bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidermoid Cyst in the Lateral Eyebrow (Frontozygomatic Suture) Region and Review of Literature
Authors: Deepthi Shetty , Prashanth Shetty
Published: April 2020

Epidermoid cysts are non odontogenic, developmental pathologies occurring in the head and neck region with an incidence ranging from 1.6% to 6.9%. Ambiguity about their exact pathogenesis exists and several theories have been postulated. Histologically they have cystic capsule lined by squamous epithelium without skin appendages. We have described a case of an epidermoid cyst in the lateral eyebrow region and its effective management with a brief review of literature.
Cutaneous Tuberculosis- probably due to mycobacterium bovis infection: A case report
Authors: Kini Sanjay , Shanbhag Aravind , Prabhu Sachidananda
Published: April 2020

Cutaneous tuberculosis is an infection caused by M. tuberculosis complex, M. bovis and bacillus Calmette- Guérin. Depending on individual immunity, environmental factors and the type of inoculum, it may present varied clinical and evolutionary aspects. Here we found a similar case where a 63 year old female patient developed cutaneous tuberculosis either due to direct inoculation or secondary to consumption of unpasteurized milk. The wound was not healing even after several courses of antibiotics and started healing only after starting anti-tubercular treatment. Hence we recommend that clinicians should keep this possibility in mind for early diagnosis and prompt treatment.
Palateless Overdenture: A Case Report
Authors: Prakyath Malli , Vinaya Bhat , Tripthi Shetty
Published: April 2020

Palateless tooth supported overdenture is a treatment modality for patients to increase comfort as it aids in good retention, enhanced stability, better chewing efficiency and decreased alveolar bone resorption. This case report gives an insight into the step wise fabrication of a tooth supported palateless overdenture rather for better comfort, temperature and taste perception which is not possible as in case of a conventional complete denture.
A comparative study on impact of dry versus moist heat application on feasibility of peripheral intravenous cannulation among the patients of a selected hospital at Mangalore
Authors: K. Jisha , S. Latha , Joseph Gincy
Published: April 2020

The present study was conducted to assess the impact of dry v/s moist heat application on feasibility of peripheral intravenous cannulation. The study design adopted was true experimental - post test only with control group design. Using randomized block sampling 60 patients were selected and equally allocated into 3 groups-dry heat (group I), moist heat (group II) and control group each with 20 samples. The baseline clinical data were collected from the patients by interview method. Dry heat with a hot water bag at temperature of 120-140 degree Fahrenheit was applied to the peripheral cannulation site in experimental group I and moist 0 heat was applied to group II by wrapping a moist towel (110-1150 F) over the site for seven minutes. Numerical Pain scale was used to measure the level of pain experienced during peripheral intravenous cannulation. Data obtained in these areas were analysed by descriptive and inferential statistics. A significant difference was found between experimental group and control group. The Mann Whitney U test scores for Impact of dry heat and moist heat on feasibility showed that the p value for the components of feasibility like (time taken for cannulation and pain score) is < 0.05, and both dry heat and moist heat is effective in improving the feasibility of IV cannulation. Comparison of dry heat and moist heat by Kruskal Wallis test revealed that dry heat is more effective than moist heat(least time for cannulation (Median =1) and least pain (Median==1).No significant association was found between the level of pain and selected variables. This study proved that dry heat application reduces the time for cannulation and level of pain experienced by the clients during intravenous cannulation.
Full mouth rehabilitation of a patient exhibiting generalized attrition - A case report
Authors: Balaji Sriram , Bhat Vinaya
Published: April 2020

Tooth wear is multifactorial and its way of presentation is complex. Many factors are to considered before arriving at a final treatment plan. Time tested philosophies of dental reconstruction must be taken as a basic foundation to which modifications can be done as per individual needs of the patient. The ultimate aim of any treating dentist is to arrive at a solution which lays emphasis on the comprehensive oral health of the patient. This case report describes one such case of managementof a patient with generalized sensitivity.
CORRELATION BETWEEN BMI AND PREGNANCY OUTCOME AMONG POSTNATAL MOTHERS WITH PREGNANCY INDUCED HYPERTENSION IN SELECTED HOSPITALS BANGALORE
Authors: P. Prathima , Anuchitra S
Published: April 2020

Title : Correlation between BMI and pregnancy Outcome among postnatal mothers with pregnancy Induced hypertension in selected hospital Bangalore.

Objectives: To identify and correlate BMI and pregnancy Outcome among postnatal mothers with pregnancy Induced hypertension.

Method: A non experimental correlation design was utilized among 80 postnatal mothers who were diagnosed as Pregnancy induced hypertension during their antenatal period selected as samples by using purposive sampling technique. Demographic data were collected by interview method, their BMI was calculated, pregnancy outcomes were identified from records by using an outcome checklist.

