bluuebunny/crossref_metadata_2025 huggingface dataset:
Jewish Mysticism
Authors: Jones Rufus M.
Published: August 2011

Professor Scholem, who is professor of Jewish Mysticism in the Hebrew University in Jerusalem, has produced a very important book, which will at once take its place in the list of the most significant books that have appeared on Mystical Religion. Baron von Hügel's The Mystical Element in Religion came at the end of 1908. My Studies in Mystical Religion came out in 1909, and Evelyn Underhill's Mysticism appeared in 1911. We all three were working independently of one another and, without knowing that anyone else was engaged in the undertaking, we produced our results almost simultaneously, and though representing three different types of religious thought, we became intimate friends through our work, and all three books went through various editions. Dean Inge had already, in 1899, published his important book on Christian Mysticism, and in 1902 William James had published his work of genius, Varieties of Religious Experience. Between 1911 and the present date there has been a remarkable output of books on Mysticism, many of them valuable contributions to the subject, and Mysticism has become an important feature of the interpretation of religion in our time. But meantime there had been no adequate interpretation of the great stream of Jewish Mysticism. In 1913 J. Abelson published a valuable little book on Jewish Mysticism, and in 1935 Jacob Minkin wrote a popular book on The Romance of Hasidism.
Edwards and the Arminians on the Freedom of the Will
Authors: Wright Conrad
Published: August 2011

Jonathan Edwards believed that the crucial point which divided Calvinists and Arminians was the freedom of the will; that by establishing the doctrine of moral necessity, the Calvinists would have a firm basis from which to confute Arminian objections to the doctrines of total depravity, efficacious grace, absolute, eternal, and particular election, and the perseverance of the saints. His treatise on the Freedom of the Will was intended to give a final and crushing reply to his opponents, and in preparation for it he read widely and thought deeply. He believed that he had answered all objections, stopped all crevices in the argument, and written an unanswerable work. It appeared in 1754.
Projections from cingulate cortex to the cat’s thalamic reticular nucleus
Authors: FITZGIBBON THOMAS , KIKUCHI NICK
Published: August 2011

The cingulate cortex (CG) and the adjacent region designated as the splenial visual area (SVA) project to areas of the extrageniculate thalamic system that are concerned with processing visual information. En route to the thalamus, they pass through the thalamic reticular nucleus (TRN), an important source of thalamic inhibition. We wished to determine whether SVA axon collaterals projected to the previously defined visual sector of the TRN or a separate projection zone and did this differ from the projection zone of CG. We iontophoretically injected different neuroanatomical tracers into several locations within CG/SVA and traced the labeled axons through the TRN. The CG and SVA have a projection zone that only partially overlaps the dorsorostral regions of the visuocortical projection zone; there was no evidence to suggest separate SVA and CG zones or tiers of label within the TRN. The projection formed only a weak topographic map in the TRN, which is largely defined in the rostrocaudal axis and is similar to that of the area 7 projection; both projections have a high degree of overlap in the dorsal TRN. We postulate that CG/SVA may be involved in the initiation of orientation behaviorsviastimulation of thalamic nuclei and attentional mechanisms of the TRN.
The divergent approaches of English and South African courts, when considering actuarial expert testimony in the matter of an award for damages for future loss of earnings after a damage-causing event
Authors: du Plessis H.L.M.
Published: August 2011

This paper analyses the driving forces behind the willingness of South African courts to hear actuarial expert testimony in even the most simple of cases, in contrast to the more circumspect approach of the English courts, when assessing the damages arising out of future loss of earnings following a damage-causing incident. The analysis may well add insight to members of other professions and scientific communities that provide expert testimony to the courts. It is argued that English substantive law of damages and those influenced by its application have something to gain from a consideration of the approach in South Africa.
Proteomic Analysis of Mitochondria in APOE Transgenic Mice and in Response to an Ischemic Challenge
Authors: James Rachel , Searcy James L , Bihan Thierry Le , Martin Sarah F , Gliddon Catherine M , Povey Joanne , Deighton Ruth F , Kerr Lorraine E , McCulloch James , Horsburgh Karen
Published: August 2011

Apolipoprotein E (APOE)-ɛ4 is associated with a deleterious outcome after ischemic brain injury, which may involve abnormal regulation of mitochondrial function. We have assessed the mitochondrial proteomic response of APOE-ɛ3 and APOE-ɛ4 transgenic mice to transient global ischemic injury in the hippocampus. A genotype-dependent increase in ApoE levels in mitochondria was observed after ischemia, with APOE-ɛ4 mice showing significantly greater increases than APOE-ɛ3 mice. Quantitative analysis of the mitochondria-enriched fractions was performed using liquid-chromatography mass spectrometry coupled to label-free analysis. Of the 1,067 identified proteins, 274 were mitochondria associated. Mitochondrial protein expression was significantly different between genotypes under basal conditions as well as in response to global ischemia. A total of 12 mitochondrial proteins (including respiratory chain proteins NDUFA11, NDUFS3, NDUF5B, ATP5J, as well as ETFA, CYB5B, ATP6V1A, HSPA1B, OXR1, GLUL, IARS2, and PHYHIPL) were significantly altered with respect to genotype, global ischemia, or their interaction ( P<0.01). A compelling interactome, created using proteins found to be significantly modulated by global ischemia ( P<0.05), involved proteins that regulate energy production and oxidative stress. Thus, APOE genotype has a differential effect on the mitochondrial protein expression in the absence and presence of an injury, which may underlie the differing genotype susceptibility.
Identification of a de novo thymidylate biosynthesis pathway in mammalian mitochondria
Authors: Anderson Donald D. , Quintero Cynthia M. , Stover Patrick J.
Published: August 2011

