bluuebunny/crossref_metadata_2025 huggingface dataset:
Breadth of Emergency Medical Training in Pakistan
Authors: Lin Janet Y. , Ahmed Saroosh , Brander Caroline
Published: January 2013

Introduction

Emergency medical care in Pakistan has not been a priority of medical education and training because of the country's need to address its lack of primary care. Resources and trained personnel are scarce. Despite these challenges, the value of emergency medical care is gaining attention. The objective of this study was to explore the breadth of Emergency Medicine training in Pakistan through an analysis of an Emergency Medicine residency in a teaching hospital. The Aga Khan University Hospital in Karachi is a teaching institution with the only Emergency Medicine residency program in the region. It was started in 2000, led by US-trained physicians, and it laid the foundation for Emergency Medicine in the country.

Methods

The study was conducted over a four-week period in January of 2009. Data collection consisted of three components: (1) a survey of the Emergency Department and hospital services; (2) a survey of the Emergency Medicine training curriculum; and (3) a retrospective chart review of every tenth patient seen in the Aga Khan Emergency Department from December 1-14, 2008.

Results

The training program is similar to that of the US models. Of the 153 patients selected for the chart review, the majority presented with GI complaints. Of these, 51 (33%) were admitted to the hospital; 20% (n = 15) left against medical advice; the remaining 57% (n = 87) were discharged.

Discussion/Conclusion

The hospital admitted patients with complaints that were expected in the region. Although Aga Khan University Hospital is a pioneer in establishing Emergency Medicine as an official medical discipline in the region, the hospital's obstetrics and gynecology, trauma, toxicology and prehospital services training do not meet current curriculum standards set forth by the Society of Academic Emergency Medicine and the Council of Emergency Medicine Residency Directors. Nevertheless, the review provides a snapshot of the development of Emergency Medical Services in a developing nation. This information may assist other nations that are interested in developing such programs.

LinJY, AhmedS, BranderC. Breadth of emergency medical training in Pakistan. Prehosp Disaster Med. 2013;28(2):1-5.
Better Understanding of SN Ia from Near Infrared Observations
Authors: Kirshner Robert P.
Published: January 2013

Type Ia supernovae (SN Ia) are explosions of white dwarfs whose distances can be measured to a precision of ~5% using luminosity information that is encoded in the light curve shape. This property has been very successfully exploited to measure the history of cosmic expansion and to infer the presence of dark energy. But to learn the properties of dark energy and determine whether it is different from the cosmological constant demands higher precision and better accuracy than optical light curves alone can provide. The largest systematic uncertainties come from light curve fitters, photometric calibration errors, and from poor knowledge of the scattering properties of dust along the line of sight. Efforts to use SN Ia spectra as luminosity indicators have had some success, but have not produced a big step forward. Fortunately, observations of SN Ia in the near infrared (NIR), from 1 to 2 microns, offer a very promising path to better knowledge of the Hubble constant, improved constraints on dark energy, and, possibly, a route to discriminating the progenitor paths for SN Ia explosions.
Studying the Progenitors of Type Ia Supernovae via Lensing with the Kepler Survey
Authors: Di Stefano Rosanne
Published: January 2013

Every model for the progenitors of Type Ia supernovae (SNe Ia) requires that binaries pass through an epoch during which a white dwarf (WD) orbits a non-degenerate star. Depending on the mass of the WD, the radius of its companion, and the orbital separation, the WD may lens its companion. The lensing event would be an antitransit, an increase in light from the companion that can rise to the level of a percent or more, during an interval of hours. Antitransits are periodic. By studying them we can determine the properties of both the WD and its companion, as well as the characteristics of the orbit. Lensing events of this type are almost certain to be observed by the Kepler mission, while some can even be detected by ground-based surveys. Antitransits and transits will both provide valuable insight into the end states of common envelope evolution and of stable mass transfer, resolving issues that must be understood before we can fully unravel the progenitor puzzle.
The Post-Nova Population
Authors: Schmidtobreick Linda , Tappert Claus , Ederoclite Alessandro , Vogt Nikolaus
Published: January 2013

We present our on-going project to unveil the post-nova population by re-discovering old novae that have been lost after the initial outburst and in which the binary itself is unobserved. We take UBVR photometry for candidate selection, long-slit spectroscopy to confirm these candidates, and time-resolved spectroscopy to measure the orbital period of the newly confirmed post-novae. Some preliminary results are shown as examples.
The Helium Abundance in the Ejecta of U Scorpii
Authors: Maxwell M. P. , Rushton M. T. , Darnley M. J. , Worters H. L. , Bode M. F. , Evans A. , Eyres S. P. S. , Kouwenhoven M. B. N. , Walter F. M. , Hassall B. J. M.
Published: January 2013

U Scorpii was observed in outburst for the tenth time in January 2010. We obtained optical and near-infrared spectroscopy from which we derive a helium abundance of N(He)/N(H) = 0.056±0.020 from the most reliable lines available; this is lower than most other estimates and indicates that the secondary is not helium-rich, as previous studies have suggested. Velocities are found to be up to 14,000 km s−1 in broad components and up to 1,800 km s−1 in narrow line components. The reddening of U Sco is found to be E(B-V) = 0.14 ± 0.12.
He-accreting WDs as SNe Ia Progenitors
Authors: Piersanti Luciano , Tornambé Amedeo , Yungelson Lev , Straniero Oscar
Published: January 2013

