling actions in cricket is particularly important from an injury perspective. Research has consistently shown that bowlers with a mixed‐action technique have an elevated risk of sustaining serious lumbar injury. In this study, 34 New Zealand bowlers (mean age 22.2±0.9 years) of premier competition standard and above were assessed using a three‐dimensional motion analysis system (240 Hz). Data were analysed using three previous classification systems before classifying bowlers into the side‐on, semi‐open, front‐on, and mixed‐action types based on a modified set of angle threshold criteria and a more intuitive angle convention system. The majority of bowlers in the sample (64.7%) used the mixed action with high levels of shoulder counter‐rotation. The strongest predictors of shoulder counter‐rotation were shoulder alignment angle and pelvic–shoulder separation angle. The current results suggest that a large proportion of fast bowlers may be at a higher risk of lumbar injury from the use of the mixed‐action technique. We believe it may be advisable to recommend the semi‐open action as an alternative to the front‐on action. In addition, the adopted angle convention is more practical than the previous convention for bowling action classification.
Perceptual and cognitive responses during exercise: Relationships with metamotivational state and dominance
Authors: Thatcher Joanne , Kuroda Yusuke , Thatcher Rhys , Legrand Fabien
Published: April 2010

In this study, we examined ratings of perceived exertion (RPE) and attentional focus during exercise in relation to telic and paratelic metamotivational dominance and state. Thirty regular exercisers (11 females, 19 males), of whom 10 were telic dominant (mean Paratelic Dominance Scale score=6.2±2.9), 10 paratelic dominant (mean PDS score=23.8±1.4), and 10 non‐dominant (mean PDS score=15.4±0.7) completed two exercise trials. In the first trial, the participants completed a maximal ramped exercise test on a motorized treadmill to determine their gas exchange threshold (the speed at which determined exercise intensity of the subsequent trial). Throughout the second trial (a 30‐min treadmill run), the participants reported their metamotivational state, RPE, and attentional focus (associative or dissociative) at 5‐min intervals. Heart rate was recorded at 3, 8, 13, 18, 23, and 28 min and expired air was analysed for oxygen consumption (VO2) between 1–3, 6–8, 11–13, 16–18, 21–23, and 26–28 min. There was no main effect of dominance or dominance×time interaction on any variables (P >0.05). Oxygen consumption did not differ between states but RPE was higher in the telic than paratelic state at 25 and 30 min (t 28=2.87, P <0.05; t 26.77=3.88, P <0.05, respectively). Attentional focus was more associative in the telic than paratelic state at 20, 25, and 30 min (t 28=− 3.73, P <0.05; t 28=− 4.85, P <0.01; t 28=− 5.15, P <0.05, respectively) and heart rate was higher at 23 min in the telic state (t 27=3.40, P <0.05). During the latter stages of exercise, the telic metamotivational state, not dominance, was related to a more associative attentional focus and higher RPE. Our results support the use of reversal theory (Apter, 2001) to understand perceptual and cognitive responses during aerobic exercise, but an experimental design in which state is manipulated is needed to examine the effects of metamotivational dominance and state on perceptual and cognitive responses.
Sleep quality in athletes under normobaric hypoxia equivalent to 1500 m altitude: A polysomnographic study
Authors: Hoshikawa Masako , Uchida Sunao , Sugo Takayuki , Kumai Yasuko , Hanai Yoshiteru , Kawahara Takashi
Published: April 2010

In the present study, we evaluated the duration of slow‐wave sleep (Stage 3 and 4) and total delta power (< 3Hz) in all‐night non‐rapid eye movement (NREM) sleep electroencephalograms (EEGs) of athletes during normobaric hypoxia at simulated altitudes of 1500 m. Seven male athletes slept for two nights in a normoxic condition and one night in an hypoxic condition equivalent to an altitude of 1500 m. Whole‐night polysomnographic recordings, thoracic and abdominal motion, nasal and oral airflow, and blood oxygen saturation (SpO2) were recorded. Visual sleep stage scoring and fast Fourier transformation analyses of EEG were performed using 30‐s epochs. Mean and minimum SpO2 decreased significantly during sleep in the hypoxic condition. Between groups, changes in heart rate, respiratory disturbance measures including apnoea and hypopnoea, slow‐wave sleep and total delta power of the all‐night NREM sleep EEG were small and non‐significant for the hypoxic condition. However, individual difference in time at an SpO2 below 90% were large in the hypoxic condition, and both slow‐wave sleep and total delta power of all‐night NREM sleep EEG decreased in three participants who spent a prolonged time below 90% SpO2. The present results suggest that monitoring time below 90% SpO2 is recommended when studying individuals' living‐high schedule even under hypoxic conditions equivalent to an altitude of 1500 m.
Developmental changes in cognitive reaction time of children aged 6–12 years
Authors: Iida Yukako , Miyazaki Makoto , Uchida Sunao
Published: April 2010

