bluuebunny/crossref_metadata_2025 huggingface dataset:
The pedagogy of design and technology at Xavier University of Louisiana, New Orleans
Authors: Blum Shayna T.
Published: May 2019

Xavier University of Louisiana (XULA) is a Science, Technology, Engineering, and Mathematics (STEM) university located in New Orleans, Louisiana. As an Historically Black University (HBCU), the university serves a diverse community of students in which many are first generation college graduates. Students enrolled in Design courses at XULA are studying in Bachelor of Science and Bachelor of Art programs and majoring in subjects such as Computer Science, Physics, Mass Communication, Art, Business, and Science. The interdisciplinary student environment offers a unique opportunity for collaboration and peer learning, whereby students are able to share diverse perspectives on a topic by relating design processes to their fields of study. In laboratory practice, students work on independent and collaborative projects in Product Design and User Experience by developing work through a design process from ideation to production.
Speech Recognition and Speech Synthesis Models for Micro Devices
Authors: Asiedu Asante Bismark , Imamura Hiroki
Published: May 2019

With the advent and breakthrough of interaction between humans and electronic devices using speech in communication, we have seen a lot of applications using speech recognition and speech synthesis technology. There are some limitations we have identified to these applications. Availability of a lot of resources and internet connectivity have made it possible in making case but with limited resources it is quite difficult to achieve this feat. As a result, it limits the application of the technology into micro devices and deploying them into areas where there are no internet connectivity. In this article, we developed a smaller Deep Neural Network models for Automatic Speech Recognition (ASR) and Text-to-Speech (TTS) for communication on micro devices such as Raspberry Pi. We tested and evaluated the models of the system. The accuracy and the performance of the models to be implemented on micro devices shows that they are good for application development in micro devices.
Effect of inspection errors on imperfect production inventory model with warranty and price discount dependent demand rate
Authors: Manna Amalesh Kumar , Dey Jayanta Kumar , Mondal Shyamal Kumar
Published: May 2019

This paper deals with selling price-discount and warranty period dependent demand in an imperfect production inventory model under the consideration of inspection errors and time dependent development cost. Normally, due to long-run, a production process deteriorates with time and here we assume that the process shifts from "in-control" to "out-of-control" state at any random time. A time dependent development cost has been constructed to increase the reliability of the production systemi.e., to decrease the deterioration of the system during the production process. As a result, a few items are rejected. Here, two types of inspection errors such as Type-I error and Type-II error, have been considered during the period of product inspection process. In Type-I error, an inspector may choose falsely a defective item as non-defective and in Type-II error an inspector may choose falsely a non-defective item as defective. Due to these phenomena, the inspection process would consist of the following costs: cost of inspection, cost of inspection errors. The purpose of this paper is to investigate the effects of time dependent development cost on the defective items, selling price-discount and warranty policy on the market demand and finally optimize the expected average profit under consideration of such inspection costs in infinite time horizon. Some numerical examples along with graphical illustrations and sensitivity analysis are provided to test the feasibility of the model.
Preclinical evaluation of peptide-based radiotracers for integrin αvβ6-positive pancreatic carcinoma
Authors: Müller Martin , Altmann Annette , Sauter Max , Lindner Thomas , Jäger Dirk , Rathke Hendrik , Herold-Mende Christel , Marmé Frederik , Babich John , Mier Walter , Haberkorn Uwe
Published: May 2019

Introduction Integrin αvβ6 shows a high expression rate in several cancer entities. As it is absent in most healthy adult tissues, it represents a promising target for tumor targeting with peptidic radiotracers. This study was performed to pave the way of the recently published αvβ6-binding peptide SFLAP3 for the clinical application in patients with pancreatic cancer.

Methods The expression of integrin αvβ6 on several pancreatic cancer cell lines was assessed using flow cytometry and cell binding assays. The affinity was determined in competition binding assays followed by internalization and efflux studies. To increase the affinity, the binding sequence was modified and trimerization of the SFLAP3 peptide was achieved by oxime ligation. PET and biodistribution assays were conducted in Capan-2 tumor bearing mice. Finally, a first pancreatic tumor patient was examined with 68Ga-DOTA-SFLAP3.

Results Flow cytometric analysis and in vitro cell binding revealed high expression of integrin αvβ6 on most pancreatic tumor cell lines. Modification of SFLAP3 led to compounds with improved in vitro binding properties. Unfortunately, these superior properties could not be transferred into improved pharmacokinetics. Consequently, the first pancreatic tumor patient was examined with 68Ga-DOTA-SFLAP3. The PET revealed specific accumulation (with SUV(max) values in the metastases ranging from 5 to 10) and a long retention in the tumor.

