bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of random discrete dopant induced variability between Ge and Si junctionless p-FinFETs
Authors: Nawaz Sk Masum , Dutta Souvik , Mallik Abhijit
Published: July 2015

In this letter, the random discrete dopant (RDD) induced variability for a Ge junctionless (JL) p-FinFET is reported. A one-to-one comparison of the RDD-induced variability between Ge and Si JL FinFETs for varying device parameters and supply voltage is made using a 3-D numerical device simulator. Results indicate that the Ge JL FinFET shows higher immunity to RDD induced threshold voltage fluctuation than its Si counterpart, which is partially due to the higher dielectric constant of Ge than Si. Because of the lower band gap of Ge than Si, a higher variation in subthreshold swing due to RDD is, however, observed for Ge devices. Technology scaling is found to reduce σSS, although it has almost no effects on σVT for both types of devices. The difference in σSS between Ge and Si devices decreases with technology scaling, which makes Ge very attractive for scaled p-type JL FinFETs.
Magnetism of Ta dichalcogenide monolayers tuned by strain and hydrogenation
Authors: Manchanda Priyanka , Sharma Vinit , Yu Hongbin , Sellmyer D. J. , Skomski Ralph
Published: July 2015

The effects of strain and hydrogenation on the electronic, magnetic, and optical properties of monolayers of Ta based dichalcogenides (TaX2; X = S, Se, and Te) are investigated using density-functional theory. We predict a complex scenario of strain-dependent magnetic phase transitions involving paramagnetic, ferromagnetic, and modulated antiferromagnetic states. Covering one of the two chalcogenide surfaces with hydrogen switches the antiferromagnetic/nonmagnetic TaX2 monolayers to a semiconductor, and the optical behavior strongly depends on strain and hydrogenation. Our research opens pathways towards the manipulation of magnetic as well as optical properties for future spintronics and optoelectronics applications.
Surface effect on resonant properties of nanowires predicted by an elastic theory for nanomaterials
Authors: Yao Yin , Chen Shaohua
Published: July 2015

A recently developed continuum theory considering surface effect in nanomaterials is adopted to investigate the resonant properties of nanowires with different boundary conditions in the present paper. The main feature of the adopted theory is that the surface effect in nanomaterials is characterized by the surface energy density of the corresponding bulk materials and the surface relaxation parameter in nanoscale. Based on a fixed-fixed beam model and a cantilever one, the governing equation of resonant frequency for corresponding nanowires is obtained. Numerical calculation of the fundamental resonant frequency is carried out, the result of which is well consistent with the existing numerical ones. Comparing to the result predicted by the conventionally structural dynamics, the resonant frequency of a fixed-fixed nanowire is improved, while that of a cantilever nanowire is weakened due to the surface effect. Both a decreasing characteristic size (height or diameter) and an increasing aspect ratio could further enhance the varying trend of resonant properties for both kinds of nanowires. The present result should be helpful for the design of nano-devices and nanostructures related to nanowires.
Enhanced energy product in Y-Co-Fe magnets intermediate between Nd-Fe-B and ferrite
Authors: Tozman P. , Venkatesan M. , Zickler G. A. , Fidler J. , Coey J. M. D.
Published: July 2015

The hysteresis of ball-milled Fe-doped YCo5 powder has been optimized by controlling the temperature and time for rapid annealing under vacuum and argon. The crystallite size is only 25 nm; yet, it has been possible to field align Y(Co,Fe) powder with a 5–20 μm grain size in a 5 T field to obtain a remanence ratio of 0.65, due to texture in the ball-milled powder. The nominal energy product of the powder is 140 kJ/m3. A pressed magnet with 78% of theoretical density has an energy product of 65 kJ/m3. This magnet could fill the gap between oriented ferrite (34 kJ/m3) and oriented Nd-Fe-B (350 kJ/m3).
Effective 90-degree magnetization rotation in Co2FeAl thin film/piezoelectric system probed by microstripline ferromagnetic resonance
Authors: Gueye M. , Zighem F. , Belmeguenai M. , Gabor M. S. , Tiusan C. , Faurie D.
Published: July 2015

Microstripline ferromagnetic resonance technique has been used to study the indirect magnetoelectric coupling occurring in an artificial magnetoelectric heterostructure consisting of a magnetostrictive thin film cemented onto a piezoelectric actuator. Two different modes (sweep-field and sweep-frequency modes) of this technique have been employed to quantitatively probe the indirect magnetoelectric coupling and to observe a voltage induced magnetization rotation (of 90°). This latter has been validated by the experimental frequency variation of the uniform mode and by the amplitude of the sweep-frequency spectra.
Effects of magnetic field and pressure in magnetoelastic stress reconfigurable thin film resonators
Authors: Staruch M. , Kassner C. , Fackler S. , Takeuchi I. , Bussmann K. , Lofland S. E. , Dolabdjian C. , Lacomb R. , Finkel P.
Published: July 2015