We investigate the thermal response of CO WDs accreting He-rich matter directly from their companions in binary systems. Our results suggest that the He-channel cannot provide progenitors for the majority of “normal” SNe Ia.
A Search for Type Ia Supernova Progenitors: the Central Stars of the Planetary Nebulae NGC 2392 and NGC 6026
Authors: Danehkar A. , Frew D. J. , De Marco O. , Parker Q. A.
Published: January 2013

We use photoionization modeling to assess the binary nature of the central stars of NGC 2392 and NGC 6026. If they are close binaries, they are potential Type Ia supernovae (SNe Ia) progenitors if the total mass exceeds the Chandrasekhar limit. We show that the nucleus of NGC 2392 likely has a hot, massive (≃1 M⊙) white dwarf companion, and a total mass of ~1.6 M⊙, making it an especially interesting system. The binary mass in NGC 6026 is less, ~1.1 M⊙. Even though its orbital period is short, it is not considered to be an SNe~Ia progenitor.
Galactic Chemical Evolution in the Context of the Recently Revealed SNe Ia Delay Time Distribution
Authors: Tsujimoto Takuji
Published: January 2013

The Galaxy is composed of four distinct structures, i.e., halo, bulge, and thick and thin disks, that are formed and evolved on different timescales; thus accordingly the speeds of chemical enrichment are different from one another, which is imprinted in individual stellar abundances. To decipher them, precise knowledge of the timing of the release of nucleosynthesis materials from various production sites is critical. The delay time distribution (DTD) of Type Ia supernovae (SNe Ia), recently revealed by the SNe Ia surveys of external galaxies, is incorporated into the models of chemical evolution for each structure. Here we report that the observed chemical properties for the thin and thick disks are compatible with a new SNe Ia DTD, and suggests a close chemical connection between the two in the way that the thin disk is formed from gas left after thick disk formation. This nicely explains the lack of thin disk stars with [Fe/H] ≲ −0.8. In this new context, a top-heavy IMF for the bulge is firmly confirmed. Finally we discuss the possibility of some modification of the DTD that might be considered for the halo case.
Towards an International Law of Brigandage: Interpretative Engineering for the Regulation of Natural Resources Exploitation
Authors: D'ASPREMONT Jean
Published: January 2013

The exploitation of natural resources in times of conflict has been the object of a prolific literature due to the extremely laconic character of the standards of conduct prescribed by the Hague and Geneva Conventions. Such laconicism has led scholars to be creative in ensuring that this central aspect of modern conflicts falls within the scope of existing legal instruments. This article starts by depicting the rich argumentative creativity developed by scholars and experts to ensure a more comprehensive regulation of what has often been perceived as a form of international brigandage. Subsequently it reflects on the biases of the professional community that has dedicated its efforts to the elaboration of a fairer framework of natural resources exploitation in times of conflict. In particular, it formulates some critical remark on the “just world business” that has dictated the methodology behind most of the interpretative engineering to be found.
The serine/threonine phosphatase PPM1B (PP2Cβ) selectively modulates PPARγ activity
Authors: Tasdelen Ismayil , van Beekum Olivier , Gorbenko Olena , Fleskens Veerle , van den Broek Niels J. F. , Koppen Arjen , Hamers Nicole , Berger Ruud , Coffer Paul J. , Brenkman Arjan B. , Kalkhoven Eric
Published: January 2013

Reversible phosphorylation is a widespread molecular mechanism to regulate the function of cellular proteins, including transcription factors. Phosphorylation of the nuclear receptor PPARγ (peroxisome-proliferator-activated receptor γ) at two conserved serine residue (Ser112 and Ser273) results in an altered transcriptional activity of this transcription factor. So far, only a very limited number of cellular enzymatic activities has been described which can dephosphorylate nuclear receptors. In the present study we used immunoprecipitation assays coupled to tandem MS analysis to identify novel PPARγ-regulating proteins. We identified the serine/threonine phosphatase PPM1B [PP (protein phosphatase), Mg2+/Mn2+ dependent, 1B; also known as PP2Cβ] as a novel PPARγ-interacting protein. Endogenous PPM1B protein is localized in the nucleus of mature 3T3-L1 adipocytes where it can bind to PPARγ. Furthermore we show that PPM1B can directly dephosphorylate PPARγ, both in intact cells and in vitro. In addition PPM1B increases PPARγ-mediated transcription via dephosphorylation of Ser112. Finally, we show that knockdown of PPM1B in 3T3-L1 adipocytes blunts the expression of some PPARγ target genes while leaving others unaltered. These findings qualify the phosphatase PPM1B as a novel selective modulator of PPARγ activity.
Identification of novel candidate phosphatidic acid-binding proteins involved in the salt-stress response of Arabidopsis thaliana roots
Authors: McLoughlin Fionn , Arisz Steven A. , Dekker Henk L. , Kramer Gertjan , de Koster Chris G. , Haring Michel A. , Munnik Teun , Testerink Christa
Published: January 2013