The de novo and salvage dTTP pathways are essential for maintaining cellular dTTP pools to ensure the faithful replication of both mitochondrial and nuclear DNA. Disregulation of dTTP pools results in mitochondrial dysfunction and nuclear genome instability due to an increase in uracil misincorporation. In this study, we identified a de novo dTMP synthesis pathway in mammalian mitochondria. Mitochondria purified from wild-type Chinese hamster ovary (CHO) cells and HepG2 cells converted dUMP to dTMP in the presence of NADPH and serine, through the activities of mitochondrial serine hydroxymethyltransferase (SHMT2), thymidylate synthase (TYMS), and a novel human mitochondrial dihydrofolate reductase (DHFR) previously thought to be a pseudogene known as dihydrofolate reductase-like protein 1 (DHFRL1). Human DHFRL1, SHMT2, and TYMS were localized to mitochondrial matrix and inner membrane, confirming the presence of this pathway in mitochondria. Knockdown of DHFRL1 using siRNA eliminated DHFR activity in mitochondria. DHFRL1 expression in CHO
glyC
, a previously uncharacterized mutant glycine auxotrophic cell line, rescued the glycine auxotrophy. De novo thymidylate synthesis activity was diminished in mitochondria isolated from
glyA
CHO cells that lack SHMT2 activity, as well as mitochondria isolated from wild-type CHO cells treated with methotrexate, a DHFR inhibitor. De novo thymidylate synthesis in mitochondria prevents uracil accumulation in mitochondrial DNA (mtDNA), as uracil levels in mtDNA isolated from
glyA
CHO cells was 40% higher than observed in mtDNA isolated from wild-type CHO cells. These data indicate that unlike other nucleotides, de novo dTMP synthesis occurs within mitochondria and is essential for mtDNA integrity.
Photoelectron spectroscopic and computational studies of the Pt@Pb101- and Pt@Pb121-/2- anions
Authors: Grubisic Andrej , Wang Haopeng , Li Xiang , Ko Yeon-Jae , Kocak F. Sanem , Pederson Mark R. , Bowen Kit H. , Eichhorn Bryan W.
Published: August 2011

A combination of anion photoelectron spectroscopy and density functional theory calculations has elucidated the geometric and electronic structure of gas-phase endohedral Pt/Pb cage cluster anions. The anions,

and

were prepared from “preassembled” clusters generated from crystalline samples of [K(2,2,2-crypt)]
2
[Pt @ Pb
12
] that were brought into the gas phase using a unique infrared desorption/photoemission anion source. The use of crystalline [K(2,2,2-crypt)]
2
[Pt @ Pb
12
] also provided access to K[Pt @ Pb

n

]
-
anions in the gas phase (i.e., the K
+
salts of the

anions). Anion photoelectron spectra of

,

, and K[Pt @ Pb
12
]
1-
are presented. Extensive density functional theory calculations on

and

provided candidate structures and anion photoelectron spectra for

and

. Together, the calculated and measured photoelectron spectra show that

and

endohedral complexes maintain their respective
D

4
d

and slightly distorted
I

h

symmetries in the gas phase even for the charge states with open shell character. Aside from the fullerenes, the

endohedral complex is the only bare cluster that has been structurally characterized in the solid state, solution, and the gas phase.
Wave drag on floating bodies
Authors: Le Merrer Marie , Clanet Christophe , Quéré David , Raphaël Élie , Chevy Frédéric
Published: August 2011

We measure the deceleration of liquid nitrogen drops floating at the surface of a liquid bath. On water, the friction force is found to be about 10 to 100 times larger than on a solid substrate, which is shown to arise from wave resistance. We investigate the influence of the bath viscosity and show that the dissipation decreases as the viscosity is increased, owing to wave damping. The measured resistance is well predicted by a model imposing a vertical force (i.e., the drop weight) on a finite area, as long as the wake can be considered stationary.
A key inactivation factor of HeLa cell viability by a plasma flow
Authors: Sato Takehiko , Yokoyama Mayo , Johkura Kohei
Published: August 2011

Recently, a plasma flow has been applied to medical treatment using effects of various kinds of stimuli such as chemical species, charged particles, heat, light, shock wave and electric fields. Among them, the chemical species are known to cause an inactivation of cell viability. However, the mechanisms and key factors of this event are not yet clear. In this study, we focused on the effect of H2O2 in plasma-treated culture medium because it is generated in the culture medium and it is also chemically stable compared with free radicals generated by the plasma flow. To elucidate the significance of H2O2, we assessed the differences in the effects of plasma-treated medium and H2O2-added medium against inactivation of HeLa cell viability. These two media showed comparable effects on HeLa cells in terms of the survival ratios, morphological features of damage processes, permeations of H2O2 into the cells, response to H2O2 decomposition by catalase and comprehensive gene expression. The results supported that among chemical species generated in a plasma-treated culture medium, H2O2 is one of the main factors responsible for inactivation of HeLa cell viability.
Enhanced negative ion yields on diamond surfaces at elevated temperatures
Authors: Kumar P , Ahmad A , Pardanaud C , Carrère M , Layet J M , Cartry G , Silva F , Gicquel A , Engeln R
Published: August 2011