Free-standing CoFe thin-film doubly clamped stress reconfigurable resonators were investigated as a function of magnetic field and pressure. A large uniaxial anisotropy resulting from residual uniaxial tensile stress, as revealed from magnetic hysteresis loops, leads to an easy magnetization axis aligned along the length of the beams. The quality factor of the driven resonator beams under vacuum is increased by 30 times, leading to an enhanced signal-to-noise ratio and a predicted reduction in the intrinsic magnetic noise by a factor of 6, potentially reaching as low as ∼25 pT/√Hz at 1 Torr. Stress reconfigurable sensors operating under vacuum could thus further improve the limit of detection and advance development of magnetic field sensing technology.
Time-resolved orbital angular momentum spectroscopy
Authors: Noyan Mehmet A. , Kikkawa James M.
Published: July 2015

We introduce pump-probe magneto-orbital spectroscopy, wherein Laguerre-Gauss optical pump pulses impart orbital angular momentum to the electronic states of a material and subsequent dynamics are studied with 100 fs time resolution. The excitation uses vortex modes that distribute angular momentum over a macroscopic area determined by the spot size, and the optical probe studies the chiral imbalance of vortex modes reflected off the sample. First observations in bulk GaAs yield transients that evolve on time scales distinctly different from population and spin relaxation, as expected, but with surprisingly large lifetimes.
Actuation performance and heat generation of shear-bending actuator based on BiScO3-PbTiO3 ceramics from 25 to 300 °C
Authors: Chen Jianguo , Liu Guoxi , Cheng Jinrong , Dong Shuxiang
Published: July 2015

The actuation performance and heat generation of the shear-bending mode actuator based on BiScO3-PbTiO3 (BS-PT) ceramics were investigated at different temperatures and under different magnitudes of applied electric field at different frequencies. The displacement of the actuator increased with the thermal and electric loadings initially, reached the maximum, and then decreased. The maximum displacement was sensitive to the coercive field of the used piezoelectric ceramics, and about 17.5 μm under an applied electric field of 5 kV/cm at 300 °C, three times higher than that measured at room temperature. The heat generation of the actuator at the frequency of 1 Hz was almost negligible, whereas it increased seriously with the measuring frequency and the magnitude of the applied electric field. These results indicated that the shear-bending actuator based on BS-PT ceramics could generate large displacement at 300 °C without serious heat generation at low frequencies.
Harvesting vibration energy using two modal vibrations of a folded piezoelectric device
Authors: Gong Li Jiao , Pan Qiao Sheng , Li Wei , Yan Gang Yi , Liu Yong Bin , Feng Zhi Hua
Published: July 2015

This letter reports a piezoelectric vibration energy harvester that uses the local lateral resonant modes of a folded structure to widen the operation frequency band. In addition, energy conversion efficiency is improved. A prototype energy harvester was fabricated and tested. The output power achieved two power peaks: 0.43 mW at 97 Hz and 6.64 mW at 120.9 Hz. The output power remained above 20 μW within the operation frequency band that ranged from 88 Hz to 177 Hz when the energy harvester was driven with a vibration of 0.7 g peak acceleration. The output power remained higher than half of one of the maximum power peaks (0.43 mW) between 95 Hz and 101 Hz. Meanwhile, it remained higher than half of the other maximum power peak (6.64 mW) between 120.5 Hz and 123.8 Hz.
Three-dimensional printed millifluidic devices for zebrafish embryo tests
Authors: Zhu Feng , Skommer Joanna , Macdonald Niall P. , Friedrich Timo , Kaslin Jan , Wlodkowic Donald
Published: July 2015

Implementations of Lab-on-a-Chip technologies for in-situ analysis of small model organisms and embryos (both invertebrate and vertebrate) are attracting an increasing interest. A significant hurdle to widespread applications of microfluidic and millifluidic devices for in-situ analysis of small model organisms is the access to expensive clean room facilities and complex microfabrication technologies. Furthermore, these resources require significant investments and engineering know-how. For example, poly(dimethylsiloxane) soft lithography is still largely unattainable to the gross majority of biomedical laboratories willing to pursue development of chip-based platforms. They often turn instead to readily available but inferior classical solutions. We refer to this phenomenon as workshop-to-bench gap of bioengineering science. To tackle the above issues, we examined the capabilities of commercially available Multi-Jet Modelling (MJM) and Stereolithography (SLA) systems for low volume fabrication of optical-grade millifluidic devices designed for culture and biotests performed on millimetre-sized specimens such as zebrafish embryos. The selected 3D printing technologies spanned a range from affordable personal desktop systems to high-end professional printers. The main motivation of our work was to pave the way for off-the-shelf and user-friendly 3D printing methods in order to rapidly and inexpensively build optical-grade millifluidic devices for customized studies on small model organisms. Compared with other rapid prototyping technologies such as soft lithography and infrared laser micromachining in poly(methyl methacrylate), we demonstrate that selected SLA technologies can achieve user-friendly and rapid production of prototypes, superior feature reproduction quality, and comparable levels of optical transparency. A caution need to be, however, exercised as majority of tested SLA and MJM resins were found toxic and caused significant developmental abnormalities in zebrafish embryos. Taken together, our data demonstrate that SLA technologies can be used for rapid and accurate production of devices for biomedical research. However, polymer biotoxicity needs to be carefully evaluated.
Optimization of the imaging response of scanning microwave microscopy measurements
Authors: Sardi G. M. , Lucibello A. , Kasper M. , Gramse G. , Proietti E. , Kienberger F. , Marcelli R.
Published: July 2015