PA (phosphatidic acid) is a lipid second messenger involved in an array of processes occurring during a plant's life cycle. These include development, metabolism, and both biotic and abiotic stress responses. PA levels increase in response to salt, but little is known about its function in the earliest responses to salt stress. In the present study we have combined an approach to isolate peripheral membrane proteins of Arabidopsis thaliana roots with lipid-affinity purification, to identify putative proteins that interact with PA and are recruited to the membrane in response to salt stress. Of the 42 putative PA-binding proteins identified by MS, a set of eight new candidate PA-binding proteins accumulated at the membrane fraction after 7 min of salt stress. Among these were CHC (clathrin heavy chain) isoforms, ANTH (AP180 N-terminal homology) domain clathrin-assembly proteins, a putative regulator of potassium transport, two ribosomal proteins, GAPDH (glyceraldehyde 3-phosphate dehydrogenase) and a PI (phosphatidylinositol) 4-kinase. PA binding and salt-induced membrane recruitment of GAPDH and CHC were confirmed by Western blot analysis of the cellular fractions. In conclusion, the approach of the present study is an effective way to isolate biologically relevant lipid-binding proteins and provides new leads in the study of PA-mediated salt-stress responses in roots.
Compact X‐band CMOS bidirectional gain amplifier without T/R switches
Authors: Cho Moon‐Kyu , Baek Donghyun , Kim Jeong‐Geun
Published: January 2013

Presented is a compact X‐band bidirectional gain amplifier in 0.18 μm CMOS, which eliminates two T/R switches in the conventional one. The gain of >14 dB and the in/output return losses of >8 dB are achieved at 8–14 GHz. The measured output P1dB is ~1 dBm at 10 GHz. The chip size is 0.62 × 0.60 mm2, which is compact due to the removal of two T/R switches for the bidirectional operation. The DC power consumption is 54 mW at 1.8 V supply voltage. Nearly identical performance is achieved in the forward and reverse operations at X‐band. To the authors’ knowledge, this is the first demonstration of an X‐band CMOS bidirectional gain amplifier with the smallest size.
Direction detector for distributed targets in unknown noise and interference
Authors: Bandiera F. , Besson O. , Ricci G.
Published: January 2013

Adaptive detection of distributed radar targets in homogeneous Gaussian noise plus subspace interference is addressed. It is assumed that the actual steering vectors lie along a fixed and unknown direction of a preassigned and known subspace, while interfering signals are supposed to belong to an unknown subspace, with directions possibly varying from one resolution cell to another. The resulting detection problem is formulated in the framework of statistical hypothesis testing and solved using an ad hoc algorithm strongly related to the generalised likelihood ratio test. A performance analysis, carried out also in comparison to natural benchmarks, is presented.
Indoor three‐dimensional location estimation based on LED visible light communication
Authors: Yang S.‐H. , Jeong E.‐M. , Kim D.‐R. , Kim H.‐S. , Son Y.‐H. , Han S.‐K.
Published: January 2013

A novel concept for integrating visible light communications (VLC) with three‐dimensional indoor positioning is presented. A VLC link based on transmitter and receiver characteristics using experimental measurements was modelled. Proposed is a three‐dimensional positioning algorithm using received signal strength indication, which changes based on the angle and distance of the location based service. To reduce inter‐cell interference, the transmitter's location code was sent using different subcarriers. A demonstration shows that the proposed algorithm can obtain a user's position, including height, accurately and without inter‐cell interference.
Hysteresis settling technique for CMOS comparators based on substrate voltage
Authors: Rodrigues C.R. , Muller C. , Neto D.J. Monteiro
Published: January 2013

A hysteresis is a widely employed solution to mitigate the effect of noise on comparators. Presented is a very simple technique, applicable to any topology of MOS differential comparator. It consists of imposing different bulk‐source voltage to the input MOS differential pair. Depending on the polarity of the input signal, one substrate is connected to the rail voltage and the other to a reference control voltage. So, when the slope inverts the connections are switched through pMOS switches. Simulation results show that the hysteresis up to 302,6 mV can be linearly controlled for bulk voltages ranging from 0 to 500 mV, for XFAB 0.35XH technology. Finally, an aproximation for the control rule is proposed.
Fast SVM‐based epileptic seizure prediction employing data prefetching
Authors: Lim Chungsoo , Nam Sang Won , Chang Joon‐Hyuk
Published: January 2013

To achieve high prediction accuracy for epileptic seizure prediction, a support vector machine (SVM) has been adopted due to its robust classification performance. However, in order to use an SVM for real‐time applications such as seizure prediction, the slow classification speed of an SVM should be addressed. For this purpose, data prefetching that enhances the classification speed of an SVM by mitigating the gap between the processor and the main memory is employed.
Terahertz zone plates with integrated laser‐ablated bandpass filters
Authors: Minkevičius L. , Voisiat B. , Mekys A. , Venckevičius R. , Kašalynas I. , Seliuta D. , Valušis G. , Račiukaitis G. , Tamošiu¯nas V.
Published: January 2013

Properties of zone plates with integrated bandpass filters were simulated numerically and demonstrated experimentally for 0.76 THz frequency. Finite‐difference time‐domain simulations were used to predict properties of a conventional zone plate and laser‐ablated zone plate with resonant filter areas. Zone plates were produced employing laser direct writing and characterised by Fourier spectroscopy and an optically pumped terahertz laser.
Discrete‐time multiserver queue with impatient customers
Authors: Kim Jeongsim , Kim Bara , Kang Jangha
Published: January 2013

This reported work considers a discrete‐time multiserver queue in which the customers wait for service for a limited time with a general distribution and leave the system if the service has not begun within that time. The customers arrive according to a Bernoulli process and the service times are geometrically distributed. Presented are exact expressions for the loss probability and the queue length distribution.
Error ratio model for synchronised‐OOK IR‐UWB receivers in AWGN channels
Authors: Crepaldi M. , Kinget P.R.
Published: January 2013