Using a visual Go/Nogo paradigm and subtraction methods, we examined detailed developmental changes in the cognitive reaction times of 153 healthy children aged 6–12 years. Three conditions were studied: simple reaction, even rate reaction (50% Go), and high rate reaction (80% Go). The subtraction of simple reaction time from even rate reaction time was considered to reflect discrimination time, while the subtraction of simple reaction time from high rate reaction time was considered to reflect the time required for inhibition. We found that simple reaction time, even rate reaction time, and high rate reaction time all declined significantly with months of age (P < 0.01). Furthermore, the times for both discrimination and inhibition also showed significant declines (P < 0.01), which could be considered developmental changes in neural mechanisms involved in discrimination and inhibition processes. The time for inhibition showed a weaker correlation (P < 0.01), which could indicate that the degree of developmental change is larger for the discriminative processes than for the inhibititory processes required for our task in the age range studied.
Supervised normalization of microarrays
Authors: Mecham Brigham H. , Nelson Peter S. , Storey John D.
Published: April 2010

Motivation: A major challenge in utilizing microarray technologies to measure nucleic acid abundances is ‘normalization’, the goal of which is to separate biologically meaningful signal from other confounding sources of signal, often due to unavoidable technical factors. It is intuitively clear that true biological signal and confounding factors need to be simultaneously considered when performing normalization. However, the most popular normalization approaches do not utilize what is known about the study, both in terms of the biological variables of interest and the known technical factors in the study, such as batch or array processing date.

Results: We show here that failing to include all study-specific biological and technical variables when performing normalization leads to biased downstream analyses. We propose a general normalization framework that fits a study-specific model employing every known variable that is relevant to the expression study. The proposed method is generally applicable to the full range of existing probe designs, as well as to both single-channel and dual-channel arrays. We show through real and simulated examples that the method has favorable operating characteristics in comparison to some of the most highly used normalization methods.

Availability: An R package called snm implementing the methodology will be made available from Bioconductor (http://bioconductor.org).

Contact:  jstorey@princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ACCUSA—accurate SNP calling on draft genomes
Authors: Fröhler Sebastian , Dieterich Christoph
Published: April 2010

Summary: Next generation sequencing technologies facilitate genome-wide analysis of several biological processes. We are interested in whole-genome genotyping. To our knowledge, none of the existing single nucleotide polymorphism (SNP) callers consider the quality of the reference genome, which is not necessary for high-quality assemblies of well-studied model organisms. However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints. Here, we present a simple yet elegant solution (‘ACCUSA’) that considers both the read qualities as well as the reference genome's quality using a Bayesian framework. We demonstrate that ACCUSA is as good as the current SNP calling software in detecting true SNPs. More importantly, ACCUSA does not call spurious SNPs, which originate from a poor reference sequence.

Availability: ACCUSA is available free of charge to academic users and may be obtained from ftp://bbc.mdc-berlin.de/software. ACCUSA is programmed in JAVA 6 and runs on any platform with JAVA support.

Contact:  christoph.dieterich@mdc-berlin.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells
Authors: Banerjee Ipsita , Maiti Spandan , Parashurama Natesh , Yarmush Martin
Published: April 2010

Motivation: Primary purpose of modeling gene regulatory networks for developmental process is to reveal pathways governing the cellular differentiation to specific phenotypes. Knowledge of differentiation network will enable generation of desired cell fates by careful alteration of the governing network by adequate manipulation of cellular environment.

Results: We have developed a novel integer programming-based approach to reconstruct the underlying regulatory architecture of differentiating embryonic stem cells from discrete temporal gene expression data. The network reconstruction problem is formulated using inherent features of biological networks: (i) that of cascade architecture which enables treatment of the entire complex network as a set of interconnected modules and (ii) that of sparsity of interconnection between the transcription factors. The developed framework is applied to the system of embryonic stem cells differentiating towards pancreatic lineage. Experimentally determined expression profile dynamics of relevant transcription factors serve as the input to the network identification algorithm. The developed formulation accurately captures many of the known regulatory modes involved in pancreatic differentiation. The predictive capacity of the model is tested by simulating an in silico potential pathway of subsequent differentiation. The predicted pathway is experimentally verified by concurrent differentiation experiments. Experimental results agree well with model predictions, thereby illustrating the predictive accuracy of the proposed algorithm.