Results : Underweight mothers had low birth weight babies and received NICU care. Among normal weight mothers 17.5 % delivered by LSCS, 15% babies were low birth weight babies 12.5 were preterm babies among them 10% received NICU care. In the overweight group 18.75% undergone LSCS, 18.75% were LBW and 1.25% VLBW, 8.75% babies were preterm, 12.5% newborn received NICU care. Among Obese mothers 8.75% delivered by LSCS, 6.25% of LBW babies, 5% were preterm and all of them received NICU care. There is a positive correlation between BMI and diagnosis and type of delivery. Significant at .01 and .05 Level (p value .008 and .019 respectively). Negative correlation between birth weight and diagnosis and gestational age. r = -.499 significant at .01 level (p value .000)

Conclusion: Obesity and under weight is a leading, preventable cause of mortality worldwide. Preeclampsia increases maternal and perinatal morbidity and mortality rates. All women who are in reproductive age group and under risk to develop pregnancy induced hypertension need to be educated about to maintenance of normal weight before pregnancy. Nurses have more responsibility on creating awareness among women how to maintain normal weight to avoid development of complications to the mother and newborn.
SAUVE - KAPANDJI PROCEDURE FOR MALUNITED DISTAL RADIUS
FRACTURE: A CASE REPORT
Authors: Shetty Sanath Kumar , John Joseph , Mathias Lawrence John , Rai H Ravindranath
Published: April 2020

Distal radioulnar joint disorders are a frequent cause of wrist pain and instability. The etiology include displaced fractures or malunions of the distal radius and tears of the triangular fibrocartilage complex with DRUJ instability.

A 47 year old gentleman presented to us with complaints of pain and deformity of the right wrist of one and half years duration. Radiographs revealed a malunited distal radius fracture.

He underwent Sauve Kapandji procedure. Follow ups were done at periodic intervals and wrist physiotherapy was instituted. He had acceptable wrist motion at six weeks.
ANTERIOR APPROACH CELIAC PLEXUS NEUROLYSIS FOR A
PATIENT WITH NECROTISING FASCIITIS OF THE BACK
Authors: Abloodu Manjunath Chikkapillappa , Pujari Vinayak Seenappa , Channasandra Tejesh Anandaswamy , Bevinaguddaiah Yatish
Published: April 2020

Celiac plexus block is a time tested method for management of pain. It is conventionally done via posterior approach. We report successful use of anterior celiac plexus to manage pain in a case of chronic pancreatitis with necrotising fasciitis of the back.
VARIATIONS OF FORAMEN TRANSVERSARIUM IN ATLAS VERTEBRAE : A MORPHOLOGICAL STUDY WITH ITS CLINICAL SIGNIFICANCE
Authors: Sultana Qudusia , Avadhani Ramakrishna , KL Varalakshmi , MH Shariff ,   Blessina
Published: April 2020

Introduction: The second part of the vertebral artery along with vertebral venous plexus and sympathetic plexus traverses through vicinity of foramen transversarium of atlas. Derangement of these structures in their course may be seen due to deformities, narrowing and presence of osteophytes in foramen transversarium.

Methods: Two hundred foramen transversarium of 100 atlas vertebrae were grossly studied for their variations.

Results: Out of hundred atlas vertebrae examined, we found that all the vertebrae had foramina transversaria. Absence of costal element was noticed in five atlas vertebrae. 2 of the vertebrae showed incomplete unilateral foramen transversarium, 3 vertebrae showed bilateral incomplete foramen, In 1 vertebra along with normal foramen transversarium, complete retroarticular foramen was observed on the left side and incomplete retroarticular foramen observed on the right side of the posterior arch.4 vertebrae showed incomplete retroarticular foramen.

Conclusion: The increasing incidence of neck injuries and related syndromes necessitates the study of bony variations of the atlas vertebra and its transverse foramina. Due to the incomplete formation of the foramen transversarium the second part of vertebral artery is prone to be damaged easily during posterior cervical injuries and Surgeries. The bony bridges embracing the vertebral artery may be responsible for vertigo and cerebrovascular accidents hence the knowledge of such variations is important for Physicians, Otirhinolaryngologists, neurologists ,Orthopaedicians and Radiologists.
A CASE REPORT OF HEAT STROKE : AN ICEBERG
Authors: Krishna Pothukuchi Venkata , Chepuri Venkata Ravikumar , Karnati Hema , Yarram Raghavareddy
Published: April 2020

Heat stroke was first recognized by the Romans in 24 BC. But it took until 1946 for it to be shown that heat stroke could lead to multiorgan damage with hemorrhage and necrosis in the lungs, heart, liver, kidneys, brain and gut with a 10% to 50% mortality rate. Patients may present with neurological impairment of varying degrees and duration, including delirium, lethargy, coma and seizures, Neurological damage is presumably attributable to metabolic disarray, cerebral edema or ischemia. Here we are presenting a case of heat stroke, with coma due to neurological involvement who recovered functionally fully though with some residual damage revealed in computerized tomogram of the brain after conservative management of heat stroke.
Dispersion and attenuation characteristics of steady-state microwave plasma waveguide
Authors: Stephan Karl D. , De La Garza Andres E. , Hua Yue
Published: April 2020