In this work, we present the analytical modeling and preliminary experimental results for the choice of the optimal frequencies when performing amplitude and phase measurements with a scanning microwave microscope. In particular, the analysis is related to the reflection mode operation of the instrument, i.e., the acquisition of the complex reflection coefficient data, usually referred as S11. The studied configuration is composed of an atomic force microscope with a microwave matched nanometric cantilever probe tip, connected by a λ/2 coaxial cable resonator to a vector network analyzer. The set-up is provided by Keysight Technologies. As a peculiar result, the optimal frequencies, where the maximum sensitivity is achieved, are different for the amplitude and for the phase signals. The analysis is focused on measurements of dielectric samples, like semiconductor devices, textile pieces, and biological specimens.
A 1 kW-class multi-stage heat-driven thermoacoustic cryocooler system operating at liquefied natural gas temperature range
Authors: Zhang L. M. , Hu J. Y. , Wu Z. H. , Luo E. C. , Xu J. Y. , Bi T. J.
Published: July 2015

This article introduces a multi-stage heat-driven thermoacoustic cryocooler capable of reaching cooling capacity about 1 kW at liquefied natural gas temperature range without any moving mechanical parts. The cooling system consists of an acoustically resonant double-acing traveling wave thermoacoustic heat engine and three identical pulse tube coolers. Unlike other traditional traveling wave thermoacoustic heat engines, the acoustically resonant double-acting thermoacoustic heat engine is a closed-loop configuration consists of three identical thermoacoustic conversion units. Each pulse tube cooler is bypass driven by one thermoacoustic heat engine unit. The device is acoustically completely symmetric and therefore “self-matching” for efficient traveling-wave thermoacoustic conversion. In the experiments, with 7 MPa helium gas as working gas, when the heating temperature reaches 918 K, total cooling capacity of 0.88 kW at 110 K is obtained with a resonant frequency of about 55 Hz. When the heating temperature is 903 K, a maximum total cooling capacity at 130 K of 1.20 kW is achieved, with a thermal-to-cold exergy efficiency of 8%. Compared to previously developed heat-driven thermoacoustic cryocoolers, this device has higher thermal efficiency and higher power density. It shows a good prospect of application in the field of natural gas liquefaction and recondensation.
A remotely operated drug delivery system with an electrolytic pump and a thermo-responsive valve
Authors: Yi Ying , Zaher Amir , Yassine Omar , Kosel Jurgen , Foulds Ian G.
Published: July 2015

Implantable drug delivery devices are becoming attractive due to their abilities of targeted and controlled dose release. Currently, two important issues are functional lifetime and non-controlled drug diffusion. In this work, we present a drug delivery device combining an electrolytic pump and a thermo-responsive valve, which are both remotely controlled by an electromagnetic field (40.5 mT and 450 kHz). Our proposed device exhibits a novel operation mechanism for long-term therapeutic treatments using a solid drug in reservoir approach. Our device also prevents undesired drug liquid diffusions. When the electromagnetic field is on, the electrolysis-induced bubble drives the drug liquid towards the Poly (N-Isopropylacrylamide) (PNIPAM) valve that consists of PNIPAM and iron micro-particles. The heat generated by the iron micro-particles causes the PNIPAM to shrink, resulting in an open valve. When the electromagnetic field is turned off, the PNIPAM starts to swell. In the meantime, the bubbles are catalytically recombined into water, reducing the pressure inside the pumping chamber, which leads to the refilling of the fresh liquid from outside the device. A catalytic reformer is included, allowing more liquid refilling during the limited valve's closing time. The amount of body liquid that refills the drug reservoir can further dissolve the solid drug, forming a reproducible drug solution for the next dose. By repeatedly turning on and off the electromagnetic field, the drug dose can be cyclically released, and the exit port of the device is effectively controlled.
Isotopic composition of polyhalomethanes from marine macrophytes – systematic effects of the halogen substituents on isotopic composition
Authors: Bahlmann Enno , Stolle Christian , Weinberg Ingo , Seifert Richard , Schulz-Bull Detlef E. , Michaelis Walter
Published: July 2015

Environmental context
Once released to the atmosphere, halocarbons are involved in key chemical reactions. Stable carbon isotope measurements of halocarbons can provide valuable information on their sources and fate in the atmosphere. Here, we report δ13C values of 13 polyhalomethanes released from brown algae, which may provide a basis for inferring their sources and fate in future studies.

