bluuebunny/crossref_metadata_2025 huggingface dataset:
Next‐generation sequencing for molecular ecology: a caveat regarding pooled samples
Authors: Anderson Eric C. , Skaug Hans J. , Barshis Daniel J.
Published: December 2013

We develop a model based on the Dirichlet‐compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next‐generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., , Molecular Ecology, 2931–2940), and show that there are many more fixed loci than expected in the absence of genetic structure. However, we show through coalescent simulations that the degree of population structure required to explain the fraction of alternatively fixed SNPs is extraordinarily high and that the surplus of fixed loci is more likely a consequence of limited representation of individual gene copies in the pooled samples, than it is of population structure. Our analysis signals that the use of NGS on pooled samples to identify divergent SNPs warrants caution. With pooled samples, it is hard to diagnose when an NGS experiment has gone awry; especially when NGS data on pooled samples are of low read depth with a limited number of individuals, it may be worthwhile to temper claims of unexpected population differentiation from pooled samples, pending verification with more reliable methods or stricter adherence to recommended sampling designs for pooled sequencing e.g. Futschik & Schlötterer , Genetics, 186, 207; Gautier et al., , Molecular Ecology, 3766–3779). Analysis of the data and diagnosis of problems is easier and more reliable (and can be less costly) with individually barcoded samples. Consequently, for some scenarios, individual barcoding may be preferable to pooling of samples.
Hell and Hope for Salvation
Authors: Grisez Germain , Ryan Peter F.
Published: December 2013

This article supplements Ralph Martin's recent book, Will
Many Be Saved? Our primary thesis is that those who hold
double predestination or universalism cannot, if consistent, hope as
Christians should for their own and others’ salvation, and therefore can
neither live their own lives with a view to reaching the heavenly kingdom
nor promote others’ salvation. We also contend that the same disabilities
are likely to subvert those who hold certain views that approximate
universalism. We go on to set out some positions regarding damnation and
salvation that, we believe, all Christians ought to hold and hand on. God
wills everyone to be saved, and those who are saved are saved by God's
grace. Entirely through their own fault, more than a few people will end in
hell. But no one still alive and able to repent need end in hell. While
created persons cannot build God's kingdom, insofar as Christians do the
Father's will in this world, they prepare materials, beginning with
themselves and their interpersonal relationships, for that kingdom.
Quantifying esophagogastric junction contractility with a novel HRM topographic metric, the EGJ‐Contractile Integral: normative values and preliminary evaluation in PPI non‐responders
Authors: Nicodème F. , Pipa‐Muniz M. , Khanna K. , Kahrilas P. J. , Pandolfino J. E.
Published: December 2013

Background

Despite its obvious pathophysiological relevance, the clinical utility of measures of esophagogastric junction (EGJ) contractility is unsubstantiated. High‐resolution manometry (HRM) may improve upon this with its inherent ability to integrate the magnitude of contractility over time and length of the EGJ. This study aimed to develop a novel HRM metric summarizing EGJ contractility and test its ability distinguish among subgroups of proton pump inhibitor non‐responders (PPI‐NRs).

Methods

75 normal controls and 88 PPI‐NRs were studied. All underwent HRM. PPI‐NRs underwent pH‐impedance monitoring on PPI therapy scored in terms of acid exposure, number of reflux events, and reflux‐symptom correlation and grouped as meeting all criteria, some criteria, or no criteria of abnormality. Control HRM studies were used to establish normal values for candidate EGJ contractility metrics, which were then compared in their ability to differentiate among PPI‐NR subgroups.

Key Results

The EGJ contractile integral (EGJ‐CI), a metric integrating contractility across the EGJ for three respiratory cycles, best distinguished the All Criteria PPI‐NR subgroup from controls and other PPI‐NR subgroups. Normal values (median, [IQR]) for this measure were 39 mmHg‐cm [25–55 mmHg‐cm]. The correlation between the EGJ‐CI and a previously proposed metric, the lower esophageal sphincter‐pressure integral, that used a fixed 10 s time frame and an atmospheric as opposed to gastric pressure reference was weak.

Conclusions & Inferences

Among HRM metrics tested, the EGJ‐CI was best in distinguishing PPI‐NRs meeting all criteria of abnormality on pH‐impedance testing. Future prospective studies are required to explore its utility in management of broader groups of gastroesophageal reflux disease patients.
Major quantitative trait loci control divergence in critical photoperiod for flowering between selfing and outcrossing species of monkeyflower (Mimulus)
Authors: Fishman Lila , Sweigart Andrea L. , Kenney Amanda M. , Campbell Samantha
Published: December 2013

Divergence in flowering time is a key contributor to reproductive isolation between incipient species, as it enforces habitat specialization and causes assortative mating even in sympatry. Understanding the genetic basis of flowering time divergence illuminates the origins and maintenance of species barriers.

We investigated the genetics of divergence in critical photoperiod for flowering between yellow monkeyflowers Mimulus guttatus (outcrosser, summer flowering) and Mimulus nasutus (selfer, spring flowering). We used quantitative trait locus (QTL) mapping of F2 hybrids and fine‐mapping in nearly isogenic lines to characterize the genomic regions underlying a > 2 h critical photoperiod difference between allopatric populations, and then tested whether the same QTLs control flowering time in sympatry.