Synchronised On/Off keying (S‐OOK) is a pulse modulation format where timing synchronisation pulses are embedded with each bit in the data stream resulting in a 1.5 pulse/bit format, but allowing for synchronisation and demodulation with a single block. In this reported work, the error ratio for S‐OOK symbols received in a non‐fading AWGN channel is analysed and a mathematical model aware of the physical parameters of a CMOS integrated prototype is introduced. Using this model, the S‐OOK RX sensitivity is shown to be close to that of a high‐threshold OOK RX for similar error‐ratios but assuming perfect synchronisation.
Gaussian process framework for pervasive estimation of swimming velocity with body‐worn IMU
Authors: Dadashi F. , Millet G.P. , Aminian K.
Published: January 2013

Presented is an accurate swimming velocity estimation method using an inertial measurement unit (IMU) by employing a simple biomechanical constraint of motion along with Gaussian process regression to deal with sensor inherent errors. Experimental validation shows a velocity RMS error of 9.0 cm/s and high linear correlation when compared with a commercial tethered reference system. The results confirm the practicality of the presented method to estimate swimming velocity using a single low‐cost, body‐worn IMU.
Woven piezoelectric structure for stretchable energy harvester
Authors: Yun D. , Yun K.‐S.
Published: January 2013

The energy harvester is an attractive power source for wireless portable electronics, especially in applications for handheld and wearable electronic devices. Proposed is a woven piezoelectric structure for possible application as a wearable energy harvester. The proposed device consists of polymer column threads and a piezoelectric film weaving them into stitches in the row. Polymer patches are alternately patterned on the upper and bottom sides of the piezoelectric film, where the charges are generated when subjected to a stretching and contraction motion. A maximum peak power density of 0.63 mW/cm2 was obtained from repeated stretching and contraction motion at an operation frequency of 8 Hz.
Improved PMEPR bound on near‐complementary sequences constructed by Yu and Gong
Authors: Wang Z. , Wu G. , Li H.
Published: January 2013

A family of near‐complementary sequences with peak‐to‐mean envelope power ratio (PMEPR) < 4 was proposed for peak power control in multicarrier communications by Yu and Gong recently. In this Letter, the PMEPR bound of these near‐complementary sequences are improved to asymptotically equivalent to 2. Based on the proof, new near‐complementary sequences constructed by other seed pairs are proposed. The PMEPR of these near‐complementary sequences are still asymptotically equivalent to 2.
8‐channel 20 kHz to 200 MHz Nyquist and compressive sampler in 0.5 μm CMOS
Authors: Murray T.S. , Pouliquen P.O. , Andreou A.G.
Published: January 2013

A report is presented on the hardware implementation of a parallel multi‐channel sampler in 0.5 μm CMOS technology. The system consists of eight parallel analogue processing channels, each one capable of modulation by a programmable binary chipping sequence. System operation is demonstrated in both Nyquist and compressive sampling of test signals.
Dual‐wavelength S‐band Tm3+:ZBLAN fibre laser with 0.6 nm wavelength spacing
Authors: Frison B. , Sarmani A.R. , Chen L.R. , Gu X. , Saad M.
Published: January 2013

A dual‐wavelength Tm3+:ZBLAN fibre laser operating around 1480 nm is demonstrated. A linear cascaded cavity with bidirectional upconversion pumping at 1064 nm was used; alternate single wavelength and dual‐wavelength operation is achieved by simple adjustment of the pump powers. A wavelength spacing of only 0.6 nm is obtained for dual‐wavelength operation.
Beyond Boussinesq-type equations: Semi-integrated models for coastal dynamics
Authors: Antuono M. , Brocchini M.
Published: January 2013

A novel approach for the description of both wave propagation and flow circulation in the nearshore zone has been defined. This is based on an integro-differential system which, at the leading-order, coincides with classical depth-averaged models (e.g., Boussinesq-type models) and, in addition, describes flow deviations from the depth-averaged values. Thanks to this feature, the proposed system enables exact calculation of the linear dispersion relation, of the linear shoaling coefficient, and of second-order nonlinear solutions for monochromatic waves. A simplified version of the original system has also been proposed. This latter model is exact up to the first order and predicts a linear shoaling coefficient which is comparable with the most advanced, fully nonlinear Boussinesq-type models. The general approach, which can be exploited to obtain a family of models, has clear computational advantages over those which solve the flow over the vertical and improves the flow description accuracy of typical depth-averaged models.
Green luminescence and room temperature ferromagnetism in Cu doped ZnO
Authors: Ahmed Khan Zaheer , Rai Abhishek , Roy Barman Sudipta , Ghosh Subhasis
Published: January 2013

We report room temperature ferromagnetism and its correlation with green luminescence band in Cu doped ZnO. Magnetic moment close to theoretical value has been obtained in high quality thin film achieved by optimizing different growth conditions. Rutherford back scattering and x-ray photoelectron spectroscopy were used to ascertain composition and the oxidation states of Cu inside the ZnO host. A correlation has been established between the Cu-induced green luminescence band and the magnetization in Cu doped ZnO.
Collection efficiency of photoelectrons injected into near- and supercritical argon gas
Authors: Borghesani A. F. , Lamp P.
Published: January 2013