Conclusion SFLAP3 showed high affinity to integrin αvβ6 on pancreatic cancer cell lines. The in vitro performance could be confirmed in tumor bearing mice and by PET imaging. These data suggest that DOTA-SFLAP3 is a promising tracer for targeting αvβ6-expressing pancreatic tumors.
Synthesis of Resolvin D6 and the Silyl Ether of the Resolvin E2 Methyl Ester via trans-Enynyl Alcohols
Authors: Morita Masao , Tanabe Shuhei , Arai Tomoya , Kobayashi Yuichi
Published: May 2019

Two trans-enynyl alcohol intermediates corresponding to the C1–C8 and C13–C22 parts of resolvin D6 (RvD6) were prepared through the Hudrlik–Peterson reaction of the TMS-substituted trans-epoxy alcohols with TMS-acetylide and subsequent TMS-desilylation. These intermediates were coupled with a 1,4-dihalo-2-butyne derivative under copper catalysis, and the resulting acetylene was reduced with Zn(Cu/Ag) to afford the TBS ether of RvD6 methyl ester. Desilylation with TBAF yielded the γ-lactone of RvD6, which was hydrolyzed to RvD6. The total yield of RvD6 was 1.9% in 19 steps from (3-trimethylsilyl)propargyl alcohol. The TBS ether of RvE2 methyl ester was also synthesized.
A New Percutaneous Endoscopic Instrument for Far-migrated Disk Herniation: A Retrospective Single-Institution Study
Authors: Nakamura Shu , Taguchi Mitsuto
Published: May 2019

Objective Compared with the traditional posterior approach, the transforaminal (TF) approach for percutaneous endoscopic lumbar diskectomy (PELD) in patients with disk herniation has a limited resection range that is problematic to treat far-migrated disk herniation. This study examined the usefulness of a newly developed percutaneous endoscopic instrument for far-migrated disk herniation.

Methods This retrospective study included 22 patients with migrated disk herniation ≥ 10 mm who underwent transforaminal PELD using the new instrument between August 2014 and May 2017. The new instrument differs from conventional forceps because it has only one jaw that rotates in a plane perpendicular to the mouth opening. The migrated herniated disk is held between the instrument and bone surface, pulled out, and subsequently removed using conventional forceps.

Results Herniated disks that had migrated up to 16 mm were removed successfully in all patients.

Conclusions The new instrument is a useful tool that can expand the resection range of the TF approach for PELD.
U-shaped Dural Flap: A Simple Method for Transcranial Skull Base Defect Repair—Technical Report
Authors: Ozdol Cagatay , Aghayev Kamran
Published: May 2019

Accidental anterior skull base defects associated with surgery are difficult to treat. There are several methods for the repair, yet postoperative rhinorrhea can occur despite the closure. A 56-year-old female patient was admitted for the treatment of a paraclinoid internal carotid artery aneurysm. The surgery included removal of the anterior clinoid process, unroofing the optic canal, decompressing the optic nerve, and clipping the aneurysm. During the surgery, the planum sphenoidale was accidentally drilled and the nasal cavity exposed. The dural defect was repaired using a U-flap technique. No postoperative cerebrospinal fluid (CSF) rhinorrhea occurred in the patient, and she was discharged on postoperative day 3. On follow-up examination the patient did not have evidence of CSF leakage.
Destruction-of-dissipation and time-scales in wall turbulence
Authors: Gerolymos G. A. , Vallet I.
Published: May 2019

This paper studies the dynamics and scalings of dissipation processes in wall turbulence, focussing on the destruction-of-dissipation tensor εεij (and its halftrace εε), which acts as destruction-by-molecular-viscosity mechanism in the transport equations for the dissipation tensor εij (or its halftrace ε). Budgets of εεij-transport (and εε-transport) are studied for low-Reynolds turbulent plane channel flow. These transport equations also include a destruction-by-molecular-viscosity mechanism, the destruction-of-destruction tensor εεεij (or its halftrace εεε), and indeed, recursively, we identify terms εij[n+1] defined by correlations of [n + 1]-derivatives which correspond to the destruction mechanism of εij[n]. Using halftraces ε[n], we may define time-scales, whose study reveals that εεε−1εε is approximately equal to the Kolmogorov time-scale. The dependence of the time-scales on the Reynolds number is discussed.
Reduction of water-molecule-induced current-voltage hysteresis in graphene field effect transistor with semi-dry transfer using flexible supporter
Authors: Jung Sungchul , Yoon Hoon Hahn , Jin Hanbyul , Mo Kyuhyung , Choi Gahyun , Lee Junghyun , Park Hyesung , Park Kibog
Published: May 2019