We identified two major QTLs that almost completely explain M. nasutus's ability to flower in early spring; they are shared by allopatric and sympatric population pairs. The smaller QTL is coincident with one that differentiates ecotypes within M. guttatus, but the larger effect QTL appears unique to M. nasutus.

Unlike floral traits associated with mating system divergence, large interspecific differences in flowering phenology depend on only a few loci. Major critical photoperiod QTLs may be ‘speciation genes’ and also restrict interspecific gene flow in secondary sympatry.
Geophysical subsurface imaging for ecological applications
Authors: Jayawickreme Dushmantha H. , Jobbágy Esteban G. , Jackson Robert B.
Published: December 2013

Ecologists, ecohydrologists, and biogeochemists need detailed insights into belowground properties and processes, including changes in water, salts, and other elements that can influence ecosystem productivity and functioning. Relying on traditional sampling and observation techniques for such insights can be costly, time consuming, and infeasible, especially if the spatial scales involved are large. Geophysical imaging provides an alternative or complement to traditional methods to gather subsurface variables across time and space. In this paper, we review aspects of geophysical imaging, particularly electrical and electromagnetic imaging, that may benefit ecologists seeking clearer understanding of the shallow subsurface. Using electrical resistivity imaging, for example, we have been able to successfully show the effect of land‐use conversions to agriculture on salt mobilization and leaching across kilometer‐long transects and to depths of tens of meters. Recent advances in ground‐penetrating radar and other geophysical imaging methods currently provide opportunities for subsurface imaging with sufficient detail to locate small (≥5 cm diameter) animal burrows and plant roots, observe soil‐water and vegetation spatial correlations in small watersheds, estuaries, and marshes, and quantify changes in groundwater storage at local to regional scales using geophysical data from ground‐ and space‐based platforms. Ecologists should benefit from adopting these minimally invasive, scalable imaging technologies to explore the subsurface and advance our collective research.
Salivary and serum level of CYFRA 21‐1 in oral precancer and oral squamous cell carcinoma
Authors: Rajkumar K , Ramya R , Nandhini G , Rajashree P , Ramesh Kumar A , Nirmala Anandan S
Published: December 2013

Background

CYFRA 21‐1, a constituent of the intermediate filament proteins of epithelial cells, is known to be increased in many cancers. This study was designed to estimate the levels of salivary and serum CYFRA 21‐1 in patients with oral precancer and oral squamous cell carcinoma (OSCC) and compare them with healthy controls.

Materials and methods

Each group comprised of 100 subjects. Saliva and blood samples were collected from patients with OSCC, premalignant subjects, and normal healthy subjects. Serum and salivary CYFRA 21‐1 levels were measured by enzyme‐linked immunosorbent assay. Appropriate statistical tests were employed to assess diagnostic potency of CYFRA 21‐1.

Results

We found a significant increase in CYFRA 21‐1 level in OSCC compared with PML and healthy subjects. Salivary CYFRA 21‐1 levels in OSCC was threefold higher when compared to serum levels. PML group showed increased salivary CYFRA 21‐1 when compared to control subjects, but it was significantly lower compared with OSCC. Receiver operator characteristic curve analysis showed salivary CYFRA 21‐1 to have superior sensitivity in detecting OSCC compared with serum CYFRA 21‐1.

Conclusions

The outcome of this study suggests that salivary CYFRA 21‐1 can be utilized as a biomarker in early detection of oral cancer.
A rapid virulence assay for the Dutch elm disease fungus Ophiostoma novo‐ulmi by inoculation of apple (Malus × domestica ‘Golden Delicious’) fruits
Authors: Plourde K. V. , Bernier L.
Published: December 2013

Large‐scale virulence tests using trees or saplings are expensive, time‐consuming and require a considerable amount of space. The suitability of using ‘Golden Delicious’ apples as a rapid screen for identifying Ophiostoma novo‐ulmi transformants with reduced virulence was thus evaluated. When a collection of O. novo‐ulmi field isolates belonging to subspecies novo‐ulmi or americana was inoculated to apples, members of subsp. novo‐ulmi induced, on average, larger necrotic lesions than subsp. americana isolates. The size of the lesions on apples was not correlated with mycelial growth rate of isolates on nutrient agar. Insertional mutants from O. novo‐ulmi subsp. novo‐ulmi isolate H327 were inoculated to ‘Golden Delicious’ apples and Ulmus parvifolia × U. americana saplings in parallel experiments. Results clearly indicated that the O. novo‐ulmi transformants included several exhibiting significantly altered levels of virulence. Variability among replicates within a treatment was reduced in apple inoculation data compared to elm sapling data. Overall, the ‘Golden Delicious’ apple assay was found to be an excellent means for rapidly assessing the virulence level of O. novo‐ulmi isolates.
Visible and invisible caring in nursing from the perspectives of patients and nurses in the gerontological context
Authors: Canzan Federica , Heilemann MarySue V. , Saiani Luisa , Mortari Luigina , Ambrosi Elisa
Published: December 2013

Aim

Just as in many countries all over the world, the number of older people in Italy has increased rapidly. Consequently, an increasing number of nurses are engaged in the care of older patients. However, due to a lack of understanding of how nurses and patients perceive caring, nursing care may be compromised. The aim of this study is to explore, describe and compare the perceptions of gerontological nurses and patients related to the dimensions of caring in nursing in an Italian hospital setting.