Boron-doped polycrystalline diamond (BDD) and highly oriented pyrolytic graphite (HOPG) surfaces were exposed to low pressure hydrogen plasma. The relative yields of surface-produced H− ions were measured by an energy analyser quadrupole mass spectrometer. The highest H− yield was obtained at 400 °C for a BDD surface and at room temperature for an HOPG surface. At low ion bombardment energy, the maximum yield on a BDD surface is about 5 times higher than that on an HOPG surface, which has been the best carbon material so far for surface production of H− ions in caesium-free plasma. Raman measurements revealed surface modifications after plasma exposure.
Reducing support loss in micromechanical ring resonators using phononic band-gap structures
Authors: Hsu Feng-Chia , Hsu Jin-Chen , Huang Tsun-Che , Wang Chin-Hung , Chang Pin
Published: August 2011

In micromechanical resonators, energy loss via supports into the substrates may lead to a low quality factor. To eliminate the support loss, in this paper a phononic band-gap structure is employed. We demonstrate a design of phononic-crystal (PC) strips used to support extensional wine-glass mode ring resonators to increase the quality factor. The PC strips are introduced to stop elastic-wave propagation by the band-gap and deaf-band effects. Analyses of resonant characteristics of the ring resonators and the dispersion relations, eigenmodes, and transmission properties of the PC strips are presented. With the proposed resonator architecture, the finite-element simulations show that the leaky power is effectively reduced and the stored energy inside the resonators is enhanced simultaneously as the operating frequencies of the resonators are within the band gap or deaf bands. Realization of a high quality factor micromechanical ring resonator with minimized support loss is expected.
High-κ field-effect transistor with copper-phthalocyanine
Authors: Roth F , Huth M
Published: August 2011

The use of SrTiO3 dielectrics as high-permittivity insulator in organic thin-film field-effect transistors (FET) is evaluated. FETs with sputtered SrTiO3 and copper-phthalocyanine (CuPc) as semiconducting layer were fabricated. The device preparation was performed in situ in an ultra-high-vacuum chamber system. The dielectric in the transistors had a permittivity of up to 200 which led to low driving voltages of 3 V. The FETs were p-type and reached mobilities of about μ = 1.5 × 10−3 cm2 V−1 s−1 and an on/off ratio of 103. These properties are compared to devices based on other dielectric materials.
Numerical analyses of hydrogen plasma generation by nanosecond pulsed high voltages at near-atmospheric pressure
Authors: Lo Chieh-Wen , Hamaguchi Satoshi
Published: August 2011

Dynamic processes of capacitively coupled hydrogen plasmas driven by nanosecond pulsed high voltages at near-atmospheric pressure are investigated with particle-in-cell simulations. It is found that propagation of an ionization front leads to a rapid increase in plasma density and the characteristics of the ionization front propagation are in good agreement with earlier experimental observations. The simulation has also revealed that electrons can form a non-Maxwellian distribution in the cathode sheath despite the high gas pressure. Therefore, the exact heating rates of such plasmas can be obtained only from such kinetic calculations as we have employed in this study.
Fringing field stretching of a pillared liquid crystal droplet
Authors: Ren Hongwen , Wu Shin-Tson
Published: August 2011

We demonstrate a liquid crystal (LC) droplet whose surface profile could be deformed by a fringing field. In the voltage-off state, the LC droplet exhibits a pillared shape by touching both substrates. As the voltage increases, such a droplet could be stretched to a cone-like shape or thin film. For a 1.5 mm aperture LC droplet, its occupied area could be expanded by ∼4.3× at 6.5 Vrms µm−1. Upon removing the voltage, the droplet could fully recover to its original shape. The shape stretching and recovering time are dependent on the expanded area. With the support of silicon oil around the droplet, the device is stable and the gravity effect is negligible.
Effects of the crystallite mosaic spread on integrated peak intensities in 2θ–ω measurements of highly crystallographically textured ZnO thin films
Authors: McCarthy E , Rajendra Kumar R T , Doggett B , Chakrabarti S , O'Haire R J , Newcomb S B , Mosnier J-P , Henry M O , McGlynn E
Published: August 2011

We report x-ray diffraction (XRD) (2θ–ω and rocking curve) and transmission electron microscopy (TEM) measurements on crystallographically textured ZnO thin films of varying thicknesses and crystallite mosaic spread deposited by pulsed-laser deposition on Si. The integrated areas of the (0 0 0 2) ZnO reflections in the 2θ–ω mode do not scale with film thickness and in some cases show discrepancies of two orders of magnitude compared with expectations based solely on sample thicknesses. Intensity differences of this type are regularly used in the literature as indications of differences in sample crystallinity or crystal quality. However TEM data of our samples show no evidence of amorphous deposits or significantly varying crystal quality in different films. X-ray rocking curves of these samples do show substantial variations in the mosaic spread of crystallites in the ZnO films which are the origin of the differences in integrated areas of the (0 0 0 2) ZnO reflections in 2θ–ω measurements. We outline a generally applicable model to treat the 2θ–ω mode peak intensities which shows good agreement with the experimental data (to within an order of magnitude) and which is much simpler than utilizing a full reciprocal space map approach to understand the XRD data. We conclude that the normalized integrated intensity of the (0 0 0 2) ZnO reflection in highly crystallographically textured ZnO thin films is strongly dependent on the rocking curve width in addition to the film thickness and the use of such intensities in isolation as measures of the thin film crystallinity or crystal quality, without reference to the rocking curve width, is likely to be misleading when making judgments of such aspects of the thin film structure.
Ag–Ti(C, N)-based coatings for biomedical applications: influence of silver content on the structural properties
Authors: Manninen N K , Galindo R Escobar , Benito N , Figueiredo N M , Cavaleiro A , Palacio C , Carvalho S
Published: August 2011