The polymethyl methacrylate-assisted wet transfer method of chemical vapor deposition (CVD) graphene has been widely used, thanks to its good coverage and simplicity. However, in the wet-transfer method, water molecules are inevitably trapped between the graphene and the substrate because the graphene is transferred to the substrate while floating in water. The trapped water molecules can cause the unwanted doping of graphene and hysteretic behavior in the current-voltage (I-V) curve. We here propose a new semidry transfer method using the Kapton tape as an additional flexible supporting layer. The N2 blowing and heating processes are added to vaporize the water molecules adsorbed on graphene layer right before the transfer step. By comparing the I-V characteristics of wet- and semidry-transferred graphene field effect transistor (GFET), the field effect mobility is found to be larger for the semidry-transferred GFET in comparison with the wet-transferred one, possibly due to the more uniform Coulomb potential landscape. Most importantly, the hysteretic behavior is found to be reduced in accordance with the decrease of the trapped water molecules. The averaged electron mobilities obtained from the GFET measurements are 1118cm2/Vs and 415cm2/Vs for semidry- and wet-transferred graphene, respectively. Our semidry transfer method can provide a simple and reliable way to transfer the CVD graphene onto an arbitrary substrate with the minimized number of trapped water molecules, which is readily applicable for large-scale substrates with potential of commercialization.
Highly efficient p-type doping of GaN under nitrogen-rich and low-temperature conditions by plasma-assisted molecular beam epitaxy
Authors: Tang H. , Sadaf S. M. , Wu X. , Jiang W.
Published: May 2019

Highly efficient and reproducible p-type doping of GaN under nitrogen-rich and low-growth-temperature conditions was demonstrated with the plasma-assisted molecular beam epitaxy technique. The low-temperature range is approximately below 650 °C and refers to growth temperatures at which the thermal desorption of any excess Ga is negligibly slow. The Mg and hole concentrations obtained with the N-rich condition were more than one order of magnitude higher than those obtained with the Ga-rich condition while keeping all other conditions identical. The Mg doping under such N-rich conditions was also found to show Mg-mediated suppression of background impurities, good epitaxy quality on GaN templates, and relatively low surface roughness. Over the investigated growth temperature range from 580 °C to 650 °C, the Mg incorporation efficiency under the N-rich condition was found to be close to unity (70%-80%) and independent of the growth temperature. High hole concentrations of up to 2×1019 cm-3 and activation efficiencies of up to 16.6% were obtained. The result rules out the Mg surface sticking probability as the limiting mechanism for Mg incorporation in this temperature range, as it would be temperature dependent. Instead, the Mg incorporation rate was more likely governed by the availability of substitutional sites for Mg on the surface, which should be abundant under the N-rich growth conditions. Excellent diode characteristics and electroluminescence results were observed when this p-type doping method was employed in the growth of full device structures.
Numerical study of the material transport in the viscous vortex dipole flow
Authors: Xu Ling
Published: May 2019

This paper presents a numerical study of the material transport of Lamb dipole(s) in the two-dimensional viscous flow. We focus on the properties of the rate of strain tensor, which has received less attention in the literature. It is noted that the eigenpairs of the tensor explicitly indicate the strength and direction of material stretching and compressing. The tensor provides a clear map of the material motion regardless of the complexity of the vortical flow. The strain rate field displays a rich structure as it contains five elliptic points and six hyperbolic points. It is interesting to observe that the left elliptic point of the strain rate field bifurcates into two at t > 0. Two kinds of material curves, circular and vertical, are used to illustrate the flow transport. The transport mechanism discussed here can be employed to explore the transport in more complex vortex flows.
Silicon carbide/phosphate ceramics composite for electromagnetic shielding applications: Whiskers vs particles
Authors: Plyushch A. , Macutkevic J. , Svirskas S. , Banys J. , Plausinaitiene V. , Bychanok Dz. , Maksimenko S. A. , Selskis A. , Sokal A. , Lapko K. N. , Kuzhir P. P.
Published: May 2019

We report on the design of highly absorptive thermostable composite materials for microwave applications. Ceramics comprising the thermostable phosphate host and silicon carbide particles or whiskers were studied in a wide frequency range from several Hertz up to microwaves. It was demonstrated that a thin layer of ceramics placed on the back-reflector absorbs perfectly at the 30 GHz frequency. In the case of a free-standing ceramic composite layer being 1 mm thick, it provides more than 50% of absorption.
Bulk viscosity of CO2 from Rayleigh-Brillouin light scattering spectroscopy at 532 nm
Authors: Wang Yuanqing , Ubachs Wim , van de Water Willem
Published: May 2019