Methods

In this qualitative descriptive study, a variety of analytic techniques were used to analyse semi‐structured interview data from a purposeful sample of 20 nurses and 20 patients from geriatric units in two different Italian hospitals.

Findings

Although both nurses and patients gave rich descriptions of caring experiences, patients described features of caring in nursing that were visible (including nurses' caring gestures, giving attention and being competent) while nurses predominantly emphasised aspects of caring that were relatively invisible (such as reflecting on the patient's past needs, evaluating the nursing care rendered, planning for more appropriate future nursing care, taking multiple complex contextual factors into account to protect the patient and being competent).

Conclusion

Our data revealed more nuanced insight into the meaning of invisible and visible caring in nursing within the gerontological context than has been previously reported in the literature. This has implications for nursing education and practice because it may help nurses meet the actual needs of older patients in hospital settings.
Association of cytochrome b5 with ETR1 ethylene receptor signaling through RTE1 in Arabidopsis
Authors: Chang Jianhong , Clay John M. , Chang Caren
Published: December 2013

Ethylene plays important roles in plant growth, development and stress responses, and is perceived by a family of receptors that repress ethylene responses when ethylene is absent. Repression by the ethylene receptor ETR1 depends on an integral membrane protein, REVERSION TO ETHYLENE SENSITIVITY1 (RTE1), which acts upstream of ETR1 in the endoplasmic reticulum (ER) membrane and Golgi apparatus. To investigate RTE1 function, we screened for RTE1‐interacting proteins using the yeast split‐ubiquitin assay, which yielded the ER‐localized cytochrome b5 (Cb5) isoform D. Cb5s are small hemoproteins that perform electron transfer reactions in all eukaryotes, but their roles in plants are relatively uncharacterized. Using bimolecular fluorescence complementation (BiFC), we found that all four ER‐localized Arabidopsis Cb5 isoforms (AtCb5–B, ‐C, ‐D and ‐E) interact with RTE1 in plant cells. In support of this interaction, atcb5 mutants exhibited phenotypic parallels with rte1 mutants in Arabidopsis. Phenotypes included partial suppression of etr1–2 ethylene insensitivity, and no suppression of RTE1‐independent ethylene receptor isoforms. The single loss‐of‐function mutants atcb5–b, ‐c and ‐d appeared similar to the wild‐type, but double mutant combinations displayed slight ethylene hypersensitivity. Over‐expression of AtCb5–D conferred reduced ethylene sensitivity similar to that conferred by RTE1 over‐expression, and genetic analyses suggested that AtCb5–D acts upstream of RTE1 in the ethylene response. These findings suggest an unexpected role for Cb5, in which Cb5 and RTE1 are functional partners in promoting ETR1‐mediated repression of ethylene signaling.
Status epilepticus attributed to inadvertent intrathecal injection of cefazolin during myelography
Authors: Griffith Carrie A. , Hoffmann Daniel E.
Published: December 2013

Objective

To describe a case of status epilepticus believed to be a consequence of inadvertent intrathecal administration of cefazolin in a dog undergoing a myelogram.

Case Summary

A 4‐year‐old, 6.5 kg, male neutered Dachshund was referred for evaluation of an acute onset hind limb paraparesis. While performing a lumbar myelogram, cefazolin was inadvertently injected into the ventral subarachnoid space. Subsequent refractory seizure activity was attributed to the epileptogenic effects of intrathecally administered cefazolin. Supportive therapy led to eventual complete recovery.

New or Unique Information Provided

Although epileptogenic effects of intrathecally administered cefazolin are well documented in the human and experimental animal model literature, to the authors’ knowledge this has not been characterized in the veterinary literature. This case highlights the need to be diligent and mindful when one administers medications, and describes the management of a dog adversely affected as a consequence of a medical error.
Myocardial injury in dogs with snake envenomation and its relation to systemic inflammation
Authors: Langhorn Rebecca , Persson Frida , Åblad Björn , Goddard Amelia , Schoeman Johan P. , Willesen Jakob L. , Tarnow Inge , Kjelgaard‐Hansen Mads
Published: December 2013

Objective

To investigate the presence of myocardial injury in dogs hospitalized for snake envenomation and to examine its relationship with systemic inflammation.

Design

Prospective case‐control study.

Setting

University teaching hospital and small animal referral hospital.

Animals

Dogs naturally envenomed by the European viper (Vipera berus; n = 24), African puff adder (Bitis arietans; n = 5), or snouted cobra (Naja annulifera; n = 9).

Interventions

Blood was collected from dogs envenomed by V. berus at admission, 12–24 hours postadmission, and 5–10 days postadmission. Blood was collected from dogs envenomed by B. arietans or N. annulifera at admission, and 12, 24, and 36 hours postadmission.