Abstract
Halocarbons are important vectors of reactive halogens to the atmosphere, where the latter participate in several key chemical processes. An improved understanding of the biogeochemical controls of the production–destruction equilibrium on halocarbons is of vital importance to address potential future changes in their fluxes to the atmosphere. Carbon stable isotope ratios of halocarbons could provide valuable additional information on their sources and fate that cannot be derived from mixing ratios alone. We determined the δ13C values of 13 polyhalomethanes from three brown algae species (Laminaria digitata, Fucus vesiculosus, Fucus serratus) and one seagrass species (Zostera noltii). The δ13C values were determined in laboratory incubations under variable environmental conditions of light, water levels (to simulate tidal events) and addition of hydrogen peroxide (H2O2). The δ13C values of the polyhalomethanes ranged from –42.2 ‰ (±3.5s.d.) for CHCl3 to 6.9 ‰ (±4.5) for CHI2Br and showed a systematic effect of the halogen substituents that could empirically be described in terms of linear free energy relationships. We further observed an enrichment in the δ13C of the polyhalomethanes with decreasing polyhalomethane yield that is attributed to the competing formation of halogenated ketones. Though variable, the isotopic composition of polyhalomethanes may provide useful additional information to discriminate between marine polyhalomethane sources.
HIV testing rate increased following recommendation of routine screening of acute medical admissions at Royal Darwin Hospital
Authors: Lallenec Laura M. , Currie Bart J. , Baird Rob W. , Pitman Matthew , Ryder Nathan
Published: July 2015

Background
To improve HIV detection, Royal Darwin Hospital implemented a guideline in 2012 recommending routine HIV testing for all adult acute medical admissions. This study aimed to determine the uptake, point prevalence and impact on late diagnosis of HIV screening following guideline implementation. Methods: Data on the number of HIV tests and number of acute medical admissions over the 8 months prior and post guideline implementation were extracted from hospital databases. A qualitative survey was conducted to ascertain clinician response to routine screening. Results: Fourteen per cent of admissions were tested post-implementation compared with 5.3% during the implementation period (P < 0.001). HIV prevalence pre-implementation was 1.4% compared with 0.3% following implementation (P < 0.05). The average CD4 count at diagnosis was <200 cells/mm3. Conclusions: There was a significant increase in HIV testing following guideline implementation; however, the overall testing rate remained low. Routine screening did not increase detection of HIV, and HIV continues to be diagnosed late at Royal Darwin Hospital. Methods for improving understanding of the rationale for routine screening and increased promotion of the guidelines are required to increase testing.
Sexual behaviour and HIV prevention needs of men attending a suburban Sex on Premises Venue
Authors: Santella Anthony J. , Schlub Timothy E. , Ooi Catriona , Varma Rick , Holt Martin , Prestage Garrett , Hillman Richard J.
Published: July 2015

Background
Sexual behaviour and HIV prevention needs of men who have sex with men (MSM) attending suburban Sex on Premises Venues (SOPVs) are understudied. Methods: A cross-sectional survey examining sexual activity, health services utilisation, sexual health services needs and STI knowledge was conducted among MSM over 18 years old attending a SOPV in Western Sydney between June and July 2013. Results: A total of 213 MSM were sampled; approximately half of the respondents (51%) reported that they only had sex with other men, and 46% had sex with both men and women. Condom use varied considerably, with ~50% of responders not using condoms consistently during anal sex. Consistent condom usage was not associated with having regular, casual or a mix of regular and casual partners during anal sex (P = 0.09). The majority (59.5%) obtained sexual health screening services from general practitioners; only 15.0% sought services from a local sexual health clinic. Over half of respondents (57.7%) believed that SOPVs should offer on-site and free testing services. Those with the highest level of previous STI diagnoses were gay men (41%), those who only had casual partners (38%) and those who did not complete high school (65%). Conclusions: Sexual health services and non-government organisations should consider targeting bisexual men with rapid HIV testing and condom usage campaigns. Low cost or free on-site HIV and STI testing at SOPVs and stronger partnerships between general practitioners and sexual health services are needed.
Body image and sexually transmissible infection prevalence among men who have sex with men
Authors: Rice Cara E. , Norris Alison H. , Davis John A. , Lynch Courtney D. , Fields Karen S. , Ervin Melissa , Turner Abigail Norris
Published: July 2015