Rayleigh-Brillouin scattering spectra of CO2 were measured at pressures ranging from 0.5 to 4 bars and temperatures from 257 to 355 K using green laser light (wavelength 532 nm, scattering angle of 55.7°). These spectra were compared to two line shape models, which take the bulk viscosity as a parameter. One model applies to the kinetic regime, i.e., low pressures, while the second model uses the continuum, hydrodynamic approach and takes the rotational relaxation time as a parameter, which translates into the bulk viscosity. We do not find a significant dependence of the bulk viscosity with pressure or temperature. At pressures where both models apply, we find a consistent value of the ratio of bulk viscosity over shear viscosity ηb/ηs = 0.41 ± 0.10. This value is four orders of magnitude smaller than the common value that is based on the damping of ultrasound and signifies that in light scattering only relaxation of rotational modes matters, while vibrational modes remain “frozen.”
Tomorrow’s micromagnetic simulations
Authors: Leliaert J. , Mulkers J.
Published: May 2019

Micromagnetic simulations are a valuable tool to increase our understanding of nanomagnetic systems and to guide experiments through parameter spaces that would otherwise be difficult and expensive to navigate. To fulfill this task, simulations have always pushed the limits of what is possible in terms of software and hardware. In this perspective, we give an overview of the current state of the art in micromagnetic simulations of ferromagnetic materials followed by our opinion of what tomorrow’s simulations will look like. Recently, the focus has shifted away from exclusively trying to achieve faster simulations, toward extending pure micromagnetic calculations to a multiphysics approach. We present an analysis of how the performance of the simulations is affected by the simulation details and hardware specifications (specific to the graphics processing unit-accelerated micromagnetic software package mumax3), which sheds light on how micromagnetic simulations can maximally exploit the available computational power. Finally, we discuss how micromagnetic simulations can benefit from new hardware paradigms like graphics cards aimed at machine learning.
Structures of stoichiometric sodium oxide cluster cations studied by ion mobility mass spectrometry
Authors: Nakano Motoyoshi , Ishimura Yudai , Hotta Riki , Hebiguchi Daiki , Nagata Toshiaki , Misaizu Fuminori
Published: May 2019

Structures of stable compositions of sodium oxide cluster cations (NanOm+, n≤11) have been investigated by ion mobility mass spectrometry. Stoichiometric compositions series, Na(Na2O)(n−1)/2+ (n=3, 5, 7, 9, and 11), were observed as stable composition series, and NaO(Na2O)(n−1)/2+ series (n=5, 7, 9, and 11) were observed as secondary stable series in the mass spectra. To assign the structures of these cluster ion series, collision cross sections between the ions and helium buffer gas were determined experimentally from the ion mobility measurements. Theoretical collision cross sections were also calculated for optimized structures of these compositions. Finally, the structures of Na(Na2O)(n−1)/2+ and NaO(Na2O)(n−1)/2+ were assigned to those having similar structural frames for each n except for n=9. All bonds in the assigned structures of Na(Na2O)(n−1)/2+ were between sodium and oxygen. On the other hand, there was one O−O bond in addition to Na−O bonds in NaO(Na2O)(n−1)/2+. This result indicates that NaO(Na2O)(n−1)/2+ have a peroxide ion (O22−) as a substitute for an oxide ion (O2−) of Na(Na2O)(n−1)/2+. As a result, both stable series, Na(Na2O)(n−1)/2+ and NaO(Na2O)(n−1)/2+, are closed-shell compositions. These closed-shell characteristics have a strong influence on the stability of sodium oxide cluster cations.
Dissociative photoionization of heterocyclic molecule-morpholine under VUV synchrotron radiation
Authors: Song Wen-tao , Hu Yong-jun , Jin Shan , Li Yu-jian
Published: May 2019

The radiation damage of biomolecules, in particular with aliphatic compound, has been extensively studied. Morpholine is a typical six-membered aliphatic heterocyclic compound. In the present work, photoionization and dissociation of the morpholine monomer and subsequent fragmentations have been investigated by synchrotron vacuum ultraviolet photoionization mass spectrometry and theoretical calculations. The vertical ionization energy of morpholine monomer is 8.37±0.05 eV, which agrees reasonably well with a theo-retical value 8.41 eV of morpholine. Experimentally observed fragmentation of morpholine (m/z=87 amu) gives rise to m/z=86 amu, m/z=57 amu, and m/z=29 amu. Based on experimental and theoretical results, it is found that the m/z=86 amu is produced by losing H atom, the m/z=57 amu is formed by the elimination of CH2O with a ring-opening process, the m/z=29 amu is generated by further dissociation of the fragment m/z=57 amu (C3H7N)+ by the elimination of C2H4. This finding would provide valuable insight into the photo-damage of aliphatic compounds, which may be related to living cells and other biological system.
Fluorescent labelling of boar spermatozoa for quantitative studies on competitive sperm–oviduct binding
Authors: Henning Heiko H. W. , Batz-Schott Julia , Grünther Benita , Le Thi Xuyen , Waberski Dagmar
Published: May 2019