Measurements and Main Results

Concentrations of cardiac troponin I (cTnI), a marker of myocardial injury, and C‐reactive protein (CRP), a marker of systemic inflammation, were measured in each blood sample. Evidence of myocardial injury was found in 58% of dogs envenomed by V. berus at one or more time points. A significant correlation between cTnI and CRP concentrations was found at all time points. Evidence of myocardial injury was found in 80% of dogs envenomed by B. arietans at one or more time points; however, no correlation was found between cTnI and CRP concentrations. Evidence of myocardial injury was found in 67% of dogs envenomed by N. annulifera at one or more time points. A significant correlation between cTnI and CRP concentrations was found at admission, but not at other time points.

Conclusions

Myocardial injury frequently occurred in dogs with snake envenomation. While the degree of systemic inflammation was significantly correlated with degree of myocardial injury in V. berus envenomation at all time points, this was not the case in dogs envenomed by N. annulifera or B. arietans. This could be due to differences in the toxic substances of the snake venoms or to differences in the cytokines induced by the venom toxins.
Plasma-Sprayed Y2O3-Stabilized ZrO2 Electrolyte With Improved Interlamellar Bonding for Direct Application to Solid Oxide Fuel Cells
Authors: Zhang Shan-Lin , Li Cheng-Xin , Li Chang-Jiu
Published: December 2013

Atmospheric plasma spraying was employed to prepare anode, cathode, and Y2O3-stabilized ZrO2 (YSZ) electrolyte to aim at reducing manufacturing cost. YSZ electrolytes were deposited on the anode at different deposition temperatures of 200 °C, 400 °C and 600 °C to optimize the gas tightness of plasma-sprayed YSZ electrolyte. The influences of the deposition temperature on the microstructure and gas-tightness of plasma-sprayed YSZ electrolyte were investigated. The effect of microstructure and the gas-tightness of YSZ electrolyte on the open circuit voltage and the output performance of solid oxide fuel cells (SOFCs) were examined. The results showed with the increase of deposition temperature, the porosity of YSZ electrolytes almost decreased by about 80% and the microstructure of YSZ electrolytes changed from the typical lamellar structure to the continuous columnar crystal structure. At a deposition temperature of 600 °C the gas permeability decreased to 1.5 × 10−7 cm4gf−1s−1, and the highest open circuit voltage can reach 1.026 V, indicating the applicability of the as-sprayed YSZ directly to the SOFC electrolyte.
Investigation of the Local Temperature Increase From the Magnetization Decay for Heat Assisted Magnetic Recording
Authors: Xiong Shaomin , Bogy David
Published: December 2013

The areal data density of magnetic recording hard disk drives (HDDs) increases year by year, following a trend similar to Moore’s law. However, the increase is not unbounded and there are some physical limits. As the density increases, the size of each magnetic grain shrinks. Finally the magnetic grain will be no longer thermally stable due to what is termed superparamagnetism. Above this point, the magnetic storage would be not reliable because the magnetic grains’ orientations fluctuate randomly. To increase magnetic recording density to more than 1 Tb/in2 and break this limit, heat assisted magnetic recording (HAMR) is proposed. In HAMR systems, a more thermally stable magnetic material, one with higher coercivity, will be used as a recording layer. But the coercivity of this material at room temperature is so high that it is difficult for the writer to switch the magnetic orientation with current magnetic transducers. However, the coercivity drops sharply if the temperature is raised close to the Curie temperature. In HAMR systems, a laser is proposed as the means to heat the disk to the Curie point. Simultaneously the magnetic field is applied from the writer to switch the magnetic bits. The success of the magnetic switching is very sensitive to the media temperature [2]. If the temperature is too low compared with the Curie point, it will not be able to write any information into the media. Conversely, heating the media over the Curie point requires more energy and may bring a greater challenge for the head disk interface (HDI). It is very important to understand the local temperature distribution during the laser heating and to calibrate the laser power input for HAMR writing. Some work has been done to evaluate the temperature increase using both numerical and experimental methods [3, 4]. Tagawa et.al. observed the disk refractive index change during laser heating and compared it with the change under conventional oven heating. This is a good method to calibrate the laser power and get the average temperature but it has some limitations for getting the accurate temperature distributions because of the averaging effect for the refractive index measurement by ellipsometry.
Mechatronic Integration of Humanoid Exoskeleton Hand Rehabilitation System
Authors: Pu Shu-Wei , Chang Jen-Yuan (James)
Published: December 2013

In the past ten years, more and more robots are developed. Some are used for hazardous operation and others are used for industrial automation purposes, such as humanoid robot and industrial robot. However, there is another type of robot which is called assistive humanoid robot. The assistive humanoid robot looks very similar to human’s body that can help human to finish some daily tasks, such as moving heavy things, walking up stairs and raising your hand, etc. Besides, the assistive robot absolutely does a great help if it is applied to the patient who are suffering from the severe diseases, or who has difficulty to move his/her arm or leg. The robot can assist the disable arm or leg in moving again. So, people can use this device to manipulate the disable hand to do some easy tasks, such as holding cup for water drinking, or picking and placing some light items [2] Also, it can be used as a device to provide a safe and intensive rehabilitation training for the patients, and it has been proved that assistive robot is effective in assisting the therapist [1][6]. The assistive humanoid robot not only helps patients for recovery or assists patients for simple everyday tasks, but also effectively promotes human’s living quality. However, even though the assistive robot for elbow, wrist or leg has already been widely developed and used in hospital trials, few projects and assistive robotic devices for hand rehabilitation are found in the market [3][7].
Numerical Simulation on Lubricant Recovery After Depletion
Authors: Yu Peng , Zhou Weidong , Yu Shengkai
Published: December 2013