Contact:  ipb1@pitt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Plasma tissue inhibitor of matrix metalloproteinase‐1 (TIMP‐1): an independent predictor of poor response to cardiac resynchronization therapy
Authors: Tolosana Jose María , Mont Lluís , Sitges Marta , Berruezo Antonio , Delgado Victoria , Vidal Bàrbara , Tamborero David , Morales Manel , Batlle Montserrat , Roig Eulalia , Castel M. Angeles , Pérez‐Villa Félix , Godoy Miguel , Brugada Josep
Published: April 2010

Aims

Matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) play a role in left ventricular structural remodelling. The aim of our study was to analyse MMP‐2 and TIMP‐1 levels as predictors of poor response to cardiac resynchronization therapy (CRT).

Methods and results

A cohort of 42 CRT patients from our centre was prospectively evaluated at baseline and after 12‐month follow‐up. MMP‐2 and TIMP‐1 assays were performed prior to CRT implant. Cardiac resynchronization therapy responders were defined as patients who survived, were not transplanted, and increased their basal 6 min walking distance test (6MWDT) by ≥10% or improved their NYHA functional class. Overall, 25 patients (60%) were classed as responders. At 12‐month follow‐up, six patients (14.2%) had died and one (2.4%) patient had been transplanted. Compared with responders, non‐responders had higher levels of TIMP‐1 (277 ± 59 vs. 216 ± 46 ng/mL, P = 0.001), MMP‐2 (325 ± 115 vs. 258 ± 56 ng/mL, P = 0.02), and creatinine (1.76 ± 0.8 vs. 1.25 ± 0.3 mg/dL, P = 0.01). In a multivariate analysis, TIMP‐1 was the only independent predictor of non‐response to CRT [OR 0.97, 95% (CI 0.96–0.99) P = 0.005]. TIMP‐1≥248 ng/mL predicted non‐response with 71% sensitivity and 72% specificity.

Conclusion

TIMP‐1 is an independent predictor of non‐response in patients treated with CRT.
Differential roles for NOD2 in osteoblast inflammatory immune responses to bacterial pathogens of bone tissue
Authors: Chauhan Vinita S. , Marriott Ian
Published: April 2010

Osteoblasts produce an array of immune molecules following bacterial challenge that can contribute to inflammation and the recruitment of leukocytes to sites of infection during bone diseases such as osteomyelitis. However, the mechanisms by which osteoblasts perceive and respond to facultative intracellular pathogens such as Salmonella species and Staphylococcus aureus have not been determined. Recently, our laboratory has described the expression in osteoblasts of members of the nucleotide-binding domain leucine-rich repeat region containing family of proteins that include nucleotide-binding oligomerization domain-2 (NOD2), a molecule that functions as an intracellular receptor for bacterial peptidoglycans. In the present study, we demonstrate that NOD2 expression is required for select inflammatory mediator production by osteoblasts following infection with the invasive pathogen Salmonella. In contrast, we have found that the inflammatory immune responses of osteoblasts to the passively internalized bacterial species Staphylococcus aureus, heat-killed pathogenic Salmonella, a non-invasive Salmonella strain and specific Toll-like receptor ligands are not reduced in the absence of NOD2 expression but are, in fact, elevated. Based upon these findings, we suggest that NOD2 serves differential roles in osteoblasts, promoting inflammatory responses to invasive bacteria while tempering cell responses to extracellular and/or passively internalized bacterial species.
Identification of molecularly defined Staphylococcus aureus strains using matrix-assisted laser desorption/ionization time of flight mass spectrometry and the Biotyper 2.0 database
Authors: Szabados Florian , Woloszyn Jaroslaw , Richter Cindy , Kaase Martin , Gatermann Sören
Published: April 2010