Injection of photoelectrons into gaseous or liquid dielectrics is a widely used technique to produce cold plasmas in weakly ionized systems for investigating the transport properties of electrons. We report measurements of the collection efficiency of photoelectrons injected into dense argon gas for T = 152.7  K, close to the critical temperature Tc ≈ 150.9  K, and for T = 200.0  K. The high-field data agree with the Young-Bradbury model and with previous measurements below Tc and at an intermediate temperature above Tc. The effective, density-dependent electron-atom momentum transfer scattering cross section can be deduced. However, the weak-field data near Tc show large deviations from the theoretical model. We show that the electron behavior at weak field is influenced by electrostriction effects that are only important near the critical point.
Free energy surface of ST2 water near the liquid-liquid phase transition
Authors: Poole Peter H. , Bowles Richard K. , Saika-Voivod Ivan , Sciortino Francesco
Published: January 2013

We carry out umbrella sampling Monte Carlo simulations to evaluate the free energy surface of the ST2 model of water as a function of two order parameters, the density and a bond-orientational order parameter. We approximate the long-range electrostatic interactions of the ST2 model using the reaction-field method. We focus on state points in the vicinity of the liquid-liquid critical point proposed for this model in earlier work. At temperatures below the predicted critical temperature we find two basins in the free energy surface, both of which have liquid-like bond orientational order, but differing in density. The pressure and temperature dependence of the shape of the free energy surface is consistent with the assignment of these two basins to the distinct low density and high density liquid phases previously predicted to occur in ST2 water.
Spin-filtering and rectification effects in a Z-shaped boron nitride nanoribbon junction
Authors: Wan Haiqing , Zhou Benhu , Liao Wenhu , Zhou Guanghui
Published: January 2013

A Z-shaped junction constructed by a few-nanometer-long armchair-edged boron nitride nanoribbon (ABNNR) sandwiched between two semi-infinite zigzag-edged BNNR electrodes with different hydrogen-passivated edge treatment is proposed, and its spin-dependent electronic transport is studied by ab initiocalculations. It is found that a short ABNNR exhibits metallic behavior and can be used as a conduction channel. Interestingly, the spin-filtering and rectification effects exist in the junctions without any edge passivation or with boron-edge passivation. The analysis on the projected density of states and spatial distribution of molecular projected self-consistent Hamiltonian eigenstates gives an insight into the observed results for the system. Our results suggest that a BNNR-based nanodevices with spin-filtering and rectification effects may be synthesized from an hexagonal boron nitride sheet by properly tailoring and edge passivation.
Effect of ion temperature on ion-acoustic solitary waves in a magnetized plasma in presence of superthermal electrons
Authors: Singh S. V. , Devanandhan S. , Lakhina G. S. , Bharuthram R.
Published: January 2013

Obliquely propagating ion-acoustic soliatry waves are examined in a magnetized plasma composed of kappa distributed electrons and fluid ions with finite temperature. The Sagdeev potential approach is used to study the properties of finite amplitude solitary waves. Using a quasi-neutrality condition, it is possible to reduce the set of equations to a single equation (energy integral equation), which describes the evolution of ion-acoustic solitary waves in magnetized plasmas. The temperature of warm ions affects the speed, amplitude, width, and pulse duration of solitons. Both the critical and the upper Mach numbers are increased by an increase in the ion temperature. The ion-acoustic soliton amplitude increases with the increase in superthermality of electrons. For auroral plasma parameters, the model predicts the soliton speed, amplitude, width, and pulse duration, respectively, to be in the range of (28.7–31.8) km/s, (0.18–20.1) mV/m; (590–167) m, and (20.5–5.25) ms, which are in good agreement with Viking observations.
Alteration of chaotic advection in blood flow around partial blockage zone: Role of hematocrit concentration
Authors: Maiti Soumyabrata , Chaudhury Kaustav , DasGupta Debabrata , Chakraborty Suman
Published: January 2013

Spatial distributions of particles carried by blood exhibit complex filamentary pattern under the combined effects of geometrical irregularities of the blood vessels and pulsating pumping by the heart. This signifies the existence of so called chaotic advection. In the present article, we argue that the understanding of such pathologically triggered chaotic advection is incomplete without giving due consideration to a major constituent of blood: abundant presence of red blood cells quantified by the hematocrit (HCT) concentration. We show that the hematocrit concentration in blood cells can alter the filamentary structures of the spatial distribution of advected particles in an intriguing manner. Our results reveal that there primarily are two major impacts of HCT concentrations towards dictating the chaotic dynamics of blood flow: changing the zone of influence of chaotic mixing and determining the enhancement of residence time of the advected particles away from the wall. This, in turn, may alter the extent of activation of platelets or other reactive biological entities, bearing immense consequence towards dictating the biophysical mechanisms behind possible life-threatening diseases originating in the circulatory system.
Soil organic carbon content and storage of raised field wetlands in different functional zones of a typical shallow freshwater lake, China
Authors: Huang Laibin , Bai Junhong , Gao Haifeng , Xiao Rong , Liu Peipei , Chen Bin
Published: January 2013