Compared with men who have sex with women, some evidence suggests that men who have sex with men (MSM) have increased prevalence of body image dissatisfaction. MSM also have a higher prevalence of sexually transmissible infections (STIs) than other population groups. As part of a cross-sectional study, body image among 104 MSM using the standardised, validated Male Body Attitudes Scale was assessed. Associations between body image and prevalent STI were examined. Body image was not associated with prevalent STI in unadjusted [prevalence ratio (PR): 1.14, 95% confidence interval (CI): 0.86–1.52] or adjusted analyses (PR: 1.17, 95% CI: 0.89–1.53).
Memory formation and retrieval of neuronal silencing in the auditory cortex
Authors: Nomura Hiroshi , Hara Kojiro , Abe Reimi , Hitora-Imamura Natsuko , Nakayama Ryota , Sasaki Takuya , Matsuki Norio , Ikegaya Yuji
Published: July 2015

Significance

Cortical neurons exhibit spontaneous activity without explicit external stimuli. Sensory stimuli not only activate specific populations of those neurons but can also silence other populations. However, it remains unclear whether neuronal silencing per se leads to memory formation and behavioral expression. Here, we used optogenetic silencing of a neuronal ensemble in the auditory cortex and found that mice exhibited a fear response to silencing that had been previously paired with footshock, and could find a reward based on the presence or absence of the silencing. These findings indicate that neuronal silencing per se, which is originally believed to be involved in neuronal modulation, is enough to elicit a cognitive behavior.
Near-infrared fluorescence molecular imaging of amyloid beta species and monitoring therapy in animal models of Alzheimer’s disease
Authors: Zhang Xueli , Tian Yanli , Zhang Can , Tian Xiaoyu , Ross Alana W. , Moir Robert D. , Sun Hongbin , Tanzi Rudolph E. , Moore Anna , Ran Chongzhao
Published: July 2015

Significance

Drug development for Alzheimer’s disease (AD) has been largely unsuccessful to date. Although numerous agents are reportedly effective in vitro, only an inadequate number of them have been tested in vivo, partially because of the lack of reliable and cost-efficient imaging methods to monitor their in vivo therapeutic effectiveness. Several amyloid beta (Aβ)-specific PET tracers have been used for clinical studies. However, their application for monitoring drug treatment in small animals is limited. Near-infrared fluorescence (NIRF) molecular imaging is a cheap, easy-to-use, and widely available technology for small animal studies. In this report we demonstrate, for the first time to our knowledge, that NIRF imaging can be used to monitor the loading changes of Aβs in an AD mouse model.
Addendum to ‘velocity-information based force-term estimation of dielectric barrier discharge plasma actuators’
Authors: Kriegseis J , Maden I , Schwarz C , Tropea C , Grundmann S
Published: July 2015

In a recent publication (Kriegseis et al 2013 J. Phys. D: Appl. Phys. 46 055202) we contrasted the variety of published strategies to estimate magnitude and distribution of the body force produced by dielectric barrier discharge plasma actuators. All approaches were applied to an identical set of velocity data, which was experimentally obtained by means of particle image velocimetry. Particularly, the determined force distributions of the above paper turned out to be beneficial for subsequent efforts to derive empirical plasma-actuator models. The purpose of this addendum, therefore, is to provide both the velocity data and the determined force distributions as discussed in the original publication. As such, a comparison of different empirical models based on identical velocity data becomes possible. In addition, numericists can directly implement the published force fields in so as to perform computational studies of discharge-based flow control.
Identifying novel associations between small molecules and miRNAs based on integrated molecular networks
Authors: Lv Yingli , Wang Shuyuan , Meng Fanlin , Yang Lei , Wang Zhifeng , Wang Jing , Chen Xiaowen , Jiang Wei , Li Yixue , Li Xia
Published: July 2015

Motivation: miRNAs play crucial roles in human diseases and newly discovered could be targeted by small molecule (SM) drug compounds. Thus, the identification of small molecule drug compounds (SM) that target dysregulated miRNAs in cancers will provide new insight into cancer biology and accelerate drug discovery for cancer therapy.

Results: In this study, we aimed to develop a novel computational method to comprehensively identify associations between SMs and miRNAs. To this end, exploiting multiple molecular interaction databases, we first established an integrated SM-miRNA association network based on 690 561 SM to SM interactions, 291 600 miRNA to miRNA associations, as well as 664 known SM to miRNA targeting pairs. Then, by performing Random Walk with Restart algorithm on the integrated network, we prioritized the miRNAs associated to each of the SMs. By validating our results utilizing an independent dataset we obtained an area under the ROC curve greater than 0.7. Furthermore, comparisons indicated our integrated approach significantly improved the identification performance of those simple modeled methods. This computational framework as well as the prioritized SM-miRNA targeting relationships will promote the further developments of targeted cancer therapies.