Ag–TiCN coatings were deposited by dc reactive magnetron sputtering and their structural and morphological properties were evaluated. Compositional analysis showed the existence of Ag–TiCN coatings with different Ag/Ti atomic ratios (ranging from 0 to 1.49). The structural and morphological properties are well correlated with the evolution of Ag/Ti atomic ratio. For the samples with low Ag/Ti atomic ratio (below 0.20) the coatings crystallize in a B1-NaCl crystal structure typical of TiC0.3N0.7. The increase in Ag/Ti atomic ratio promoted the formation of Ag crystalline phases as well as amorphous CN
x
phases detected in both x-ray photoelectron spectroscopy and Raman spectroscopy analysis. Simultaneously to the formation of Ag crystalline phases and amorphous carbon-based phases, a decrease in TiC0.3N0.7 grain size was observed as well as the densification of coatings.
Controlling the quality factor of a tuning-fork resonance between 9 and 300 K for scanning-probe microscopy
Authors: Ctistis G , Frater E H , Huisman S R , Korterik J P , Herek J L , Vos W L , Pinkse P W H
Published: August 2011

We study the dynamic response of a mechanical quartz tuning fork in the temperature range from 9 to 300 K. Since the quality factor Q of the resonance strongly depends on temperature, we implement a procedure to control the quality factor of the resonance. We show that we are able to dynamically change the quality factor and keep it constant over the whole temperature range. This procedure is suitable for applications in scanning-probe microscopy.
Separation of VUV/UV photons and reactive particles in the effluent of a He/O2atmospheric pressure plasma jet
Authors: Schneider S , Lackmann J-W , Narberhaus F , Bandow J E , Denis B , Benedikt J
Published: August 2011

The incorrect surface density of bacteria (4 × 106cm-2) on the agar plate was given in the right column, line 16, on page 3 in section 3 'Substrate preparation'. The correct surface coverage was 2.2 × 103cm-2. This surface coverage was selected to obtain a homogeneous surface coverage after 18 hours of incubation at 37 °C. The term 'monolayer surface coverage' in the same section is used to stress the fact that there is no multilayer of bacteria during the treatment and that the shadowing effects can be neglected. However, the surface is not fully covered by one continuous layer of bacteria. This error and ambiguity in the use of the term 'monolayer surface coverage' does not affect the interpretation of the results and conclusions in the article.

Additionally, the names of Volker Schulz-von der Gathen and Nikolas Knake have been misspelled in the 'Acknowledgments'. The authors apologize for any inconvenience and confusion they may have caused.
Volumetric reconstruction of the 3D boundary of stream tubes with general topology using tracer particles
Authors: Rossi M , Cierpka C , Segura R , Kähler C J
Published: August 2011

A general method is proposed to reconstruct the volumetric interface between two fluid flows using tracer particles and 3D particle tracking techniques. The method relies on the fact that a homogeneous dispersion of tracer particles introduced in a stream tube remains confined in that tube so that the cloud of particles can be used to reconstruct the boundary of the flow covered by the stream tube. Thus it becomes possible to quantitatively determine the interface between laminar and turbulent flow regions in boundary or shear layers as well as the interface between two mixing fluids. Tracer particles, as opposed to dye tracers, have negligible diffusion and their position in the measurement volume can be precisely localized by means of 3D particle tracking methods. On the other hand, they provide a discrete representation of a continuous volume and the reconstruction of the interface cannot be implemented in a straight forward fashion. In this work, the problem of interface reconstruction, from a randomly scattered particle cloud, is addressed and two different reconstruction algorithms are proposed: one based on numeric diffusion and one based on Delaunay triangulation. The two methods are qualified and compared by means of numerical simulations using the Monte Carlo method. The simulations are used to estimate the accuracy of the method and to provide guidelines for the choice of parameter settings. Finally, results on the interface between two mixing fluids in a microfluidic mixer are shown. A resolution of 2.5 µm in the optical-axis direction, with a maximum estimated error of 5.5 µm in the three directions, was obtained.
A new mechanism preventing proarrhythmia in chronic heart failure: rapid phase‐III repolarization explains the low proarrhythmic potential of amiodarone in contrast to sotalol in a model of pacing‐induced heart failure
Authors: Frommeyer Gerrit , Milberg Peter , Witte Patricia , Stypmann Jörg , Koopmann Matthias , Lücke Martin , Osada Nani , Breithardt Günter , Fehr Michael , Eckardt Lars
Published: August 2011

Aims

Life‐threatening arrhythmias are a major problem in chronic heart failure (CHF). The aim of the present study was to investigate the mechanism underlying the low proarrhythmic potential of amiodarone in a model of pacing‐induced heart failure.