Near the electrostatic plasma frequency, plasma exhibits a relative permittivity near zero, and this property has been used to make transient plasma waveguides at microwave and optical wavelengths by ionizing gases with pulsed electromagnetic fields and laser radiation. However, to our knowledge, no one has constructed a steady-state RF-excited plasma waveguide for the purpose of studying its microwave attenuation and dispersion characteristics. We report here the results of investigations at 2.8–3.7 GHz of a variable-length plasma waveguide up to 30 cm long in which the plasma’s relative permittivity was as low as 0.2. De-embedded S-parameter power loss is as low as 4.6 dB and the dispersion is largely consistent with theory, although further work remains to be done.
Thermoelectric properties, phonon, and mechanical stability of new half-metallic quaternary Heusler alloys: FeRhCrZ (Z = Si and Ge)
Authors: Khandy Shakeel Ahmad , Chai Jeng-Da
Published: April 2020

Computer simulations within the framework of density functional theory are performed to study the electronic, dynamic, elastic, magnetic, and thermoelectric properties of a newly synthesized FeRhCrGe alloy and a theoretically predicted FeRhCrSi alloy. From the electronic structure simulations, both FeRhCrZ (Z = Si and Ge) alloys at their equilibrium lattice constants exhibit half-metallic ferromagnetism, which is established from the total magnetic moment of 3.00 μB, and that the spin moment of FeRhCrGe is close to the experimental value (2.90 μB). Their strength and stability with respect to external pressures are determined by simulated elastic constants. The Debye temperatures of FeRhCrSi and FeRhCrGe alloys are predicted to be 438 K and 640 K, respectively, based on elastic and thermal studies. The large power factors (PFs) of the two investigated alloys are in contour with those of the previously reported Heusler compounds. Besides, the conservative estimate of relaxation time speculated from the experimental conductivity value is 0.5 × 10−15 s. The room temperature PF values of FeRhCrSi and FeRhCrGe compounds are 2.3 μW/cm K2 and 0.83 μW/m K2, respectively. Present investigations certainly allow the narrow bandgap, spin polarization, and high PF values to be looked upon for suitable applications in thermoelectrics and spintronics.
High-speed electroluminescence from semiconducting carbon nanotube films
Authors: Takahashi Hidenori , Suzuki Yuji , Yoshida Norito , Nakagawa Kenta , Maki Hideyuki
Published: April 2020

High-speed light emitters integrated on silicon chips can enable novel architectures for silicon-based optoelectronics, such as on-chip optical interconnects and silicon photonics. However, conventional light sources based on compound semiconductors face major challenges for their integration with the silicon-based platforms because of the difficulty of their direct growth on a silicon substrate. Here, we report high-speed, ultra-small-size on-chip electroluminescence (EL) emitters based on semiconducting single-walled carbon nanotube (SWNT) thin films. The peaks of the EL emission spectra are about 0.15-eV redshifted from the peaks of the absorption and photoluminescence emission spectra, which probably suggest emission from trions. High-speed responses of ∼100 ps were experimentally observed from the EL emitters, which indicate the possibility of several-GHz modulation. The pulsed light generation was also obtained by applying the pulse voltage. These high-speed and ultra-small-size EL emitters can enable novel on-chip optoelectronic devices for highly integrated optoelectronics and silicon photonics.
2D hole gas mobility at diamond/insulator interface
Authors: Daligou G. , Pernot J.
Published: April 2020

The hole mobility of two-dimensional (2D) gas at (001) and (111) diamond/insulator interfaces is investigated theoretically and compared with experimental data from the literature. It is shown that the surface impurity scattering is the limiting mechanism at room temperature in most of the H-terminated diamond field effect transistors, where the negative charges created by transfer doping are in the vicinity of the 2D gas. By repelling the negative charges at the metal/insulator interface, as recently reported for the (111) h-BN/diamond interface, we demonstrate that it is possible to achieve high mobility values of the order of 3000 cm2/V s when a pure phonon scattering occurs. This work confirms the potential of two-dimensional hole gas diamond field effect transistors for high power and high frequency applications.
Variations of belowground C and N cycling between arbuscular mycorrhizal and ectomycorrhizal forests across China
Authors: Li Jiwei , Shangguan Zhouping , Deng Lei
Published: April 2020

Forests associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi may have distinct belowground carbon (C) and nitrogen (N) cycle processes. However, there are little available data providing evidence for the effects of trees associating with mycorrhizal type on belowground C and N cycling in forest ecosystems in China. Here, we collected a database of 26 variables related to belowground C and N cycling from 207 studies covering 209 sampling sites in China, to better understand the variations in belowground C and N cycling between the two mycorrhizal types in forest ecosystems along a climatic gradient. The AM forests had significantly lower soil total C and N contents, and soil microbial biomass C and N, than ECM forests, probably due to differences in litter quality (N and C/N) between AM and ECM forest types. In contrast, AM forests had significantly higher litter input, litter decomposition and soil respiration than ECM forests. Temperature and precipitation had significant positive effects on litter input and decomposition, soil total C and N contents, and soil respiration in AM and ECM forests. Overall, our results indicated that mycorrhizal type strongly affected belowground C and N cycle processes in forest ecosystems. Moreover, AM forests are likely more sensitive and ECM forests have a greater ability to adapt to global climate change.
Sterol biosensor reveals LAM-family Ltc1-dependent sterol flow to endosomes upon Arp2/3 inhibition
Authors: Marek Magdalena , Vincenzetti Vincent , Martin Sophie G.
Published: April 2020