Invitro sperm–oviduct binding assays enable assessment of the capacity of spermatozoa to form a ‘reservoir’ in the oviduct. Competitive approaches, such as experimental set-ups that test multiple males or semen samples simultaneously on the same tissue explants, are desirable because they reduce the likelihood of bias when using material from different females. Therefore, we established a fluorescent labelling technique that allows tagging and storage of spermatozoa before competitive studies of sperm–oviduct binding invitro. Fluorescent markers were tested for reliability and compatibility with parameters of boar spermatozoa viability. The addition of seminal plasma after density gradient centrifugation was essential to counteract centrifugation stress during the labelling procedure. It was demonstrated that sperm tagged with MitoTracker Green FM or MitoTracker Red FM can be successfully used in competitive sperm–oviduct binding studies. The assay was sensitive enough to indicate subtle effects of semen storage temperature on the ability of the spermatozoa to contribute to the female sperm reservoir.
Patronin-mediated minus end growth is required for dendritic microtubule polarity
Authors: Feng Chengye , Thyagarajan Pankajam , Shorey Matthew , Seebold Dylan Y. , Weiner Alexis T. , Albertson Richard M. , Rao Kavitha S. , Sagasti Alvaro , Goetschius Daniel J. , Rolls Melissa M.
Published: May 2019

Microtubule minus ends are thought to be stable in cells. Surprisingly, in Drosophila and zebrafish neurons, we observed persistent minus end growth, with runs lasting over 10 min. In Drosophila, extended minus end growth depended on Patronin, and Patronin reduction disrupted dendritic minus-end-out polarity. In fly dendrites, microtubule nucleation sites localize at dendrite branch points. Therefore, we hypothesized minus end growth might be particularly important beyond branch points. Distal dendrites have mixed polarity, and reduction of Patronin lowered the number of minus-end-out microtubules. More strikingly, extra Patronin made terminal dendrites almost completely minus-end-out, indicating low Patronin normally limits minus-end-out microtubules. To determine whether minus end growth populated new dendrites with microtubules, we analyzed dendrite development and regeneration. Minus ends extended into growing dendrites in the presence of Patronin. In sum, our data suggest that Patronin facilitates sustained microtubule minus end growth, which is critical for populating dendrites with minus-end-out microtubules.
Complementarity via Minimum Error Measurement in a Two-Path Interferometer*
Authors: Liu Junzhao , Liu Yanjun , Lu Jing
Published: May 2019

We study the fringe visibility and the which-path information (WPI) of a general Mach–Zehnder interferometer with an asymmetric beam splitter (BS). A minimum error measurement in the detector is used to extract the WPI. Both the fringe visibility V and the WPI Ipath are affected by the initial state of the photon and the second asymmetric BS. The condition in which the WPI takes the maximum is obtained. The complementarity relationship

V
2

+

I

path

2

≤
1

is found, and the conditions for equality are also presented.
Interplay of Strain and Magnetism in FeSe Monolayers*
Authors: Xie Yun , Feng Junsheng , Xiang Hongjun , Gong Xingao
Published: May 2019

Superconductivity and its relationship with strain remains elusive in the monolayer FeSe superconductor. Based on first-principles calculations and model studies, we investigate the magnetic properties of FeSe and FeTe monolayers and find that tensile strain induces changes to magnetic phases for both materials. Furthermore, we reveal that electron doping will decrease the difference of effective magnetic interactions between the a and b directions in an FeSe monolayer and hence suppress its nematicity. We suggest that the overall effect of tensile strain combined with electron doping hinders the appearance of both magnetic and nematic orders in an FeSe monolayer, which paves the way for the emergence of superconductivity.
Absorption Enhancement of Silicon Solar Cell in a Positive-Intrinsic-Negative Junction*
Authors: Yue Gen , Deng Zhen , Wang Sen , Xu Ran , Li Xinxin , Ma Ziguang , Du Chunhua , Wang Lu , Jiang Yang , Jia Haiqiang , Wang Wenxin , Chen Hong
Published: May 2019

Absorption coefficient is a physical parameter to describe electromagnetic energy absorption of materials, which is closely related to solar cells and photodetectors. We grow a series of positive-intrinsic-negative (PIN) structures on silicon wafer by a gas source molecule beam epitaxy system and the investigate the absorption coefficient through the photovoltaic processes in detail. It is found that the absorption coefficient is enhanced by one order and can be tuned greatly through the thickness of the intrinsic layer in the PIN structure, which is also demonstrated by the 730-nm-wavelength laser irradiation. These results cannot be explained by the traditional absorption theory. We speculate that there could be some uncovered mechanism in this system, which will inspire us to understand the absorption process further.
Molecules with dipoles in periodic boundary conditions in a tetragonal cell
Authors: Rutter M J
Published: May 2019