Methods and results

Heart failure was induced in 35 female rabbits by rapid ventricular pacing, resulting in a significant decrease of ejection fraction. Thirty‐four rabbits were sham‐operated. In 17 of 35 CHF‐rabbits and 20 of 34 ‘sham’‐rabbits, amiodarone (50 mg/kg/day) was fed for 6 weeks. Eight monophasic action potentials and a simultaneously recorded 12‐lead electrocardiogram showed prolongation of QT‐interval and action potential duration (APD90) in all failing hearts (P< 0.05). Amiodarone pre‐treatment led to a prolongation of APD90 (+19 ms) as compared with sham‐controlled hearts but showed only a marginal effect on APD90 in failing hearts. Infusion of sotalol (50–100 µM) led to a significant prolongation of APD90 in sham and a further prolongation of APD90 in failing hearts [+55 ms (50 µM); +70 ms (100 µM); P< 0.01 as compared with sham hearts]. Sotalol led to a triangular action potential configuration in sham and failing hearts, whereas amiodarone did not cause triangularization but caused a rapid phase‐III repolarization. Moreover, amiodarone did not increase dispersion of repolarization either in sham or in failing hearts. Infusion of sotalol led to a significant increase in dispersion of repolarization in sham (+29 ms) and a further increase in failing hearts (+67 ms; P< 0.05).

Conclusion

Chronic amiodarone results in a rapid phase‐III‐repolarization and does not increase dispersion of repolarization. These electrophysiological findings are present in healthy hearts and are preserved in heart failure. This contributes to the low proarrhythmic potential of amiodarone in heart failure.
Design and preliminary results of the Heart Function Assessment Registry Trial in Saudi Arabia (HEARTS) in patients with acute and chronic heart failure†
Authors: AlHabib Khalid F. , Elasfar Abdelfatah A. , AlBackr Hanan , AlFaleh Hussam , Hersi Ahmad , AlShaer Fayez , Kashour Tarek , AlNemer Khalid , Hussein Gamal A. , Mimish Layth
Published: August 2011

Aims

The heart function assessment registry trial in Saudi Arabia (HEARTS) is the first multicentre national quality improvement initiative in the Arab population to study the clinical features, management, and outcomes of inpatients admitted with acute heart failure (AHF) and outpatients with high‐risk chronic heart failure (HCHF).

Methods and results

We conducted a prospective pilot phase for the registry that included consecutive patients with AHF and HCHF in five tertiary care hospitals in Saudi Arabia between October 2009 and December 2010. The study enrolled 1090 patients, 722 (66.2%) of whom were admitted with AHF and 368 (33.8%) had HCHF. The mean age ± SD of AHF patients was 60.6 ± 15.3 years; 65.2% were men, 55.3% were de novo heart failure, 60.7% had diabetes mellitus, 72.5% had moderate or severe left ventricular (LV) systolic dysfunction, and 51.5% had coronary artery disease as the main aetiology. More than 80% of AHF and HCHF patients were treated with beta‐blockers and angiotensin‐converting enzyme inhibitors/angiotensin receptor blockers. Patients with HCHF had a similar clinical profile, but only one‐third had implantable cardioverter defibrillators. In‐hospital mortality was 5.3% for AHF patients and 7.5% at 30 days after hospital discharge.

Conclusion

Heart failure patients in Saudi Arabia present at a relatively younger age, have a much higher rate of diabetes mellitus, and predominantly have LV systolic dysfunction, which is mainly ischaemic in origin, compared with  patients in developed countries. The preliminary results of the study show potential targets for improvement in care.
The effect of cardiac resynchronization therapy on left ventricular diastolic function assessed with speckle‐tracking echocardiography
Authors: Shanks Miriam , Antoni M. Louisa , Hoke Ulas , Bertini Matteo , Ng Arnold C.T. , Auger Dominique , Marsan Nina Ajmone , van Erven Lieselot , Holman Eduard R. , Schalij Martin J. , Bax Jeroen J. , Delgado Victoria
Published: August 2011

Aims

Changes in left ventricular (LV) diastolic function after cardiac resynchronization therapy (CRT) in relation to LV reverse remodelling and heart failure aetiology have not been extensively characterized. The aims of the study were to evaluate changes in LV diastolic function with speckle‐tracking echocardiography in relation to: (i) cardiac resynchronization therapy response (LV remodelling) and (ii) heart failure aetiology.

Methods and results

A total of 192 heart failure patients undergoing CRT implantation were evaluated. Speckle‐tracking echocardiography was performed before and 6 months after implantation and reliable analysis was obtained in 188 patients. Left ventricular diastolic function was assessed by measuring diastolic strain rate during the isovolumic relaxation period (SRIVR) and by calculating the ratio of peak transmitral E‐wave to SRIVR (E/SRIVR). Changes in LV diastolic parameters were evaluated in responders and non‐responders and in patients with ischaemic and non‐ischaemic cardiomyopathy. Response to CRT was defined as ≥15% reduction in LV end‐systolic volume at 6 months follow‐up. One‐hundred and nine patients (58%) were defined as responders. Significant improvements in LV diastolic performance were observed in responders with improvement in SRIVR (from 0.14 ± 0.08 to 0.18 ± 0.12 s−1, P= 0.001) and E/SRIVR (from 834 ± 840 to 641 ± 612, P= 0.04). In addition, LV relaxation improved in patients with non‐ischaemic aetiology (SRIVR: from 0.15 ± 0.08 to 0.19 ± 0.13 s−1, P= 0.004). In contrast, LV relaxation did not improve in non‐responders and in patients with ischaemic heart disease.