Contact:  yxli@sibs.ac.cn, lixia@hrbmu.edu.cn or jiangwei@hrbmu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
The application of a novel ‘rising activity, multi-level mixed effects, indicator emphasis’ (RAMMIE) method for syndromic surveillance in England
Authors: Morbey Roger A. , Elliot Alex J. , Charlett Andre , Verlander Neville Q. , Andrews Nick , Smith Gillian E.
Published: July 2015

Motivation: Syndromic surveillance is the real-time collection and interpretation of data to allow the early identification of public health threats and their impact, enabling public health action. The ‘rising activity, multi-level mixed effects, indicator emphasis’ method was developed to provide a single robust method enabling detection of unusual activity across a wide range of syndromes, nationally and locally.

Results: The method is shown here to have a high sensitivity (92%) and specificity (99%) compared to previous methods, whilst halving the time taken to detect increased activity to 1.3 days.

Availability and implementation: The method has been applied successfully to syndromic surveillance systems in England providing realistic models for baseline activity and utilizing prioritization rules to ensure a manageable number of ‘alarms’ each day.

Contact: roger.morbey@phe.gov.uk
Big biomedical data as the key resource for discovery science
Authors: Toga Arthur W , Foster Ian , Kesselman Carl , Madduri Ravi , Chard Kyle , Deutsch Eric W , Price Nathan D , Glusman Gustavo , Heavner Benjamin D , Dinov Ivo D , Ames Joseph , Van Horn John , Kramer Roger , Hood Leroy
Published: July 2015

Modern biomedical data collection is generating exponentially more data in a multitude of formats. This flood of complex data poses significant opportunities to discover and understand the critical interplay among such diverse domains as genomics, proteomics, metabolomics, and phenomics, including imaging, biometrics, and clinical data. The Big Data for Discovery Science Center is taking an “-ome to home” approach to discover linkages between these disparate data sources by mining existing databases of proteomic and genomic data, brain images, and clinical assessments. In support of this work, the authors developed new technological capabilities that make it easy for researchers to manage, aggregate, manipulate, integrate, and model large amounts of distributed data. Guided by biological domain expertise, the Center’s computational resources and software will reveal relationships and patterns, aiding researchers in identifying biomarkers for the most confounding conditions and diseases, such as Parkinson’s and Alzheimer’s.
A design principle for a single-stranded RNA genome that replicates with less double-strand formation
Authors: Usui Kimihito , Ichihashi Norikazu , Yomo Tetsuya
Published: July 2015

Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive double-stranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Qβ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the β-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.
Detecting and Segregating Black Tip‐Damaged Wheat Kernels Using Visible and Near‐Infrared Spectroscopy
Authors: Armstrong Paul R. , Maghirang Elizabeth B. , Pearson Tom C.
Published: July 2015

Detection of individual wheat kernels with black tip symptom (BTS) and black tip damage (BTD) was demonstrated with near‐infrared reflectance spectroscopy (NIRS) and silicon light‐emitting‐diode (LED) based instruments. The two instruments tested, a single‐kernel NIRS instrument (SKNIRS) and a silicon LED‐based single‐kernel high‐speed sorter (SiLED‐SKS) were both developed by the Stored Product Insect and Engineering Research Unit, Center for Grain and Animal Health Research, USDA Agricultural Research Service. BTD was classified into four levels for the study ranging from sound, symptomatic (BTS) at two levels, and damaged (BTD). Discriminant analysis models for the SKNIRS instrument could distinguish sound undamaged kernels well, correctly classifying kernels 80% of the time. Damaged kernels were classified with 67% accuracy and symptomatic kernels at about 44%. Higher classification accuracy (81–87%) was obtained by creating only two groupings: 1) combined sound and lightly symptomatic kernels and 2) combined heavily symptomatic and damaged kernels. A linear regression model was developed from the SiLED‐SKS sorted fractions to predict the percentage of combined BTS and BTD kernels in a sample. The model had an R2 of 0.64 and a standard error of prediction of 7.4%, showing it had some measurement ability for BTS and BTD. The SiLED‐SKS correctly classified and sorted out 90% of BTD and 66% of BTS for all 28 samples after three passes through the sorter. These instruments can serve as important tools for plant breeders and grading facilities of the wheat industry that require timely and objective determination and sorting of different levels of black tip present in wheat samples.
Feasibility of a Sexual Health Clinic Within Cancer Care
Authors: Tracy Myrna , McDivitt Karmen , Ryan Maureen , Tomlinson Jamie , Brotto Lori A.
Published: July 2015

Background:

As cancer survival rates increase, so does the imperative for a satisfying quality of life, including a fulfilling sexual life.

Objective:

The feasibility and effectiveness of a newly formed Sexual Health Clinic were determined using a nurse-led format, which provided support to survivors in a cancer care setting.