Sterols are crucial components of biological membranes, which are synthetized in the ER and accumulate in the plasma membrane (PM). Here, by applying a genetically encoded sterol biosensor (D4H), we visualize a sterol flow between PM and endosomes in the fission yeast Schizosaccharomyces pombe. Using time-lapse and correlative light-electron microscopy, we found that inhibition of Arp2/3-dependent F-actin assembly promotes the reversible relocalization of D4H from the PM to internal sterol-rich compartments (STRIC) labeled by synaptobrevin Syb1. Retrograde sterol internalization to STRIC is independent of endocytosis or an intact Golgi, but depends on Ltc1, a LAM/StARkin-family protein localized to ER-PM contact sites. The PM in ltc1Δ cells over-accumulates sterols and upon Arp2/3 inhibition forms extended ER-interacting invaginations, indicating that sterol transfer contributes to PM size homeostasis. Anterograde sterol movement from STRIC is independent of canonical vesicular trafficking but requires Arp2/3, suggesting a novel role for this complex. Thus, transfer routes orthogonal to vesicular trafficking govern the flow of sterols in the cell.
Demonstration of dynamic thermal compensation for parametric instability suppression in Advanced LIGO
Authors: Hardwick T , Hamedan V J , Blair C , Green A C , Vander-Hyde D
Published: April 2020

Advanced LIGO and other ground-based interferometric gravitational-wave detectors use high laser power to minimize shot noise and suspended optics to reduce seismic noise coupling. This can result in an opto-mechanical coupling which can become unstable and saturate the interferometer control systems. The severity of these parametric instabilities scales with circulating laser power and first hindered LIGO operations in 2014. Static thermal tuning and active electrostatic damping have previously been used to control parametric instabilities at lower powers but are insufficient as power is increased. Here we report the first demonstration of dynamic thermal compensation to avoid parametric instability in an Advanced LIGO detector. Annular ring heaters that compensate central heating are used to tune the optical mode away from multiple problematic mirror resonance frequencies. We develop a single-cavity approximation model to simulate the optical beat note frequency during the central heating and ring heating transient. An experiment of dynamic ring heater tuning at the LIGO Livingston detector was carried out at 170 kW circulating power and, in agreement with our model, the third order optical beat note is controlled to avoid instability of the 15 and 15.5 kHz mechanical modes. We project that dynamic thermal compensation with ring heater input conditioning can be used in parallel with acoustic mode dampers to control the optical mode transient and avoid parametric instability of these modes up to Advanced LIGO’s design circulating power of 750  kW. The experiment also demonstrates the use of three mode interaction monitoring as a sensor of the cavity geometry, used to maintain the g-factor product to g
1
g
2 = 0.829 ± 0.004.
Exact eigenvectors and eigenvalues of the finite Kitaev chain and its topological properties
Authors: Leumer Nico , Marganska Magdalena , Muralidharan Bhaskaran , Grifoni Milena
Published: April 2020

We present a comprehensive, analytical treatment of the finite Kitaev chain for arbitrary chemical potential and chain length. By means of an exact analytical diagonalization in the real space, we derive the momentum quantization conditions and present exact analytical formulas for the resulting energy spectrum and eigenstate wave functions, encompassing boundary and bulk states. In accordance with an analysis based on the winding number topological invariant, and as expected from the bulk-edge correspondence, the boundary states are topological in nature. They can have zero, exponentially small or even finite energy. Further, for a fixed value of the chemical potential, their properties are ruled by the ratio of the decay length to the chain length. A numerical analysis confirms the robustness of the topological states against disorder.
Observation of spatiotemporal structures of temperature fluctuations by using of a statistical phase detection method in a linear magnetized plasma
Authors: Kawachi Yuichi , Inagaki Shigeru , Kin Fumiyoshi , Yamasaki Kotaro , Kosuga Yusuke , Sasaki Makoto , Nagashima Yoshihiko , Yamada Takuma , Arakawa Hiroyuki , Kasuya Naohiro , Moon Chanho , Hasamada Kazunobu , Fujisawa Akihide
Published: April 2020

In this paper, we evaluated electron temperature fluctuations by using a conditional sampling and a statistical phase detection method. These methods allow us to reconstruct probe I − V characteristics at each time delay; that is, we can extract electron temperature and ion saturation current fluctuations in high temporal resolution without complex electronic circuits. Our method was applied to two quasi-coherent fluctuations observed in a linear magnetized plasma device, PANTA. We observed spatiotemporal structures of electron temperature and ion saturation current fluctuations. The results revealed the amplitudes and phase relation between electron temperature and density fluctuations.
Pseudo-2D superconducting quantum computing circuit for the surface code: proposal and preliminary tests
Authors: Mukai Hiroto , Sakata Keiichi , Devitt Simon J , Wang Rui , Zhou Yu , Nakajima Yukito , Tsai Jaw-Shen
Published: April 2020