In magnetic recording, the hard disk rotates at a high speed, with the slider flying above it. To protect the disk and slider from corrosion damage, contact scratching, high friction and wear, a thin lubricant layer is coated on the disk surface. With the continuous increase in the hard disk drive (HDD) areal density, the spacing between the head and the media is rapidly approaching the sub-nanometer regime, which demands the thickness of lubricant to be molecularly-thin. At such a nanoscale head-disk interface, the short-range forces and the air shear force may cause significant lubricant migration [1, 2]. The lubricant may pile up, and/or be picked up by the slider [3], which in turn affects the flyability of the slider. Meanwhile, the short-range forces such as Van de Waals forces may cause lubricant instability issues [1].
Intelligence Compensation Algorithm for Data Restoration in Holographic Data Storage System
Authors: Jeong Wooyoung , Kim Jang Hyun , Lim Sung-Yong , Lee Jae-Seong , Yang Hyunseok , Park No-Cheol , Park Young-Pil , Park Kyoung-Su
Published: December 2013

In holographic data storage system, misalignment of optical components causes fluctuation of path and angle of laser. These phenomena generate data distortion like rotation, barrel, pincushion and mustache distortion, because holographic data storage system has very sensitive tolerance with incident angle of reference beam. Because it is difficult to align perfectly, data distortion occurs inevitably by misalignment. It is important to acquire accurate data page from holographic data storage system without distortion. In this paper, we propose intelligence compensation algorithm for data restoration in holographic data storage system. We used fuzzy system and sub-clustering algorithm to generate fuzzy rules for this compensation algorithm. This proposed algorithm acquires the value how much the data image has barrel distortion. With acquired data form this algorithm, data distortion can be compensated. Barrel image is used for this simulation and it shows good performance.
A Battery Charge Controller for a Flyback Converter With Digital Primary Side Regulation
Authors: Chao Paul C.-P. , Chen W. D. , Wu R. H.
Published: December 2013

The market of electronic products such as mobile phones and portable devices grows rapidly while the demand of lithium battery for fast charge, long duration, and long life cycle increases significantly as well. There are several charge methods for lithium battery, such as constant current (CC)/constant voltage (CV) charge [1], pulse charge [2] and reflex charge [3], etc. In general, a flyback converter has been widely adopted as the front-end converter of battery charger due to its low-cost, wide power range, and galvanic isolation between input and output stage. The battery charge controller with flyback converter has been developed in digital control with opto-coupler feedback [4]–[6]. The conventional flyback converter with CC or CV applications always requires two sensed ADC channels for regulating [7]–[9]. An improved control method is proposed in this study to achieve CC/CV by only one ADC channel. This study presents a battery charge mechanism with a flyback converter and associated trickle charge method for the temperature compensation. The PSR is adopted for switching the charge modes within trickle current (TC), constant current (CC) and constant voltage (CV). The TC charging method is used to avoid the rapid increase in the temperature of the battery which is based on the characteristics of the internal resistance of the battery [10]. The proposed system circuit contains two stages in topology. The first stage is a front-end flyback converter which operates in DC-DC discontinuous current mode (DCM) by using PSR to sense the output voltage from auxiliary winding. It is adopted to replace the opto-coupler for avoiding temperature limitation for operations and reducing cost. The software Powersim is used to simulate the proposed flyback converter and PSR method. The second stage is the digital feedback loop, which processes the controlled signal by a digital processor (DSP) TMS320F2812. The experimental results were compared with general CC/CV method. The results show favorable performance of the propose charging method.
Contact Between a Disk Asperity and the Touchdown Sensor in a Thermal Flying-Height Control Slider
Authors: Zhang Chuanwei , Ovcharenko Andrey , Talke Frank E.
Published: December 2013

The contact between a touchdown sensor and an asperity on a disk is investigated using finite element analysis. The touchdown sensor is embedded in the area of the thermal protrusion of a thermal flying-height control (TFC) slider. A transient thermo-elastic-plastic finite element contact model is developed to simulate the temperature rise of the touchdown sensor due to frictional heating.
Position-Error-Based Shock Protection in HDDs
Authors: Jia Qingwei , Guo Guoxiao , Yu Jie
Published: December 2013

This paper studies off-track write protection in HDDs. The system data integrity requirement is formulated based on the head/media and data track pitch configurations and a servo-mechanical system track misregistration (TMR) under various conditions. A write fault protection scheme is formulated based on position estimation through the current and predicted future PES (position error signal). The write fault trigger threshold determination and its impact on the system trade-offs are qualitatively discussed. The shock protection method applies to both conventional magnetic recording (CMR) and shingled magnetic recording (SMR).
Molecular Dynamics Simulation to Study the Effect of Empirical Potential Functions on Modeling of Diamond-Like Carbon
Authors: Li Longqiu , Xu Ming , Song Wenping , Zhang Guangyu , Ovcharenko Andrey
Published: December 2013