When a system which contains a dipole, and whose dimensionality is less than three, is studied in a code which imposes periodic boundary conditions in all three dimensions, an artificial electric field arises which keeps the potential periodic. This has an impact on the total energy of the system, and on any other attribute which would respond to an electric field. Simple corrections are known for 0D systems embedded in a cubic geometry, and 2D slab systems. This paper shows how the 0D result can be extended to tetragonal geometries, and that for a particular c/a ratio the correction is zero. It also considers an exponential error term absent from the usual consideration of 2D slab geometries, and discusses an empirical form for this.
Optimal parameters for radiation reaction experiments
Authors: Arran C , Cole J M , Gerstmayr E , Blackburn T G , Mangles S P D , Ridgers C P
Published: May 2019

As new laser facilities are developed with intensities on the scale of

10

22

–

10

24

W

cm

−
2

, it becomes ever more important to understand the effect of strong field quantum electrodynamic processes, such as quantum radiation reaction, which will play a dominant role in laser-plasma interactions at these intensities. Recent all-optical experiments, where GeV electrons from a laser wakefield accelerator encountered a counter-propagating laser pulse with a
0 > 10, have produced evidence of radiation reaction, but have not conclusively identified quantum effects nor their most suitable theoretical description. Here we show the number of collisions and the conditions required to accomplish this, based on a simulation campaign of radiation reaction experiments under realistic conditions. We conclude that while the critical energy of the photon spectrum distinguishes classical and quantum-corrected models, a better means of distinguishing the stochastic and deterministic quantum models is the change in the electron energy spread. This is robust against shot-to-shot fluctuations and the necessary laser intensity and electron beam energies are already available. For example, we show that so long as the electron energy spread is below 25%, collisions at a
0 = 10 with electron energies of

500

MeV

could differentiate between different quantum models in under 30 shots, even with shot-to-shot variations at the 50% level.
One large glitch in PSR B1737−30 detected with the TMRT
Authors: Liu Jie , Yan Zhen , Yuan Jian-Ping , Zhao Ru-Shuang , Huang Zhi-Peng , Wu Xin-Ji , Wang Na , Shen Zhi-Qiang
Published: May 2019

One large glitch was detected in PSR B1737–30 using data spanning from MJD 57999 to 58406 obtained with the newly built Shanghai Tian Ma Radio Telescope (TMRT). The glitch took place at the time around MJD 58232.4 when the pulsar underwent an increase in the rotation frequency of Δν about 1.38× 10−6 Hz, corresponding to a fractional step change of Δν/ν ∼ 8.39× 10−7. Post-glitch ν gradually decreased to the pre-glitch value. The frequency derivative was observed to undergo a step change of about −9× 10−16 s−2. Since July 1987, there have been 36 glitches already reported in PSR B1737−30 including this one. According to our analysis, the glitch size distribution is well described by a power law with an index of 1.13. The distribution of the interval between two adjacent glitches (waiting time ΔT) follows a Poisson probability density function. For PSR B1737−30, the interval is prone to be long after a large glitch. However, no correlation is found between glitch size and the interval since the previous glitch.
Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose–response experiments
Authors: Labelle Caroline , Marinier Anne , Lemieux Sébastien
Published: May 2019

Motivation

The efficacy of a chemical compound is often tested through dose–response experiments from which efficacy metrics, such as the IC50, can be derived. The Marquardt–Levenberg algorithm (non-linear regression) is commonly used to compute estimations for these metrics. The analysis are however limited and can lead to biased conclusions. The approach does not evaluate the certainty (or uncertainty) of the estimates nor does it allow for the statistical comparison of two datasets. To compensate for these shortcomings, intuition plays an important role in the interpretation of results and the formulations of conclusions. We here propose a Bayesian inference methodology for the analysis and comparison of dose–response experiments.

Results

Our results well demonstrate the informativeness gain of our Bayesian approach in comparison to the commonly used Marquardt–Levenberg algorithm. It is capable to characterize the noise of dataset while inferring probable values distributions for the efficacy metrics. It can also evaluate the difference between the metrics of two datasets and compute the probability that one value is greater than the other. The conclusions that can be drawn from such analyzes are more precise.

Availability and implementation

We implemented a simple web interface that allows the users to analyze a single dose–response dataset, as well as to statistically compare the metrics of two datasets.
Learning a mixture of microbial networks using minorization–maximization
Authors: Tavakoli Sahar , Yooseph Shibu
Published: May 2019

Motivation

The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose nodes represent microbial taxa and edges represent pairwise interactions. A microbial network is typically constructed from a sample-taxa count matrix that is obtained by sequencing multiple biological samples and identifying taxa counts. From large-scale microbiome studies, it is evident that microbial community compositions and interactions are impacted by environmental and/or host factors. Thus, it is not unreasonable to expect that a sample-taxa matrix generated as part of a large study involving multiple environmental or clinical parameters can be associated with more than one microbial network. However, to our knowledge, microbial network inference methods proposed thus far assume that the sample-taxa matrix is associated with a single network.