Among the major hardware platforms for large-scale quantum computing, one of the leading candidates is superconducting quantum circuits. Current proposed architectures for quantum error-correction with the promising surface code require a two-dimensional layout of superconducting qubits with nearest-neighbor interactions. A major hurdle for the scalability in such an architecture using superconducting systems is the so-called wiring problem, where qubits internal to a chipset become difficult to access by the external control/readout lines. In contrast to the existing approaches which address the problem through intricate three-dimensional wiring and packaging technology, leading to a significant engineering challenge, here we address this problem by presenting a modified microarchitecture in which all the wiring can be realized through a newly introduced pseudo two-dimensional resonator network which provides the inter-qubit connections via airbridges. Our proposal is completely compatible with current standard planar circuit technology. We carried out experiments to examine the feasibility of the new airbridge component. The measured quality factor of the airbridged resonator is below the simulated surface-code threshold required for a coupling resonator, and it should not limit simulated gate fidelity. The measured crosstalk between crossed resonators is at most −49 dB in resonance. Further spatial and frequency separation between the resonators should result in relatively limited crosstalk between them, which would not increase as the size of the chipset increases. This architecture and the preliminary tests indicate the possibility that a large-scale, fully error-corrected quantum computer could be constructed by monolithic integration technologies without additional overhead or special packaging know-how.
Effect of antimony on low-temperature tensile deformation behaviour of high-grade non-oriented silicon steel
Authors: Dechao Li , Junhui Dong , Haipeng Chen , Haiyan Wang
Published: April 2020

The effects of antimony (Sb) on the deformation behaviour of high-grade non-oriented silicon steel at a low temperature were studied by using a Gleeble-3800 thermal simulator and the field-emission scanning-electron microscope. The tensile strength of the high-grade non-oriented silicon steel without Sb was significantly lower than that of the high-grade non-oriented silicon steel with Sb within the tensile temperature range of 25 °C–240 °C. It is possible for Sb atoms near the grain boundary to diffuse at hundreds of atoms through dislocations as a rapid diffusion channel, which is driven by thermal activation with an increase in temperature. Atomic diffusion can weaken the damage to bonding forces on the grain boundary and crack propagation along the grain boundary under load action. The segregation of Sb atoms at the grain boundary decreased gradually, which weakened the cleavage characteristics of the fracture morphology and enhanced its dimple characteristics. For a stretching temperature of 80 °C, the fracture dimple of high-grade non-oriented silicon steel without Sb was significantly more than the high-grade non-oriented silicon steel with Sb. Because of the weakening effect of Sb segregation at the grain boundary, the suitable low-temperature deformation range for high-grade non-oriented silicon steel with Sb was 120 °C–160 °C.
On initial and terminal value problems for fractional nonclassical diffusion equations
Authors: Tuan Nguyen Huy , Caraballo Tomás
Published: April 2020

In this paper, we consider fractional nonclassical diffusion equations under two forms: initial value problem and terminal value problem. For an initial value problem, we study local existence, uniqueness, and continuous dependence of the mild solution. We also present a result on unique continuation and a blow-up alternative for mild solutions of fractional pseudo-parabolic equations. For the terminal value problem, we show the well-posedness of our problem in the case

0
>
α
≤
1

0>\alpha \le 1

and show the ill-posedness in the sense of Hadamard in the case

α
>
1

\alpha > 1

. Then, under the a priori assumption on the exact solution belonging to a Gevrey space, we propose the Fourier truncation method for stabilizing the ill-posed problem. A stability estimate of logarithmic-type in

L
q

L^q

norm is first established.
Mediation of the Associations of Physical Activity With Cardiovascular Events and Mortality by Diabetes in Older Mexican Americans
Authors: Inoue Kosuke , Mayeda Elizabeth R , Paul Kimberly C , Shih I-Fan , Yan Qi , Yu Yu , Haan Mary , Ritz Beate R
Published: April 2020

Low physical activity (PA) among older adults increases the risk of cardiovascular disease (CVD) and mortality through metabolic disorders such as type 2 diabetes. We aimed to elucidate the extent to which diabetes mediates the effect of nonoccupational PA levels on CVD and mortality among older Mexican Americans. This study included 1,676 adults from the Sacramento Area Latino Study on Aging (1998–2007). We employed Cox proportional hazards regression models to investigate associations of PA level with all-cause mortality, fatal CVD, and nonfatal CVD events. Utilizing causal mediation analysis within a counterfactual framework, we decomposed the total effect of PA into natural indirect and direct effects. Over a median of 8 years of follow-up, low PA (<25th percentile) was associated with increased risks of all-cause mortality (hazard ratio (HR) = 1.36, 95% confidence interval (CI): 1.06, 1.75), fatal CVD (HR = 2.05, 95% CI: 1.42, 2.97), and nonfatal CVD events (HR = 1.67, 95% CI: 1.18, 2.37) in comparison with high PA (>75th percentile). Diabetes mediated 11.0%, 7.4%, and 5.2% of the total effect of PA on all-cause mortality, fatal CVD, and nonfatal CVD events, respectively. Our findings indicate that public health interventions targeting diabetes prevention and management would be a worthwhile strategy for preventing CVD and mortality among older Mexican Americans with insufficient PA levels.
Race and the Rise of a Mass Visual Culture: The Case of David Hunter Strother’s Virginia Illustrated
Authors: Lukasik Christopher
Published: April 2020