Methods:

Twenty-one cancer survivors received assessment, education, and tailored sexual health support by an oncology nurse with specialized skills in sexual health. Two months later, semistructured interviews focused on patients’ personal experiences. Questionnaires were also administered to healthcare providers involved in providing the follow-up care.

Results:

Participants presented with sexual concerns that were psychological, physical, and/or relational. Scores on validated measures of sexual functioning were in the range comparable to those with a sexual dysfunction. Participants were open to being asked about sexual health and wanted professionals available who were skilled in dealing with sexual health services. Most participants experienced an improvement in their well-being and/or sexual life following participation. Some noted more confidence when speaking with their partner about sexual concerns.

Conclusion:

Our pilot Sexual Health Clinic was feasible, and evidence for its effectiveness was based on qualitative feedback. Participants and providers identified a strong need for the inclusion of sexual health services in cancer care.

Implications for Practice:

Oncology nurses are in a key position to initiate discussions surrounding sexual health issues related to cancer treatment. Self-awareness, sensitivity, and a nonjudgmental approach are required to address this dimension of holistic cancer care.
Rational Manual and Automated Scoring Thresholds for the Immunohistochemical Detection of TP53 Missense Mutations in Human Breast Carcinomas
Authors: Taylor Nicholas J. , Nikolaishvili-Feinberg Nana , Midkiff Bentley R. , Conway Kathleen , Millikan Robert C. , Geradts Joseph
Published: July 2015

Missense mutations in TP53 are common in human breast cancer, have been associated with worse prognosis, and may predict therapy effect. TP53 missense mutations are associated with aberrant accumulation of p53 protein in tumor cell nuclei. Previous studies have used relatively arbitrary cutoffs to characterize breast tumors as positive for p53 staining by immunohistochemical assays. This study aimed to objectively determine optimal thresholds for p53 positivity by manual and automated scoring methods using whole tissue sections from the Carolina Breast Cancer Study. p53-immunostained slides were available for 564 breast tumors previously assayed for TP53 mutations. Average nuclear p53 staining intensity was manually scored as negative, borderline, weak, moderate, or strong and percentage of positive tumor cells was estimated. Automated p53 signal intensity was measured using the Aperio nuclear v9 algorithm combined with the Genie histology pattern recognition tool and tuned to achieve optimal nuclear segmentation. Receiver operating characteristic curve analysis was performed to determine optimal cutoffs for average staining intensity and percent cells positive to distinguish between tumors with and without a missense mutation. Receiver operating characteristic curve analysis demonstrated a threshold of moderate average nuclear staining intensity as a good surrogate for TP53 missense mutations in both manual (area under the curve=0.87) and automated (area under the curve=0.84) scoring systems. Both manual and automated immunohistochemical scoring methods predicted missense mutations in breast carcinomas with high accuracy. Validation of the automated intensity scoring threshold suggests a role for such algorithms in detecting TP53 missense mutations in high throughput studies.
Significance of p27 Immunostaining in B-Cell Neoplasm
Authors: El-kerdany Tahany A. , Shams Eldin El Telbany Manal A. , Esmaeel Manal M. , Mahmoud Hanan M.
Published: July 2015

P27Kip1is an important cell cycle regulatory protein. Many reports have validated the utility of p27 as a prognostic marker in different human cancers and to prove its prognostic role in B-cell neoplasm; 80 newly diagnosed B-cell neoplasm patients with mean age of 46.6 years recruited from Hematology/Oncology Unit of Ain Shams University Hospitals during the period from January 2008 till June 2010 were studied for their p27 immunostaining results which showed that all cases of chronic lymphocytic leukemia (CLL) were positive for p27, whereas all mantly cell lymphoma cases were negative for it. There was significantly higher p27 positivity in CLL cases compared with non-Hodgkin lymphoma and that indolent cases showed significantly higher rate of positivity when compared with aggressive and highly aggressive cases. So, we can use this marker to differentiate CLL and mantly cell lymphoma in cases of confusion.
Haplotype-phased synthetic long reads from short-read sequencing
Authors: Stapleton James A. , Kim Jeongwoon , Hamilton John P. , Wu Ming , Irber Luiz C. , Maddamsetti Rohan , Briney Bryan , Newton Linsey , Burton Dennis R. , Brown C. Titus , Chan Christina , Buell C. Robin , Whitehead Timothy A.
Published: July 2015

Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIVenvgene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.
Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes
Authors: Gossmann Toni I , Saleh Dounia , Schmid Marc W , Spence Michael A , Schmid Karl J
Published: July 2015

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterise evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analysed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species,Arabidopsis thaliana, rice (Oryza sativa) and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as ``evolutionary bulge'' during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.
Virtual assembly with physical information: a review
Authors: Liu Keyan , Yin Xuyue , Fan Xiumin , He Qichang
Published: July 2015

Purpose

– The purpose of this paper is to give a comprehensive survey on the physics-based virtual assembly (PBVA) technology in a novel perspective, to analyze current drawbacks and propose several promising future directions.