Conclusions

Novel diastolic strain rate indices are useful for evaluating changes in LV diastolic function after CRT. Improvement in diastolic function was only observed in responders to CRT and patients with non‐ischaemic aetiology.
Masculinized female yellow-bellied marmots initiate more social interactions
Authors: Monclús Raquel , Cook Taylor , Blumstein Daniel T.
Published: August 2011

The presence of male siblings
in utero
influences female morphology and life-history traits because testosterone transferred among foetuses may masculinize females. Similarly, litter sex composition might alter the display of sexually dimorphic behaviour, such as play and allogrooming, since they are modulated by androgens. We explored whether masculinization alters the frequency of play and sociopositive behaviour in female yellow-bellied marmots (
Marmota flaviventris
). We found that masculinized juvenile females were more likely to initiate play and allogrooming, but yearling females exhibited higher levels of oestrogen-modulated sociopositive behaviours. Additionally, the more they interacted, the greater number of different partners they interacted with. Our results suggest that masculinization increases the rate of age-dependent social behaviour. This probably works by increasing exploration that predisposes individuals to higher encounter rates. Further support comes from previous findings showing that masculinized females were more likely to disperse. Our study stresses the importance of considering litter sex composition as a fitness modulator.
From non-local gap solitary waves to bound states in periodic media
Authors: Akylas T. R. , Hwang Guenbo , Yang Jianke
Published: August 2011

Solitary waves in one-dimensional periodic media are discussed by employing the nonlinear Schrödinger equation with a spatially periodic potential as a model. This equation admits two families of gap solitons that bifurcate from the edges of Bloch bands in the linear wave spectrum. These fundamental solitons may be positioned only at specific locations relative to the potential; otherwise, they become non-local owing to the presence of growing tails of exponentially small amplitude with respect to the wave peak amplitude. Here, by matching the tails of such non-local solitary waves, high-order locally confined gap solitons, or bound states, are constructed. Details are worked out for bound states comprising two non-local solitary waves in the presence of a sinusoidal potential. A countable set of bound-state families, characterized by the separation distance of the two solitary waves, is found, and each family features three distinct solution branches that bifurcate near Bloch-band edges at small, but finite, amplitude. Power curves associated with these solution branches are computed asymptotically for large solitary-wave separation, and the theoretical predictions are consistent with numerical results.
Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus

Verrucosispora
Authors: Xi Lijun , Zhang Limin , Ruan Jisheng , Huang Ying
Published: August 2011

A

Micromonospora

-like strain, RtIII47T, was isolated from a mangrove swamp in Sanya, Hainan Province, China. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus

Verrucosispora

and shared the highest sequence similarity with

Verrucosispora lutea

YIM 013T (98.0 %). The strain also showed high 16S rRNA gene sequence similarities to

Micromonospora olivasterospora

DSM 43868T (97.9 %),

Plantactinospora mayteni

YIM 61359T (97.9 %),

Salinispora tropica

CNB-440T (97.8 %),

Micromonospora peucetia

DSM 43363T (97.7 %),

Micromonospora auratinigra

TT1-11T (97.7 %),

Verrucosispora sediminis

CGMCC 4.3550T (97.6 %) and

Salinispora arenicola

CNH-643T (97.5 %). Phylogenetic analysis based on the gyrB gene sequence supported the conclusion that strain RtIII47T should be assigned to the genus

Verrucosispora

. DNA–DNA relatedness between strain RtIII47T and the most closely related type strain,

V. lutea

YIM 013T, was less than 40 %. Chemotaxonomic results confirmed the taxonomic position of the isolate in the genus

Verrucosispora

, and revealed differences at the species level in polar lipids, whole-cell sugars and DNA G+C content. A combination of physiological and biochemical tests also distinguished this strain from other

Verrucosispora

species. Based on genotypic and phenotypic observations, strain RtIII47T ( = CGMCC 4.5826T  = NBRC 106684T) is proposed as the type strain of a novel species, Verrucosispora qiuiae sp. nov. An emended description of the genus

Verrucosispora

is also provided.
Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil
Authors: Lin Shih-Yao , Shen Fo-Ting , Lai Wei-An , Zhu Zhi-Long , Chen Wen-Ming , Chou Jui-Hsing , Lin Zih-Yu , Young Chiu-Chung
Published: August 2011

In the present study, a yellow-pigmented, Gram-negative, short rod-shaped novel bacterium that was capable of degrading a wide range of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) was isolated from agricultural soil located in Yunlin County, Taiwan. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus

Sphingomonas

as an independent lineage adjacent to a subclade containing

Sphingomonas fennica

K101T,

Sphingomonas histidinilytica

UM2T,

Sphingomonas wittichii

RW1T and

Sphingomonas haloaromaticamans

A175T. 16S rRNA gene sequence analysis of strain CC-Nfb-2T showed highest sequence similarity to

S. fennica

K101T (96.2 %),

S. histidinilytica

UM2T (96.1 %),

S. wittichii

RW1T (95.9 %),

S. haloaromaticamans

A175T (95.7 %), and

Sphingobium ummariense

RL-3T (94.7 %); lower sequence similarities were observed with strains of all other