Results

We present a mixture model framework to address the scenario when the sample-taxa matrix is associated with K microbial networks. This count matrix is modeled using a mixture of K Multivariate Poisson Log-Normal distributions and parameters are estimated using a maximum likelihood framework. Our parameter estimation algorithm is based on the minorization–maximization principle combined with gradient ascent and block updates. Synthetic datasets were generated to assess the performance of our approach on absolute count data, compositional data and normalized data. We also addressed the recovery of sparse networks based on an l1-penalty model.

Availability and implementation

MixMPLN is implemented in R and is freely available at https://github.com/sahatava/MixMPLN.

Supplementary information

Supplementary data are available at Bioinformatics online.
MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks
Authors: Miraskarshahi Reza , Zabeti Hooman , Stephen Tamon , Chindelevitch Leonid
Published: May 2019

Motivation

Constraint-based modeling of metabolic networks helps researchers gain insight into the metabolic processes of many organisms, both prokaryotic and eukaryotic. Minimal cut sets (MCSs) are minimal sets of reactions whose inhibition blocks a target reaction in a metabolic network. Most approaches for finding the MCSs in constrained-based models require, either as an intermediate step or as a byproduct of the calculation, the computation of the set of elementary flux modes (EFMs), a convex basis for the valid flux vectors in the network. Recently, Ballerstein et al. proposed a method for computing the MCSs of a network without first computing its EFMs, by creating a dual network whose EFMs are a superset of the MCSs of the original network. However, their dual network is always larger than the original network and depends on the target reaction. Here we propose the construction of a different dual network, which is typically smaller than the original network and is independent of the target reaction, for the same purpose. We prove the correctness of our approach, minimal coordinated support (MCS2), and describe how it can be modified to compute the few smallest MCSs for a given target reaction.

Results

We compare MCS2 to the method of Ballerstein et al. and two other existing methods. We show that MCS2 succeeds in calculating the full set of MCSs in many models where other approaches cannot finish within a reasonable amount of time. Thus, in addition to its theoretical novelty, our approach provides a practical advantage over existing methods.

Availability and implementation

MCS2 is freely available at https://github.com/RezaMash/MCS under the GNU 3.0 license.

Supplementary information

Supplementary data are available at Bioinformatics online.
Weighing up Work Willingness in Social Assistance: A Balancing Act on Multiple Levels
Authors: De Wilde Marjolijn , Marchal Sarah
Published: May 2019

In all European countries, social assistance legislation specifies that the receipt of benefits is conditional upon the willingness to work. Nevertheless, the manner in which such policies are implemented in practice has remained a black box. From the literature on social policy, social work, and social administration, we know that implementation is the result of decisions at multiple levels. To our knowledge, however, this study is the first quantitative attempt to bring together the insights from these various strands of literature into a combined assessment of factors that determine willingness-to-work assessments. We build on an innovative and purpose-designed survey of social workers in Belgium. We identified factors determining the perceptions of 584 case managers, clustered in 89 municipalities, with regard to sanction decisions upon job refusal, based on almost 5,000 experimentally varied client cases (vignette experiment). These unique data make it possible to distinguish between the effects of case managers who assess individual cases and characteristics of the local welfare agencies and municipalities in which they operate. The results reveal relatively little variation between municipalities, which can be largely explained by characteristics of the municipalities (e.g. political ideology and organizational setting). Surprisingly, however, we find extensive variation at the case-manager level. Although some of this variation remains unexplained, a substantial share can be explained by characteristics of individual case managers (e.g. age and attitudes concerning the welfare state). This finding raises concerns about the unintended consequences of the broad discretion granted to case managers within contemporary social assistance schemes.
Associations between Swiss Needle Cast Severity and Foliar Nutrients in Young-Growth Douglas-Fir in Coastal Western Oregon and Southwest Washington, USA
Authors: Lan Yung-Hsiang , Shaw David C , Ritóková Gabriela , Hatten Jeff A
Published: May 2019