Soil samples were collected in raised-field wetlands of five typical functional zones (inlet zone, water reserve zone, outlet zone, aquaculture zone, industrial zone) in Baiyangdian Lake, China, from a depth of 0–30 cm. The soil organic carbon (SOC) content, density, and storage, and carbon pool index (CPI) were calculated for each typical zone, and spatial distribution of SOC storage in the region was estimated using the ordinary kriging, interpolated value method. Our results showed that the average values of SOC content and storage decreased with depth along the soil profiles. Lowest values of SOC content and storage were observed in the inlet zone, whereas the outlet zone showed the highest SOC content and the water reserve zone showed the highest SOC storage. Surface soils had higher heterogeneity with higher values of SOC content and storage than deeper soils. Storage of SOC was much lower in the south-east of the water reserve zone and the east of the inlet zone than in the north-west of the water reserve zone or in the east of the whole Baiyangdian Lake. Values of CPI followed the order water reserve zone > aquaculture zone > outlet zone > industrial zone > inlet zone. The SOC was positively correlated with water content and negatively correlated with soil bulk density (P < 0.01), but had no significant correlation with other soil properties.
Wnt5a cooperates with canonical Wnts to generate midbrain dopaminergic neurons in vivo and in stem cells
Authors: Andersson Emma R. , Saltó Carmen , Villaescusa J. Carlos , Cajanek Lukas , Yang Shanzheng , Bryjova Lenka , Nagy Irina I. , Vainio Seppo J. , Ramirez Carmen , Bryja Vitezslav , Arenas Ernest
Published: January 2013

Wnts are a family of secreted proteins that regulate multiple steps of neural development and stem cell differentiation. Two of them, Wnt1 and Wnt5a, activate distinct branches of Wnt signaling and individually regulate different aspects of midbrain dopaminergic (DA) neuron development. However, several of their functions and interactions remain to be elucidated. Here, we report that loss of
Wnt1
results in loss of Lmx1a and
Ngn2
expression, as well as agenesis of DA neurons in the midbrain floor plate. Remarkably, a few ectopic DA neurons still emerge in the basal plate of
Wnt1

−/−

mice, where Lmx1a is ectopically expressed. These results indicate that
Wnt1
orchestrates DA specification and neurogenesis in vivo. Analysis of
Wnt1

−/−

;Wnt5a

−/−

mice revealed a greater loss of Nurr1
+
cells and DA neurons than in single mutants, indicating that
Wnt1
and
Wnt5a
interact genetically and cooperate to promote midbrain DA neuron development in vivo. Our results unravel a functional interaction between
Wnt1
and
Wnt5a
resulting in enhanced DA neurogenesis. Taking advantage of these findings, we have developed an application of Wnts to improve the generation of midbrain DA neurons from neural and embryonic stem cells. We thus show that coordinated Wnt actions promote DA neuron development in vivo and in stem cells and suggest that coordinated Wnt administration can be used to improve DA differentiation of stem cells and the development of stem cell-based therapies for Parkinson’s disease.
The 10-Year Course of Alcoholics Anonymous Participation and Long-Term Outcomes: A Follow-Up Study of Outpatient Subjects in Project MATCH
Authors: Pagano Maria E. , White William L. , Kelly John F. , Stout Robert L. , Tonigan J. Scott
Published: January 2013

This study investigates the 10-year course and impact of Alcoholics Anonymous (AA)-related helping (AAH), step-work, and meeting attendance on long-term outcomes. Data were derived from 226 treatment-seeking alcoholics recruited from an outpatient site in Project MATCH and followed for 10 years post treatment. Alcohol consumption, AA participation, and other-oriented behavior were assessed at baseline, end of the 3-month treatment period, and 1, 3, and 10 years post treatment. Controlling for explanatory baseline and time-varying variables, results showed significant direct effects of AAH and meeting attendance on reduced alcohol outcomes and a direct effect of AAH on improved other-oriented interest.
Do Changes in Selfishness Explain 12-Step Benefit? A Prospective Lagged Analysis
Authors: Tonigan J. Scott , Rynes Kristina , Toscova Radka , Hagler Kylee
Published: January 2013

12-Step attendance is associated with increased abstinence. A strong claim made in 12-step literature is that alcoholics are pathologically selfish and that working the 12 steps reduces this selfishness, which, in turn, leads to sustained alcohol abstinence. This study tested this assumption by investigating the linkages between 12-step attendance, pathological narcissism, and drinking. One hundred thirty early Alcohol Anonymous (AA) affiliates with limited AA and treatment histories were recruited from treatment and community-based AA. A majority of the sample was alcohol dependent and reported illicit drug use before recruitment. Participants were interviewed at intake and at 3, 6, and 9 months. A majority of participants attended AA meetings throughout follow-up and such attendance predicted increased abstinence and reduced drinking intensity. 12-Step affiliates were significantly higher on pathological narcissism (PN) relative to general population samples and their PN remained elevated. Contrary to predictions, PN was unrelated to 12-step meeting attendance and did not predict later abstinence or drinking intensity. The findings did not support the hypothesis that reductions in PN explain 12-step benefit. An alternative function for the emphasis placed on pathological selfishness in 12-step programs is discussed and a recommendation is made to use unobtrusive measures of selfishness in future research.
Olanzapine Abuse
Authors: Kumsar Neslihan Akkişi , Erol Atila
Published: January 2013