Sphingomonas

species. The strain contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and diphosphatidylglycerol. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) C16 : 0 and 11-methyl C18 : 1ω7c; C14 : 0 2-OH was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus

Sphingomonas

. The serine palmitoyl transferase gene (spt) was also detected and sphingolipid synthesis was confirmed. The predominant isoprenoid quinone system was ubiquinone (Q-10) and the isolate contained sym-homospermidine as the major polyamine. The DNA G+C content of the isolate was 62.8±0.8 mol%. On the basis of chemotaxonomic, phenotypic and phylogenetic data, strain CC-Nfb-2T represents a novel species within the genus

Sphingomonas

, for which the name Sphingomonas formosensis sp. nov. is proposed; the type strain is CC-Nfb-2T ( = BCRC 80272T = DSM 24164T).
Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family Desulfovibrionaceae isolated from marine mangrove sediment
Authors: Zhao Chao , Gao Zhaoming , Qin Qiwei , Li Fuying , Ruan Lingwei
Published: August 2011

A taxonomic study was carried out on strain P1T, which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5–2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22–44 °C (optimum, 35–40 °C) and pH range 5.5–8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5 % (w/v) (optimum, 0.5 %). Strain P1Tutilized hydrogen, succinate,l-malate, citrate, oxalate,dl-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H2and CO2. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1Tformed a distinct evolutionary lineage within the familyDesulfovibrionaceae. Strain P1Twas most closely related to members of the generaDesulfovibrio(92.0–94.3 % 16S rRNA gene sequence similarity),Desulfocurvus(91.1 %),Bilophila(87.9 %) andLawsonia(86.0 %) of the familyDesulfovibrionaceae. The DNA G+C content of strain P1Twas 64.5 mol% and the major cellular fatty acids were iso-C15 : 0(18.8 %), anteiso-C15 : 0(5.0 %), C16 : 0(14.2 %) and iso-C17 : 1ω9c(24.4 %). The predominant menaquinone was MK-7 (97 %). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1Twas distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1Trepresents a novel species of a new genus, for which the nameDesulfobaculum xiamenensisgen. nov., sp. nov. is proposed. The type strain ofDesulfobaculum xiamenensisis P1T( = CGMCC 1.5166T = DSM 24233T).
Analysis of two-component sensor proteins involved in the response to acid stimuli in Streptococcus pyogenes
Authors: Ichikawa Mariko , Minami Masaaki , Isaka Masanori , Tatsuno Ichiro , Hasegawa Tadao
Published: August 2011

The virulence of Streptococcus pyogenes depends on proteins that are produced by this bacterium. The production of virulence proteins depends on environmental factors, and two-component regulatory systems are considered to be involved in sensing these factors. One of the environmental factors is acid stimuli. We established knockout strains in all speculated two-component regulatory sensor proteins of the M1 clinical strain of S. pyogenes and examined their relevance to acid stimuli. The parental strain and its derived knockout strains were cultured in a medium adjusted to pH 7.6 or 6.0, and their growth in broth was compared. The spy1622 sensor knockout strain showed significant growth reduction compared with the parental strain in broth at pH 6.0, suggesting that the Spy1622 two-component sensor protein is involved in sensing acid stimuli. To further examine the role of the Spy1622 two-component sensor protein in virulence, blood bactericidal assays and mouse infection model experiments were performed. We found that the spy1622 knockout strain was less virulent than the parental strain, which suggests that the Spy1622 two-component sensor protein could play an important role in virulence.
Structure–function analysis of HsiF, a gp25-like component of the type VI secretion system, in Pseudomonas aeruginosa
Authors: Lossi Nadine S. , Dajani Rana , Freemont Paul , Filloux Alain
Published: August 2011

Bacterial pathogens use a range of protein secretion systems to colonize their host. One recent addition to this arsenal is the type VI secretion system (T6SS), which is found in many Gram-negative bacteria. The T6SS involves 12–15 components, including a ClpV-like AAA+ ATPase. Moreover, the VgrG and Hcp components have been proposed to form a puncturing device, based on structural similarity to the tail spike components gp5/gp27 and the tail tube component gp19 of the T4 bacteriophage, respectively. Another T6SS component shows similarity to a T4 phage protein, namely gp25. The gp25 protein has been proposed to have lysozyme activity. Other T6SS components do not exhibit obvious similarity to characterized T4 phage components. The genome of Pseudomonas aeruginosa contains three T6SS gene clusters. In each cluster a gene encoding a putative member of the gp25-like protein family was identified, which we called HsiF. We confirmed this similarity by analysing the structure of the P. aeruginosa HsiF proteins using secondary and tertiary structure prediction tools. We demonstrated that HsiF1 is crucial for the T6SS-dependent secretion of Hcp and VgrG. Importantly, lysozyme activity of HsiF proteins was not detectable, and we related this observation to the demonstration that HsiF1 localizes to the cytoplasm of P. aeruginosa. Finally, our data showed that a conserved glutamate, predicted to be required for proper HsiF folding, is essential for its function. In conclusion, our data confirm the central role of HsiF in the T6SS mechanism, provide information on the predicted HsiF structure, and call for reconsideration of the function of gp25-like proteins.
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
Authors: Skelly Daniel A. , Johansson Marnie , Madeoy Jennifer , Wakefield Jon , Akey Joshua M.
Published: August 2011