Design/methodology/approach

– To provide a deep insight of PBVA, a discussion of the developing context of PBVA and a comparison against constraint-based virtual assembly (CBVA) is put forward. The core elements and general structure are analyzed based on typical PBVA systems. Some common key issues as well as common drawbacks are discussed, based on which the research trend and several promising future directions are proposed.

Findings

– Special attention is paid to new research progresses and new ideas concerning recent development as well as new typical systems of the technology. Advantages of PBVA over CBVA are investigated. Based on the analysis of typical PBVA systems and the evolution of PBVA, the core elements of the technology and the general structure of its implementation are identified. Then, current PBVA systems are summarized and classified. After that, key issues in the technology and current drawbacks are explored in detail. Finally, promising future directions are given, including both the further perfecting of the technology and the combination with other technologies.

Originality/value

– The PBVA technology is put into a detailed review and analysis in a novel way, providing a better insight of both the theory and the implementation of the technology.
Recent innovations in adhesive technology
Authors: Bogue Robert
Published: July 2015

Purpose

– This paper aims to provide an insight into recent innovations in adhesive technology by considering a selection of commercial developments and academic research activities.

Design/methodology/approach

– Following an introduction, this paper first discusses a selection of commercially developed adhesives used in the healthcare, photovoltaics and aerospace industries. It then considers biomimetic adhesive research, specifically dry adhesives which mimic the principles of gecko adhesion and wet adhesives based on the chemistry which underpins mussel adhesion. Finally, brief concluding comments are drawn.

Findings

– This shows that new adhesives continue to be developed to meet a growing range of industrial requirements, and a major research effort into biologically inspired adhesion mechanisms is poised to yield new families of high-performance adhesives.

Originality/value

– This provides details of recent commercial and academic developments in adhesive technology.
Financial inclusion of the poor: from microcredit to Islamic microfinancial services
Authors: Hassan Abul
Published: July 2015

Purpose

– The purpose of this paper is to initiate a direct discourse towards an Islamic microfinance focus agenda for the economic enlistment of the poor minority community and to allow poorer households in the financial inclusion. The issue of the Indian conventional microfinance institutions in failing to attract the poorest of the poor amongst Muslims is important for the purpose of this paper. This study explores a Shari’ah-compliant microfinance system which will create a level of playing-field with respect to the financial inclusion of the poor.

Design/methodology/approach

– The paper is a theoretical discussion on Islamic microfinancial services for financial inclusion of the poor. Therefore, there is little to say about “methodology” other than the conventional microfinance model is reviewed, and an alternative model of Islamic microfinancial service has been suggested to allow poorer households in the financial inclusion.

Findings

– The paper finds that there are some opportunities capable of improving the economic condition of the poor Muslim communities through some innovative approaches. To illustrate this finding, the paper emphasises on designing and delivering Islamic microfinancial products suitable for the poor based on the principle of Islamic solidarity. It argues that this service will help the poor and turn their savings into sums large enough to satisfy a wide range of personal, social and asset-building needs as well as needs relating to small businesses and consumption.

Research limitations/implications

– The paper’s findings are limited to the matter of financial inclusion of the poor through Islamic microfinancial services in India.

Originality/value

– Combining the Islamic social principle of solidarity for the less fortunate with the power of microfinance to provide financial access to the poor has the potential to reach out to millions more people. The ideas presented in this paper are designed to direct discourse towards an Islamic microfinance focus agenda for the economic enlistment of the poor Muslims in India.
From partner selection to trust dynamics
Authors: Pao Huei-Wen , Wu Hsueh-Liang , Ho Shih-Ping , Lee Cheng-Yu
Published: July 2015

Purpose

– To heed the calls for more inquiries into the tacit behavior in the partnering process and the latent rules underpinning the success of partnerships, the purpose of this paper is to develop a process model that explains when and how partner fit triggers the generation of trust through the sense making of fairness and similarity, and then yields performance by overcoming uncertainties jeopardizing the collaboration.

Design/methodology/approach

– To develop a comprehensive but parsimonious model for international partnership, the study involves observing and interpreting the accounts of project managers, which suggest the use of an exploratory approach based on case studies. The research setting is six cross-country partnerships operating in East Asian countries during 2005-2009 with each joint project involving Taiwanese construction companies and at least one local partner.

Findings

– The evidence shows that inter-partner trust conduces to project performance by reducing the threat of behavioral and environmental uncertainty. The findings confirm the general thesis that the performance implication of inter-partner trust is not uniform but contingent on both the types of trust and the uncertainty in the partnering process.

Originality/value

– Although not the first in the literature of collaborative dynamics, the paper contributes to identifying the latent constructs in the partnering process and highlighting the context-dependent nature of a successful partnership.