The publication of David Hunter Strother’s Virginia Illustrated under the pseudonym Porte Crayon in Harper’s Monthly (1854–56) provides a compelling case study through which to consider the role of race in the development of a US mass visual culture. The media combinations found within and the reception history of Virginia Illustrated demonstrate the importance of racialized viewing to the early success of Harper’s Monthly at a critical moment in media history. To be sure, Virginia Illustrated circulated racist stereotypes to be mass consumed, but the image/text operations of Strother’s literary sketches and illustrations also extended the privileges and pleasures inherent in the performance of the white male gaze to the expanding readership of Harper’s Monthly despite the differences in region, gender, and class of that audience. The case study of Virginia Illustrated challenges us to revisit the oddly marginalized relationship of nineteenth-century illustration to literary, art, and media history and invites us to situate nineteenth-century US literature into the wider media landscape of which it was undoubtedly a part.
Assessing the variation in manganese use efficiency traits in Scottish barley landrace Bere (Hordeum vulgare L.)
Authors: Cope Jonathan E , Russell Joanne , Norton Gareth J , George Timothy S , Newton Adrian C
Published: April 2020

Background and Aims

Manganese (Mn) deficiency in barley is a global problem. It is difficult to detect in the early stages of symptom development and is commonly pre-emptively corrected by Mn foliar sprays that can be costly. Landraces adapted to marginal lands around the world represent a genetic resource for potential sustainability traits including mineral use efficiency. This research aims to confirm novel Mn use efficiency traits from the Scottish landrace Bere and use an association mapping approach to identify genetic loci associated with the trait.

Methods

A hydroponic system was developed to identify and characterize the Mn deficiency tolerance traits in a collection of landraces, including a large number of Scottish Bere barleys, a group of six-rowed heritage landraces grown in the highlands and islands of Scotland. Measuring chlorophyll fluorescence, the effect of Mn deficiency was identified in the early stages of development. Genotypic data, generated using the 50k Illumina iSelect genotyping array, were coupled with the Mn phenotypic data to create a genome-wide association study (GWAS) identifying candidate loci associated with Mn use efficiency.

Key Results

The Bere lines generally had good Mn use efficiency traits. Individual Bere lines showed large efficiencies, with some Bere lines recording almost double chlorophyll fluorescence readings in limited Mn conditions compared with the elite cultivar Scholar. The Mn-efficient Bere lines had increased accumulation of Mn in their shoot biomass compared with elite cultivars, which was highly correlated to the chlorophyll fluorescence. Several candidate genes were identified as being associated with Mn use efficiency in the GWAS.

Conclusions

Several genomic regions for Mn use efficiency traits originating from the Bere lines were identified. Further examination and validation of these regions should be undertaken to identify candidate genes for future breeding for marginal lands.
A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging
Authors: Tar P D , Thacker N A , Deepaisarn S , O’Connor J P B , McMahon A W
Published: April 2020

Motivation

Probabilistic latent semantic analysis (pLSA) is commonly applied to describe mass spectra (MS) images. However, the method does not provide certain outputs necessary for the quantitative scientific interpretation of data. In particular, it lacks assessment of statistical uncertainty and the ability to perform hypothesis testing. We show how linear Poisson modelling advances pLSA, giving covariances on model parameters and supporting χ2 testing for the presence/absence of MS signal components. As an example, this is useful for the identification of pathology in MALDI biological samples. We also show potential wider applicability, beyond MS, using magnetic resonance imaging (MRI) data from colorectal xenograft models.

Results

Simulations and MALDI spectra of a stroke-damaged rat brain show MS signals from pathological tissue can be quantified. MRI diffusion data of control and radiotherapy-treated tumours further show high sensitivity hypothesis testing for treatment effects. Successful χ2 and degrees-of-freedom are computed, allowing null-hypothesis thresholding at high levels of confidence.

Availability and implementation

Open-source image analysis software available from TINA Vision, www.tina-vision.net.

Supplementary information

Supplementary data are available at Bioinformatics online.
PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning
Authors: Zhang Yu P , Zou Quan
Published: April 2020

Motivation

Peptide is a promising candidate for therapeutic and diagnostic development due to its great physiological versatility and structural simplicity. Thus, identifying therapeutic peptides and investigating their properties are fundamentally important. As an inexpensive and fast approach, machine learning-based predictors have shown their strength in therapeutic peptide identification due to excellences in massive data processing. To date, no reported therapeutic peptide predictor can perform high-quality generic prediction and informative physicochemical properties (IPPs) identification simultaneously.