Variation in gene expression is thought to make a significant contribution to phenotypic diversity among individuals within populations. Although high-throughput cDNA sequencing offers a unique opportunity to delineate the genome-wide architecture of regulatory variation, new statistical methods need to be developed to capitalize on the wealth of information contained in RNA-seq data sets. To this end, we developed a powerful and flexible hierarchical Bayesian model that combines information across loci to allow both global and locus-specific inferences about allele-specific expression (ASE). We applied our methodology to a large RNA-seq data set obtained in a diploid hybrid of two diverse Saccharomyces cerevisiae strains, as well as to RNA-seq data from an individual human genome. Our statistical framework accurately quantifies levels of ASE with specified false-discovery rates, achieving high reproducibility between independent sequencing platforms. We pinpoint loci that show unusual and biologically interesting patterns of ASE, including allele-specific alternative splicing and transcription termination sites. Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes.
Epigenetic regulation of normal human mammary cell type–specific miRNAs
Authors: Vrba Lukas , Garbe James C. , Stampfer Martha R. , Futscher Bernard W.
Published: August 2011

Epigenetic mechanisms are important regulators of cell type–specific genes, including miRNAs. In order to identify cell type–specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type–specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA genes were epigenetically repressed in nonexpressing cells by DNA methylation (38%) and H3K27me3 (58%), with only a small set of miRNAs (21%) showing a dual epigenetic repression where both DNA methylation and H3K27me3 were present at their promoters, such as MIR10A and MIR10B. Individual miRNA clusters of closely related miRNA gene families can each display cell type–specific repression by the same or complementary epigenetic mechanisms, such as the MIR200 family, and MIR205, where fibroblasts repress MIR200C/141 by DNA methylation, MIR200A/200B/429 by H3K27me3, and MIR205 by both DNA methylation and H3K27me3. Since deregulation of many of the epigenetically regulated miRNAs that we identified have been linked to disease processes such as cancer, it is predicted that compromise of the epigenetic control mechanisms is important for this process. Overall, these results highlight the importance of epigenetic regulation in the control of normal cell type–specific miRNA expression.
Generation of Human Fab Antibody Libraries: PCR Amplification and Assembly of Light- and Heavy-Chain Coding Sequences
Authors: Andris-Widhopf Jennifer , Steinberger Peter , Fuller Roberta , Rader Christoph , Barbas Carlos F.
Published: August 2011

INTRODUCTION

The development of therapeutic antibodies for use in the treatment of human diseases has long been a goal for many researchers in the antibody field. One way to obtain these antibodies is through phage-display libraries constructed from human lymphocytes. This protocol describes the construction of human Fab (fragment antigen binding) antibody libraries. In this method, the individual rearranged heavy- and light-chain variable regions are amplified separately and are linked through a series of overlap polymerase chain reaction (PCR) steps to give the final Fab products that are used for cloning.
Live Cell Imaging of Yeast
Authors: Rines Daniel R. , Thomann Dominik , Dorn Jonas F. , Goodwin Paul , Sorger Peter K.
Published: August 2011

INTRODUCTION

The development of cloning vectors for green fluorescent protein (GFP) and the simplicity of yeast reverse genetics allow straightforward labeling of yeast proteins in living cells. Budding and fission yeast are therefore attractive organisms in which to study dynamic cellular processes such as growth, cell division, and morphogenesis using live cell fluorescence microscopy. This article focuses on methods to culture, mount, and observe budding yeast cells using three-dimensional (3D) microscopy, but the methods are broadly applicable to other types of cells and other imaging techniques. The emphasis is on 3D imaging, because yeast cells are roughly spherical, and most organelles in yeast move in three dimensions. Three-dimensional imaging also makes it possible to apply image restoration methods (e.g., deconvolution) to obtain sharper images with better definition. This is important, because yeast cells are small (haploid Saccharomyces cerevisiae cells have a diameter of ~4–5 µm) relative to the resolution of even the best optical microscope (~0.25 µm).
Stress-Responsive Mitogen-Activated Protein Kinases Interact with the EAR Motif of a Poplar Zinc Finger Protein and Mediate Its Degradation through the 26S Proteasome
Authors: Hamel Louis-Philippe , Benchabane Meriem , Nicole Marie-Claude , Major Ian T. , Morency Marie-Josée , Pelletier Gervais , Beaudoin Nathalie , Sheen Jen , Séguin Armand
Published: August 2011

Mitogen-activated protein kinases (MAPKs) contribute to the establishment of plant disease resistance by regulating downstream signaling components, including transcription factors. In this study, we identified MAPK-interacting proteins, and among the newly discovered candidates was a Cys-2/His-2-type zinc finger protein named PtiZFP1. This putative transcription factor belongs to a family of transcriptional repressors that rely on an ERF-associated amphiphilic repression (EAR) motif for their repression activity. Amino acids located within this repression motif were also found to be essential for MAPK binding. Close examination of the primary protein sequence revealed a functional bipartite MAPK docking site that partially overlaps with the EAR motif. Transient expression assays in Arabidopsis (Arabidopsis thaliana) protoplasts suggest that MAPKs promote PtiZFP1 degradation through the 26S proteasome. Since features of the MAPK docking site are conserved among other EAR repressors, our study suggests a novel mode of defense mechanism regulation involving stress-responsive MAPKs and EAR repressors.