Molecular dynamics (MD) simulations is an effective method to investigate the mechanical and tribological properties of amorphous carbon since the coordinates of all atoms can be calculated as a function of time. Several empirical potentials can be used to model the interatomic interactions of carbon atoms, including the Tersoff potential, the Reactive Bond Order (REBO) potential and its revised versions, and the Reactive Force Field (ReaxFF) potential. The choice of empirical potential is one of the fundamental and important assumptions in the MD approach since it can affect the properties of amorphous carbon during the MD simulations. In this study, liquid quenching method is used to model amorphous carbon for computational efficiency. We will study the influence of the three types of potentials, specifically the Tersoff potential, the 2nd REBO potential and the ReaxFF potential on DLC parameters. These parameters include the sp3 content as a function of density, the arrangement of the amorphous carbon atoms, hybridization and the radial distribution functions G(r).
Dual-Stage Servo Control for an Optical Pointing System
Authors: Miller Eric D. , de Callafon Raymond A.
Published: December 2013

In the realm of hard disk drives (HDD), dual-stage servo control has been shown to achieve increased control bandwidth and reduced power consumption compared to single-stage architectures [1]–[4]. Motivated by these results, we seek to apply dual-stage control to an analogous case of an optical pointing system, which has similar objectives of high-bandwidth control over a wide spatial range.
Hybrid Variable Damping Control: Design, Simulation, and Optimization
Authors: Ribeiro Roberto , Khamesee Mir Behrad , Khajepour Amir
Published: December 2013

Damping in a multitude of engineering applications has a variable threshold requirement based on system excitation. Since system excitation is also variable; dampers are designed such that a maximum amount of damping is provided (based on the worst case for a structure), opposed to an optimal amount as a function of excitation. By implementing a hybrid damper design based on a bias component provided through a hydraulic medium and a variable component provided by electromagnetics; an optimal damping quantity can be obtained for a given excitation.
Position Alignment of Micro Manipulator Using Root Mean Square Errors for Maskless Lithography System
Authors: Ihn Yong Seok , Park Sae Whan , Koo Ja Choon
Published: December 2013

A precision optical exposure process of lithography has become one of the essential processes to manufacture and develop micro electro mechanical system (MEMS) devices, flat panel display (FPD), and semiconductor. For a typical exposure process for the lithography, a photomask that is often very expensive is required to generate patterns[1]. So it is very inefficient not only in terms of cost but also the time due to the reliance on the photomasks in development. The alternative solution is the maskless lithography system, which does not use photomasks since the patterns are generated by using a digital mirror device (DMD). The unit mirror of a digital mirror device has two kinds of status which are on and off, then the status of unit mirrors configures a pattern called point array method. The maskless lithography system can reduce the amount of work forces significantly and save money as well. However, the maskless lithography system has a critical drawback, which is a low throughput since the patterns are generated in a line. This is an intrinsic problem of point array method. So in most volume production processes of maskless lithography system, a number of optical heads are used in order to maximize throughput of the expositing process. And to guarantee the exposure quality, multiple numbers of optical heads should be accurately aligned to each other, and then the focal plane of each optical head is also well aligned with chuck.
Slit Design for the Thermal Flying Height Control Slider
Authors: Li Hui , Shen Shengnan
Published: December 2013

Thermal flying height control (TFC) has recently been implemented in magnetic recording disk drives to reduce the flying height at the read/write element for high areal density magnetic recording. In this work, we propose a novel thermal flying height control slider, by designing a slit near the thermal heater in the slider. The thermal-structure simulation coupled with air bearing simulation is used to simulate the actuation by the thermal actuator, as well as the effects on flying performance of slider being actuated.
Carbon Overcoat Loss From the Surface of a Heat Assisted Magnetic Storage Disk due to Laser Irradiation
Authors: Jones Paul M. , Ahner Joachim , Platt Christopher L. , Tang Huan , Hohlfeld Julius
Published: December 2013

A pump-probe experimental technique that incorporated a 527nm wavelength pump laser and a 476nm probe laser was applied to a magnetic storage disk having a magnetic layer comprised of a FePt alloy and coated with a hydrogenated carbon overcoat (COC). The pump laser power was systematically increased while sweeping the applied field with an electromagnet to observe the temperature dependent magnetization, which is proportional to the change in the polarization of the reflected beam. In this way the laser power required to heat the media to the Curie temperature (Tc) was determined, with the Curie temperature of the media determined from a separate magnetometry measurement. Such a single point laser power-to-media temperature calibration allowed the determination of the media temperature over a small laser power range near Tc. The carbon over-coated FePt media was then irradiated for varying durations at temperatures pertinent to a Heat Assisted Magnetic Recording (HAMR) device [1]. The COC surface topography and carbon bonding structure within each irradiated zone was probed with AFM and micro-spot Raman. A subtle, systematic temperature and duration dependent change in the COC was observed. With increasing temperature and duration, the Raman D-peak became increasingly pronounced, signaling an increase of the sp2 (disorder) content in the film in the irradiated region. At incrementally higher temperatures, the loss of the carbon overcoat becomes apparent as a shallow depression in the COC film in the irradiated area. A clearer picture of the possible sensitivity and kinetics of the loss of COC on the HAMR media surface was obtained by measuring its loss over a range of irradiation temperatures and durations. The activation energy and COC loss rate were obtained and a possible mechanism for COC failure-loss was discussed within the bounds of the operating HAMR device [2].
Right Place, Right Time
Authors: Voight Benjamin F.
Published: December 2013