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced for bacterial identification. To our knowledge, this is the first study where the Biotyper 2.0 database (Bruker Daltonics) has been applied for bacterial identification in a local strain collection of molecularly defined Staphylococcus aureus. We showed that the accuracy of the Biotyper 2.0-based identification for 602 molecularly defined strains of S. aureus, irrespective of meticillin resistance, was equivalent to that of the molecularly defined reference even at a score cut-off value of 2. Also, 412 isolates of 20 different species of non-S. aureus staphylococci were all correctly identified to species level compared to the molecularly defined reference. Moreover, the MALDI-TOF MS-based S. aureus identification approach was clearly faster than more time-consuming methods such as a molecular identification approach.
Nosocomial infection by VIM-2 metallo-β-lactamase-producing Pseudomonas putida
Authors: Treviño M. , Moldes L. , Hernández M. , Martínez-Lamas L. , García-Riestra C. , Regueiro B. J.
Published: April 2010

Nosocomial infections caused by multidrug-resistant and carbapenem-resistant Pseudomonas putida isolates have been reported occasionally in severely ill or immunocompromised patients. Here we report the microbiological characteristics of what are believed to be the two first carbapenem-resistant VIM metallo-β-lactamase (MBL)-producing P. putida strains in Spain, which were isolated from patients at the University Hospital Complex of Santiago de Compostela. Both patients were immunocompromised with severe underlying diseases and had been hospitalized for more than 15 days. One of them had previously been treated with a broad-spectrum therapy. Antimicrobial susceptibility testing showed that both strains were resistant to piperacillin/tazobactam, ceftazidime, cefepime, imipenem, meropenem, gentamicin, tobramycin, aztreonam, trimethoprim/sulfamethoxazole and ciprofloxacin, but sensitive to amikacin and colistin. For both isolates PCR and sequencing was positive for the bla
VIM-2 gene. Fingerprinting analysis revealed these were two different strains. One patient recovered clinically and one died; no direct link could be established between the isolation of P. putida and death. Our data expose the emergence of multidrug-resistant P. putida VIM-2 MBL, probably arising by independent horizontal transfer of resistance genes. So, although P. putida is not frequently isolated, it may survive easily in the hospital setting and occasionally cause difficult-to-treat nosocomial infections in severely ill patients.
Genetic diversity in Campylobacter jejuni is associated with differential colonization of broiler chickens and C57BL/6J IL10-deficient mice
Authors: Wilson David L. , Rathinam Vijay A. K. , Qi Weihong , Wick Lukas M. , Landgraf Jeff , Bell Julia A. , Plovanich-Jones Anne , Parrish Jodi , Finley Russell L. , Mansfield Linda S. , Linz John E.
Published: April 2010

Previous studies have demonstrated that Campylobacter jejuni, the leading causative agent of bacterial food-borne disease in the USA, exhibits high-frequency genetic variation that is associated with changes in cell-surface antigens and ability to colonize chickens. To expand our understanding of the role of genetic diversity in the disease process, we analysed the ability of three C. jejuni human disease isolates (strains 11168, 33292 and 81-176) and genetically marked derivatives to colonize Ross 308 broilers and C57BL/6J IL10-deficient mice. C. jejuni colonized broilers at much higher efficiency (all three strains, 23 of 24 broilers) than mice (11168 only, 8 of 24 mice). C. jejuni 11168 genetically marked strains colonized mice at very low efficiency (2 of 42 mice); however, C. jejuni reisolated from mice colonized both mice and broilers at high efficiency, suggesting that this pathogen can adapt genetically in the mouse. We compared the genome composition in the three wild-type C. jejuni strains and derivatives by microarray DNA/DNA hybridization analysis; the data demonstrated a high degree of genetic diversity in three gene clusters associated with synthesis and modification of the cell-surface structures capsule, flagella and lipo-oligosaccharide. Finally, we analysed the frequency of mutation in homopolymeric tracts associated with the contingency genes wlaN (GC tract) and flgR (AT tracts) in culture and after passage through broilers and mice. C. jejuni adapted genetically in culture at high frequency and the degree of genetic diversity was increased by passage through broilers but was nearly eliminated in the gastrointestinal tract of mice. The data suggest that the broiler gastrointestinal tract provides an environment which promotes outgrowth and genetic variation in C. jejuni; the enhancement of genetic diversity at this location may contribute to its importance as a human disease reservoir.
Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses
Authors: Picozzi Claudia , Bonacina Gaia , Vigentini Ileana , Foschino Roberto
Published: April 2010

Lactobacillus sanfranciscensisis a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh,gyrA, mapA, nox, pgmAandpta) was developed for this study. PFGE with the restriction enzymeApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population inL. sanfranciscensis.The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.