Results

In this work, Physicochemical Property-based Therapeutic Peptide Predictor (PPTPP), a Random Forest-based prediction method was presented to address this issue. A novel feature encoding and learning scheme were initiated to produce and rank physicochemical property-related features. Besides being capable of predicting multiple therapeutics peptides with high comparability to established predictors, the presented method is also able to identify peptides’ informative IPP. Results presented in this work not only illustrated the soundness of its working capacity but also demonstrated its potential for investigating other therapeutic peptides.

Availability and implementation

https://github.com/YPZ858/PPTPP.

Supplementary information

Supplementary data are available at Bioinformatics online.
PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing
Authors: Jeong Hyundoo , Liu Zhandong
Published: April 2020

Single-cell RNA sequencing technology provides a novel means to analyze the transcriptomic profiles of individual cells. The technique is vulnerable, however, to a type of noise called dropout effects, which lead to zero-inflated distributions in the transcriptome profile and reduce the reliability of the results. Single-cell RNA sequencing data, therefore, need to be carefully processed before in-depth analysis. Here, we describe a novel imputation method that reduces dropout effects in single-cell sequencing. We construct a cell correspondence network and adjust gene expression estimates based on transcriptome profiles for the local subnetwork of cells of the same type. We comprehensively evaluated this method, called PRIME (PRobabilistic IMputation to reduce dropout effects in Expression profiles of single-cell sequencing), on synthetic and eight real single-cell sequencing datasets and verified that it improves the quality of visualization and accuracy of clustering analysis and can discover gene expression patterns hidden by noise.

Availability and implementation

The source code for the proposed method is freely available at https://github.com/hyundoo/PRIME.

Supplementary information

Supplementary data are available at Bioinformatics online.
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
Authors: Guil Francisco , Hidalgo José F , García José M
Published: April 2020

Motivation

Elementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are known to be very efficient if the main interest lies in computing large enough sets of EFMs.

Results

Here, we propose a new method called EFM-Ta that boosts the efficiency rate by analyzing the information provided by the LP solver. We base our method on a further study of the final tableau of the simplex method. By performing additional elementary steps and avoiding trivial solutions consisting of two cycles, we obtain many more EFMs for each LP problem posed, improving the efficiency rate of previously proposed methods by more than one order of magnitude.

Availability and implementation

Software is freely available at https://github.com/biogacop/Boost_LP_EFM.

Contact

fguil@um.es

Supplementary information

Supplementary data are available at Bioinformatics online.
The Motor Cortex Has Independent Representations for Ipsilateral and Contralateral Arm Movements But Correlated Representations for Grasping
Authors: Downey John E , Quick Kristin M , Schwed Nathaniel , Weiss Jeffrey M , Wittenberg George F , Boninger Michael L , Collinger Jennifer L
Published: April 2020

Motor commands for the arm and hand generally arise from the contralateral motor cortex, where most of the relevant corticospinal tract originates. However, the ipsilateral motor cortex shows activity related to arm movement despite the lack of direct connections. The extent to which the activity related to ipsilateral movement is independent from that related to contralateral movement is unclear based on conflicting conclusions in prior work. Here we investigate bilateral arm and hand movement tasks completed by two human subjects with intracortical microelectrode arrays implanted in the left hand and arm area of the motor cortex. Neural activity was recorded while they attempted to perform arm and hand movements in a virtual environment. This enabled us to quantify the strength and independence of motor cortical activity related to continuous movements of each arm. We also investigated the subjects’ ability to control both arms through a brain–computer interface. Through a number of experiments, we found that ipsilateral arm movement was represented independently of, but more weakly than, contralateral arm movement. However, the representation of grasping was correlated between the two hands. This difference between hand and arm representation was unexpected and poses new questions about the different ways the motor cortex controls the hands and arms.
High Rates of Recurrent Tuberculosis Disease: A Population-level Cohort Study
Authors: Hermans Sabine M , Zinyakatira Nesbert , Caldwell Judy , Cobelens Frank G J , Boulle Andrew , Wood Robin
Published: April 2020

Background

Retreatment tuberculosis (TB) disease is common in high-prevalence settings. The risk of repeated episodes of recurrent TB is unknown. We calculated the rate of recurrent TB per subsequent episode by matching individual treatment episodes over a period of 13 years.

Methods

All recorded TB episodes in Cape Town between 2003 and 2016 were matched by probabilistic linkage of personal identifiers. Among individuals with a first episode notified in Cape Town and who completed their prior treatment successfully we estimated the recurrence rate stratified by subsequent episode and HIV status. We adjusted person-time to background mortality by age, sex, and HIV status.

Results

A total of 292 915 TB episodes among 263 848 individuals were included. The rate of recurrent TB was 16.4 per 1000 person-years (95% CI, 16.2–16.6), and increased per subsequent episode (8.4-fold increase, from 14.6 to 122.7 per 1000 from episode 2 to 6, respectively). These increases were similar stratified by HIV status. Rates among HIV positives were higher than among HIV negatives for episodes 2 and 3 (2- and 1.5-fold higher, respectively), and the same thereafter.