Olanzapine is a thienobenzodiazepine that blocks especially the serontonin (5-hydroxytryptamine [5-HT]) 5-HT2A and the dopamine D2 receptors as well as muscarinic (M1), histamine (H1), 5-HT2C, 5-HT3 to 5-HT6, adrenergic (αl), and D4 receptors. This case report presents an olanzapine abuse. A 48-year-old, primary school graduate, married woman applied to psychiatry clinic with tachycardia, insomnia, and anxiety complaints. In psychiatric evaluations, it was determined that these complaints have been continuing for 15 years at intervals and that she has been using citalopram 40 mg/day and olanzapine 50 mg/day for the last 3 years. As diabetes mellitus was diagnosed in follow-ups, interruption of olanzapine treatment was planned. The patient stated that she started taking the medicine again upon discomfort, increase in anxiety, dysphoria, insomnia, and nervousness, which started just after olanzapine was interrupted. She said that she was feeling dense stress when she did not take the medicine, and she thought that this situation would recover only by taking that medicine and hence she could not discontinue the medicine. In addition to medications with obvious abuse potential such as benzodiazepines and methylphenidate, and other stimulants, abuse of a number of commonly prescribed psychiatric medications has been reported. There are only 2 cases of olanzapine abuse in literature.
Egypt at the crossroads. Egypt’s future: three scenarios
Authors: Abdul-Majid Wahid
Published: January 2013

Egypt is undergoing dramatic changes and the shifts in its politics are wide ranging, touching upon almost the whole political system, which also includes the aspirations of the Egyptian people at this point. The hopes and fears of the Egyptian people have been high and subject to competing forces and agendas. There are many scenarios that reflect the dynamism that have characterized the Egyptian revolution and its aftermath. Furthermore, the fear barrier has been overcome and a larger segment of Egypt’s society has become acquainted with the principle of political participation, especially when today’s electronic age has provided the youth with the tools that enable that participation. This article seeks to explain the interaction of the dynamics that have been at play since the fall of the Hosni Mubarak regime and it provides an analysis of their positions. Three possible scenarios are provided, while an attempt at defining the newly emerging paradigm in Egyptian politics is explained.
Collagen remodeling by phagocytosis is determined by collagen substrate topology and calcium-dependent interactions of gelsolin with nonmuscle myosin IIA in cell adhesions
Authors: Arora P. D. , Wang Y. , Bresnick A. , Dawson J. , Janmey P. A. , McCulloch C. A.
Published: January 2013

We examine how collagen substrate topography, free intracellular calcium ion concentration ([Ca2+]i, and the association of gelsolin with nonmuscle myosin IIA (NMMIIA) at collagen adhesions are regulated to enable collagen phagocytosis. Fibroblasts plated on planar, collagen-coated substrates show minimal increase of [Ca2+]i, minimal colocalization of gelsolin and NMMIIA in focal adhesions, and minimal intracellular collagen degradation. In fibroblasts plated on collagen-coated latex beads there are large increases of [Ca2+]i, time- and Ca2+-dependent enrichment of NMMIIA and gelsolin at collagen adhesions, and abundant intracellular collagen degradation. NMMIIA knockdown retards gelsolin recruitment to adhesions and blocks collagen phagocytosis. Gelsolin exhibits tight, Ca2+-dependent binding to full-length NMMIIA. Gelsolin domains G4–G6 selectively require Ca2+to interact with NMMIIA, which is restricted to residues 1339–1899 of NMMIIA. We conclude that cell adhesion to collagen presented on beads activates Ca2+entry and promotes the formation of phagosomes enriched with NMMIIA and gelsolin. The Ca2+-dependent interaction of gelsolin and NMMIIA in turn enables actin remodeling and enhances collagen degradation by phagocytosis.
Sparsely correlated hidden Markov models with application to genome-wide location studies
Authors: Choi Hyungwon , Fermin Damian , Nesvizhskii Alexey I. , Ghosh Debashis , Qin Zhaohui S.
Published: January 2013

Motivation: Multiply correlated datasets have become increasingly common in genome-wide location analysis of regulatory proteins and epigenetic modifications. Their correlation can be directly incorporated into a statistical model to capture underlying biological interactions, but such modeling quickly becomes computationally intractable.

Results: We present sparsely correlated hidden Markov models (scHMM), a novel method for performing simultaneous hidden Markov model (HMM) inference for multiple genomic datasets. In scHMM, a single HMM is assumed for each series, but the transition probability in each series depends on not only its own hidden states but also the hidden states of other related series. For each series, scHMM uses penalized regression to select a subset of the other data series and estimate their effects on the odds of each transition in the given series. Following this, hidden states are inferred using a standard forward–backward algorithm, with the transition probabilities adjusted by the model at each position, which helps retain the order of computation close to fitting independent HMMs (iHMM). Hence, scHMM is a collection of inter-dependent non-homogeneous HMMs, capable of giving a close approximation to a fully multivariate HMM fit. A simulation study shows that scHMM achieves comparable sensitivity to the multivariate HMM fit at a much lower computational cost. The method was demonstrated in the joint analysis of 39 histone modifications, CTCF and RNA polymerase II in human CD4+ T cells. scHMM reported fewer high-confidence regions than iHMM in this dataset, but scHMM could recover previously characterized histone modifications in relevant genomic regions better than iHMM. In addition, the resulting combinatorial patterns from scHMM could be better mapped to the 51 states reported by the multivariate HMM method of Ernst and Kellis.

Availability: The scHMM package can be freely downloaded from http://sourceforge.net/p/schmm/ and is recommended for use in a linux environment.