Integrating human genetics and brain coexpression patterns provides insight into autism pathogenesis.
Diabetes Shrinks the Brain
Authors: Jastreboff Ania M.
Published: December 2013

Type 2 diabetes is associated with loss of brain volume and cognitive deficits.
Oncogenic Driver Mutations: Neither Tissue-Specific nor Independent
Authors: Margolin Adam A.
Published: December 2013

Genomic analysis of 12 cancers identifies common somatic mutations across tumor types.
Finding the Proverbial Needle
Authors: Seker Erkin
Published: December 2013

A microfluidic platform generates different types of nanoparticles to identify particle features that could enhance therapeutic efficacy.
What do measures of agreement (κ) tell us about quality of exposure assessment? Theoretical analysis and numerical simulation
Authors: Burstyn Igor , de Vocht Frank , Gustafson Paul
Published: December 2013

Background

The reliability of binary exposure classification methods is routinely reported in occupational health literature because it is viewed as an important component of evaluating the trustworthiness of the exposure assessment by experts. The Kappa statistics (κ) are typically employed to assess how well raters or classification systems agree in a variety of contexts, such as identifying exposed participants in a population-based epidemiological study of risks due to occupational exposures. However, the question we are really interested in is not so much the reliability of an exposure assessment method, although this holds value in itself, but the validity of the exposure estimates. The validity of binary classifiers can be expressed as a method's sensitivity (SN) and specificity (SP), estimated from its agreement with the error-free classifier.

Methods and results

We describe a simulation-based method for deriving information on SN and SP that can be derived from κ and the prevalence of exposure, since an analytic solution is not possible without restrictive assumptions. This work is illustrated in the context of comparison of job-exposure matrices assessing occupational exposures to polycyclic aromatic hydrocarbons.

Discussion

Our approach allows the investigators to evaluate how good their exposure-assessment methods truly are, not just how well they agree with each other, and should lead to incorporation of information of validity of expert assessment methods into formal uncertainty analyses in epidemiology.
Primary prevention of diabetic retinopathy with fibrates: a retrospective, matched cohort study
Authors: Morgan Christopher Ll , Owens David R , Aubonnet Patrick , Carr Emma S M , Jenkins-Jones Sara , Poole Chris D , Currie Craig J
Published: December 2013

Objectives

To compare the progression of diabetic retinopathy (DR) in people with type 2 diabetes treated with fibrates with that of non-exposed controls.

Design

Retrospective, matched cohort study.

Setting

UK Clinical Practice Research Datalink (CPRD).

Participants

5038 people with type 2 diabetes with a history of fibrate exposure but without evidence of DR were identified. Three thousand one hundred and seventy-six (63%) people could be randomly matched to one non-exposed control; of these, 2599 (81.8%) were matched without any missing blood pressure or glycated haemoglobin (HbA1c) values.

Main outcome measures

The primary endpoint was first recorded DR with a secondary endpoint of all-cause mortality or first DR. Time to clinical endpoints was compared using Cox proportional hazards models.

Results

Mean follow-up was 5.1 and 5.0 years for fibrate-exposed and non-exposed patients, respectively. For fibrate-exposed participants, there was a reduction in DR: 33.4 events/1000 person-years vs 40.4 (p=0.002), and in death or DR: 50.6 vs 60.2 (p<0.001). For those matched with full systolic blood pressure and HbA1c data, crude event rates were 34.3 versus 43.9 for DR (p<0.001) and 51.2 vs 63.4 (p<0.001) for death or DR. Following adjustment, DR was significantly delayed for those treated with fibrates, with an adjusted HR (aHR) of 0.785 (p<0.001) for participants with complete data and an aHR of 0.802 (p<0.001) for all participants.

Conclusions

The treatment with fibrates in people with type 2 diabetes was independently associated with reduced progression to a first diagnosis of DR.
Factors influencing trust in doctors: a community segmentation strategy for quality improvement in healthcare
Authors: Gopichandran Vijayaprasad , Chetlapalli Satish Kumar
Published: December 2013

Background

Trust is a forward-looking covenant between the patient and the doctor where the patient optimistically accepts his/her vulnerability. Trust is known to improve the clinical outcomes.

Objectives

To explore the factors that determine patients’ trust in doctors and to segment the community based on factors which drive their trust.

Setting

Resource-poor urban and rural settings in Tamil Nadu, a state in southern India.

Participants

A questionnaire was administered to a sample of 625 adult community-dwelling respondents from four districts of Tamil Nadu, India, chosen by multistage sampling strategy.

Outcome measures

The outcomes were to understand the main domains of factors influencing trust in doctors and to segment the community based on which of these domains predominantly influenced their trust.

Results

Factor analysis revealed five main categories, namely, comfort with the doctor, doctor with personal involvement with the patient, behaviourally competent doctor, doctor with a simple appearance and culturally competent doctor, which explained 49.3% of the total variance. Using k-means cluster analysis the respondents were segmented into four groups, namely, those who have ‘comfort-based trust’, ‘emotionally assessed trust’, who were predominantly older and belonging to lower socioeconomic status, those who had ‘personal trust’, who were younger people from higher socioeconomic strata of the community and the group who had ‘objectively assessed trust’, who were younger women.