Conclusions

TB recurrence rates were high and increased per subsequent episode, independent of HIV status. This suggests that HIV infection is insufficient to explain the high burden of recurrence; it is more likely due to a high annual risk of infection combined with an increased risk of infection or progression to disease associated with a previous TB episode. The very high recurrence rates would justify increased TB surveillance of patients with >1 episode.
Methodological Considerations for Cost of Illness Studies of Enteric Fever
Authors: Mejia Nelly , Ramani Enusa , Pallas Sarah W , Song Dayoung , Abimbola Taiwo , Mogasale Vittal
Published: April 2020

This article presents a selection of practical issues, questions, and tradeoffs in methodological choices to consider when conducting a cost of illness (COI) study on enteric fever in low- to lower-middle-income countries. The experiences presented are based on 2 large-scale COI studies embedded within the Surveillance for Enteric Fever in Asia Project II (SEAP II), in Bangladesh, Nepal, and Pakistan; and the Severe Typhoid Fever Surveillance in Africa (SETA) Program in Burkina Faso, Ethiopia, Ghana, and Madagascar. Issues presented include study design choices such as controlling for background patient morbidity and healthcare costs, time points for follow-up, data collection methods for sensitive income and spending information, estimating enteric fever–specific health facility cost information, and analytic approaches in combining patient and health facility costs. The article highlights the potential tradeoffs in time, budget, and precision of results to assist those commissioning, conducting, and interpreting enteric fever COI studies.
HotSpotAnnotations—a database for hotspot mutations and annotations in cancer
Authors: Trevino Victor
Published: April 2020

Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes like BRAF, IDH1, KRAS and NRAS among many other genes. Hotspots are attractive because provide opportunities for biomedical research and novel treatments. Nevertheless, recent evidence, such as DNA hairpins for APOBEC3A, suggests that a considerable fraction of hotspots seem to be passengers rather than drivers. To document hotspots, the database HotSpotsAnnotations is proposed. For this, a statistical model was implemented to detect putative hotspots, which was applied to TCGA cancer datasets covering 33 cancer types, 10 182 patients and 3 175 929 mutations. Then, genes and hotspots were annotated by two published methods (APOBEC3A hairpins and dN/dS ratio) that may inform and warn researchers about possible false functional hotspots. Moreover, manual annotation from users can be added and shared. From the 23 198 detected as possible hotspots, 4435 were selected after false discovery rate correction and minimum mutation count. From these, 305 were annotated as likely for APOBEC3A whereas 442 were annotated as unlikely. To date, this is the first database dedicated to annotating hotspots for possible false functional hotspots.
Population- and Species-Based Variation of Webworm–Parasitoid Interactions in Hogweeds (Heracelum spp.) in the Netherlands
Authors: Harvey Jeffrey A , Ode Paul J , Gols Rieta
Published: April 2020

In three Dutch populations of the native small hogweed (Heracleum sphondylium L. [Apiales: Apiaceae]), and one of the invasive giant hogweed (H. mantegazzianum Sommeier & Levier [Apiales: Apiaceae]), interactions between a specialist herbivore, the parsnip webworm (Depressaria radiella), and its associated parasitoids were compared during a single growing season. We found host plant species-related differences in the abundance of moth pupae, the specialist polyembryonic endoparasitoid, Copidosoma sosares, the specialist pupal parasitoid, Barichneumon heracliana, and a potential hyperparasitoid of C. sosares, Tyndaricus scaurus Walker (Hymenoptera: Encyrtidae). Adult D. radiella body mass was similar across the three small hogweed populations, but moths and their pupal parasitoid B. heracliana were smaller when developing on giant than on small hogweeds where the two plants grew in the same locality (Heteren). Mixed-sex and all-male broods of C. sosares were generally bigger than all-female broods. Furthermore, adult female C. sosares were larger than males and adult female mass differed among the three small hogweed populations. The frequency of pupal parasitism and hyperparasitism also varied in the different H. sphondylium populations. These results show that short-term (intra-seasonal) effects of plant population on multitrophic insects are variable among different species in a tightly linked food chain.
The EACVI survey on cardiac imaging in cardio-oncology
Authors: Stankovic Ivan , Dweck Marc R , Marsan Nina Ajmone , Bergler-Klein Jutta , Holte Espen , Manka Robert , Schulz-Menger Jeanette , Sitges Marta , Haugaa Kristina H
Published: April 2020

Early and late cardiovascular (CV) toxicities related to many cancer treatments may complicate the clinical course of patients, offsetting therapeutic benefits, and altering prognosis. The early detection, monitoring, and treatment of cardiotoxicity have therefore become essential parts of cancer patient care. CV imaging is a cornerstone of every cardio-oncology unit, but its use may vary across Europe because of the non-uniform availability of advanced imaging techniques and differences in the organization and logistics of cardio-oncology services. The purpose of this EACVI survey in cardio-oncology is to obtain real-world data on the current usage of cardiac imaging in cancer patients. Data from 104 centres and 35 different countries confirmed that cardiac imaging plays a pivotal role in the detection and monitoring of cardiac toxicity in oncology patients in Europe and beyond. However, it also revealed gaps between guidelines recommendations and everyday clinical practice, highlighting some of the challenges that need to be overcome in this rapidly advancing field.