Contact:  ghoshd@psu.edu or zhaohui.qin@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The emerging issue of cardiac dysfunction induced by antineoplastic angiogenesis inhibitors
Authors: Tocchetti Carlo G. , Gallucci Giuseppina , Coppola Carmela , Piscopo Giovanna , Cipresso Clemente , Maurea Carlo , Giudice Aldo , Iaffaioli Rosario V. , Arra Claudio , Maurea Nicola
Published: January 2013

Left ventricular dysfunction from anticancer drugs has emerged as a relevant problem in the clinical and scientific communities. Anthracycline toxicity has always been the most relevant, but with the increasing use of biological targeted therapies in treatment protocols, with an increasing number of cancer survivors, new toxicities have been increasing in more recent years. Cardiomyopathy after ErbB2 inhibitors has been intensively studied. Another important class of biological anticancer drugs are vascular endothelial growth factor (VEGF) inhibitors. VEGF signalling is crucial for vascular growth, but it also has a major impact on myocardial function. Also, it is important to note that such angiogenesis inhibitors are multitargeted in most cases, and can produce a broad spectrum of cardiovascular side effects. Here we review the mechanisms and pathophysiology of the most significant cardiotoxic effects of antiangiogenic drugs, and particular attention is drawn to LV dysfunction, discussing the assessment and management on the basis of the most recent cardio‐oncological findings and heart failure guidelines.
Providence virus (family: Carmotetraviridae) replicates vRNA in association with the Golgi apparatus and secretory vesicles
Authors: Short James R. , Nakayinga Ritah , Hughes Gareth E. , Walter Cheryl T. , Dorrington Rosemary A.
Published: January 2013

Providence virus (PrV) is the sole member of the family Carmotetraviridae (formerly Tetraviridae) sharing the characteristic T = 4 capsid architecture with other tetravirus families. Despite significant structural similarities, PrV differs from other tetraviruses in terms of genome organization, non-structural protein sequence and regulation of gene expression. In addition, it is the only tetravirus that infects tissue culture cells. Previous studies showed that in persistently infected Helicoverpa zea MG8 cells, the PrV replicase associates with detergent-resistant membranes in punctate cytosolic structures, which is similar to the distribution of an alpha-like tetravirus replicase (Helicoverpa armigera stunt virus). Here, we demonstrate that the site of PrV vRNA replication coincides with the presence of PrV p40/p104 proteins in infected cells and that these replication proteins associate with the Golgi apparatus and secretory vesicles in transfected cells.
Dynamic DNA methylation across diverse human cell lines and tissues
Authors: Varley Katherine E. , Gertz Jason , Bowling Kevin M. , Parker Stephanie L. , Reddy Timothy E. , Pauli-Behn Florencia , Cross Marie K. , Williams Brian A. , Stamatoyannopoulos John A. , Crawford Gregory E. , Absher Devin M. , Wold Barbara J. , Myers Richard M.
Published: January 2013

As studies of DNA methylation increase in scope, it has become evident that methylation has a complex relationship with gene expression, plays an important role in defining cell types, and is disrupted in many diseases. We describe large-scale single-base resolution DNA methylation profiling on a diverse collection of 82 human cell lines and tissues using reduced representation bisulfite sequencing (RRBS). Analysis integrating RNA-seq and ChIP-seq data illuminates the functional role of this dynamic mark. Loci that are hypermethylated across cancer types are enriched for sites bound by NANOG in embryonic stem cells, which supports and expands the model of a stem/progenitor cell signature in cancer. CpGs that are hypomethylated across cancer types are concentrated in megabase-scale domains that occur near the telomeres and centromeres of chromosomes, are depleted of genes, and are enriched for cancer-specific EZH2 binding and H3K27me3 (repressive chromatin). In noncancer samples, there are cell-type specific methylation signatures preserved in primary cell lines and tissues as well as methylation differences induced by cell culture. The relationship between methylation and expression is context-dependent, and we find that CpG-rich enhancers bound by EP300 in the bodies of expressed genes are unmethylated despite the dense gene-body methylation surrounding them. Non-CpG cytosine methylation occurs in human somatic tissue, is particularly prevalent in brain tissue, and is reproducible across many individuals. This study provides an atlas of DNA methylation across diverse and well-characterized samples and enables new discoveries about DNA methylation and its role in gene regulation and disease.
Timing and cue competition in conditioning of the nictitating membrane response of the rabbit (Oryctolagus cuniculus)
Authors: Kehoe E. James , Ludvig Elliot A. , Sutton Richard S.
Published: January 2013

Rabbits were classically conditioned using compounds of tone and light conditioned stimuli (CSs) presented with either simultaneous onsets (Experiment 1) or serial onsets (Experiment 2) in a delay conditioning paradigm. Training with the simultaneous compound reduced the likelihood of a conditioned response (CR) to the individual CSs (“mutual overshadowing”) but left CR timing unaltered. CR peaks were consistently clustered around the time of unconditioned stimulus (US) delivery. Training with the serial compound (CSA→CSB→US) reduced responding to CSB (“temporal primacy/information effect”) but this effect was prevented by prior CSB→US pairings. In both cases, serial compound training altered CR timing. On CSA→CSB test trials, the CRs were accelerated; the CR peaks occurred after CSB onset but well before the time of US delivery. Conversely, CRs on CSB– trials were decelerated; the distribution of CR peaks was variable but centered well after the US. Timing on CSB– trials was at most only slightly accelerated. The results are discussed with respect to processes of generalization and spectral timing applicable to the cerebellar and forebrain pathways in eyeblink preparations.