Conclusions

Trust in doctors seems to be influenced by the doctor's behaviuor, perceived comfort levels, personal involvement with the patient, and to a lesser extent by cultural competence and doctor's physical appearance. On the basis of these dimensions, the community can be segmented into distinct groups, and trust building can happen in a strategic manner which may lead to improvement in perceived quality of care.
Integrating patient safety into health professionals’ curricula: a qualitative study of medical, nursing and pharmacy faculty perspectives
Authors: Tregunno Deborah , Ginsburg Liane , Clarke Beth , Norton Peter
Published: December 2013

Background

As efforts to integrate patient safety into health professional curricula increase, there is growing recognition that the rate of curricular change is very slow, and there is a shortage of research that addresses critical perspectives of faculty who are on the ‘front-lines’ of curricular innovation. This study reports on medical, nursing and pharmacy teaching faculty perspectives about factors that influence curricular integration and the preparation of safe practitioners.

Methods

Qualitative methods were used to collect data from 20 faculty members (n=6 medical from three universities; n=6 pharmacy from two universities; n=8 nursing from four universities) engaged in medical, nursing and pharmacy education. Thematic analysis generated a comprehensive account of faculty perspectives.

Results

Faculty perspectives on key challenges to safe practice vary across the three disciplines, and these different perspectives lead to different priorities for curricular innovation. Additionally, accreditation and regulatory requirements are driving curricular change in medicine and pharmacy. Key challenges exist for health professional students in clinical teaching environments where the culture of patient safety may thwart the preparation of safe practitioners.

Conclusions

Patient safety curricular innovation depends on the interests of individual faculty members and the leveraging of accreditation and regulatory requirements. Building on existing curricular frameworks, opportunities now need to be created for faculty members to act as champions of curricular change, and patient safety educational opportunities need to be harmonises across all health professional training programmes. Faculty champions and practice setting leaders can collaborate to improve the culture of patient safety in clinical teaching and learning settings.
A numerical investigation of overstrength and ductility factors of moment resisting steel frames retrofitted with GFRP plates
Authors: Siddique Mohammad Al Amin , El Damatty Ashraf A. , El Ansary Ayman M.
Published: December 2013

This paper reports the results of an investigation conducted to assess the effectiveness of using glass fiber reinforced polymer (GFRP) plates to enhance the overstrength and ductility factors of moment resisting steel frames. The GFRP plates are bonded to the flanges of steel beams of the frame with an aim to enhance their local buckling capacities and consequently their ductility. The flexural behaviour of GFRP retrofitted beams is first determined using a nonlinear finite element model developed in-house. In this numerical model, consistent shell elements are used to simulate the flanges and web of the steel beam as well as the GFRP plate. The interface between the steel and the GFRP plate is simulated using a set of continuous linear spring system representing both the shear and peeling stiffness of the adhesive based on values obtained from a previous experimental study. The moment–rotation characteristics of the retrofitted beams are then implemented into the frame model to carry out nonlinear static (pushover) analyses. The seismic performance level of the retrofitted frames in terms of overstrength and ductility factors is then compared with that of the bare frame. The results show a significant enhancement in strength and ductility capacities of the retrofitted frames, especially when the beams of the frame are slender.
Late Wisconsinan helmeted muskoxen (Bootherium bombifrons) from southwestern Alberta, Canada
Authors: Hills L.V. , Tolman Shayne , McNeil P. , Kooyman B.
Published: December 2013

The first known occurrence of helmeted muskox in the Late Wisconsinan (ca. 16 000–11 000 radiocarbon years BP) of Alberta is recorded and described. 14C dating places the specimen at 10 980 ± 80 radiocarbon years BP (uncorrected). The distribution of the species is mapped, the widespread distribution implying that these animals probably occupied diverse habitats. Evidence from Wally’s Beach, including associated fauna and floral remains and eolian deposits, indicates a dry windswept steppe–grassland with intermittent patches of low woody shrubs.
PARTICLE PHYSICS, FROM RUTHERFORD TO THE LHC
Authors: WEINBERG STEVEN
Published: December 2013

Our understanding of fundamental particles has developed in ways that were unimaginable 100 years ago, when the atomic nucleus was first glimpsed.
GOLDEN RATIO CONTROLLED CHAOS IN SUPERSYMMETRIC DYNAMICS
Authors: HÜBSCH TRISTAN , KATONA GREGORY A.
Published: December 2013

We construct supersymmetric Lagrangians for the recently constructed off-shell worldline N = 3 supermultiplet [Formula: see text] for I = 1, 2, 3, where [Formula: see text] and [Formula: see text] are standard, Salam–Strathdee superfields: [Formula: see text] fermionic and [Formula: see text] bosonic. Already the Lagrangian bilinear in component fields exhibits a total of thirteen free parameters, seven of which specify Zeeman-like coupling to external (magnetic) fluxes. All but special subsets of this parameter space describe aperiodic oscillatory response, some of which are controlled by the "golden ratio," φ≈1.61803. We also show that all of these Lagrangians admit an N = 3 →4 supersymmetry extension, while a subset admits two inequivalent such extensions.