Swiss needle cast (SNC) is a foliage disease of Douglas-fir (Pseudotsuga menziesii) caused by Nothophaeocryptopus gaeumannii, an ascomycete fungus (Mycosphaerellaceae) that causes tree growth reductions in the Pacific Northwest. The epidemiology of the fungus is generally well known, but the relations between disease expression and foliar nutrition are unclear. In this study, we used data from the Swiss Needle Cast Cooperative research and monitoring plot network in western Oregon and SW Washington to assess associations between SNC severity, carbon, and nine foliage nutrients (nitrogen, Na, K, P, Ca, Mg, Mn, Al, S). Foliage samples were collected from midcrown of selected Douglas-firs from each plot. SNC severity was determined on 2-year-old needles by multiplying disease incidence and fungal reproductive (pseudothecia) density. Disease severity and nutrient relations were determined using linear mixed models. SNC severity showed statistically significant positive trends with concentrations of carbon, nitrogen, Na, K, and S, no relation with concentrations of Ca, Mg, or Al, and slightly negative trends that were not significant for P and Mn. This is the first such analysis of associations between a conifer foliage disease and foliage nutrients across a landscape; subsequently, there is little published literature on how or why these nutrients may interact with disease.
Longevity-Associated Variant of BPIFB4 Mitigates Monocyte-Mediated Acquired Immune Response
Authors: Ciaglia Elena , Montella Francesco , Maciag Anna , Scala Pasqualina , Ferrario Anna , Banco Carlotta , Carrizzo Albino , Spinelli Chiara Carmela , Cattaneo Monica , De Candia Paola , Vecchione Carmine , Villa Francesco , Puca Annibale Alessandro
Published: May 2019

One of the basis of exceptional longevity is the maintaining of the balance between inflammatory and anti-inflammatory networks. The monocyte-macrophages activation plays a major role in tuning the immune responses, by oscillating between patrolling-protective to inflammatory status. Longevity-associated variant (LAV) of bactericidal/permeability-increasing fold-containing family B member 4 (BPIFB4) activates calcium, PKC-alpha, and eNOS, rescuing endothelial dysfunction in aged mice and inducing revascularization. The BPIFB4’s increment in serum of healthy long-living individuals (LLIs) compared to nonhealthy ones, its therapeutic potential in improving vascular homeostasis, which depends on immune system, together with its expression in bone marrow myeloid cells, suggests that LAV-BPIFB4 may improve immune regulation. Here we show that human monocytes exposed to LAV-BPIFB4 protein increased co-stimulatory molecules in resting state and reduced pro-inflammatory cytokine tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) after activating stimuli. Accordingly, a low percentage of CD69+ activated lymphocytes are found among LAV-BPIFB4-treated peripheral blood mononuclear cells (PBMCs). Moreover, human monocyte-derived dendritic cells (DCs) generated in presence of LAV-BPIFB4 secreted higher anti-(IL-10 and TGF-β) and lower pro-inflammatory (TNF-α and IL-1β) cytokines. Accordingly, LLIs’ plasma showed higher levels of circulating IL-10 and of neutralizing IL-1 receptor antagonist (IL-1RA) compared to controls. Thus, LAV-BPIFB4 effects on myeloid compartment could represent one example of a genetic predisposition carried by LLIs to protect from immunological dysfunctions.
New Insights Into the Kinetics and Variability of Egg Excretion in Controlled Human Hookworm Infections
Authors: Hoogerwerf Marie-Astrid , Coffeng Luc E , Brienen Eric A T , Janse Jacqueline J , Langenberg Marijke C C , Kruize Yvonne C M , Gootjes Chelsea , Manurung Mikhael D , Dekker Mark , Becker Luke , Erkens Marianne A A , van der Beek Martha T , Ganesh Munisha S , Feijt Carola , Winkel Beatrice M F , Westra Inge M , Meij Pauline , Loukas Alex , Visser Leo G , de Vlas Sake J , Yazdanbakhsh Maria , van Lieshout Lisette , Roestenberg Meta
Published: May 2019

Four healthy volunteers were infected with 50 Necator americanus infective larvae (L3) in a controlled human hookworm infection trial and followed for 52 weeks. The kinetics of fecal egg counts in volunteers was assessed with Bayesian multilevel analysis, which revealed an increase between weeks 7 and 13, followed by an egg density plateau of about 1000 eggs/g of feces. Variation in egg counts was minimal between same-day measurements but varied considerably between days, particularly during the plateau phase. These analyses pave the way for the controlled human hookworm model to accelerate drug and vaccine efficacy studies.
Anti-Inflammatory Interleukin 10 Inversely Relates to Coronary Atherosclerosis in Persons With Human Immunodeficiency Virus
Authors: Fourman Lindsay T , Saylor Charles F , Cheru Lediya , Fitch Kathleen , Looby Sara , Keller Kiana , Robinson Jake A , Hoffmann Udo , Lu Michael T , Burdo Tricia , Lo Janet
Published: May 2019

Interleukin 10 (IL-10) is an anti-inflammatory cytokine that may be protective against coronary atherosclerosis. In an observational study of persons with human immunodeficiency virus (PWH) and uninfected controls, IL-10 was measured in serum samples by means of enzyme-linked immunosorbent assay, and coronary atherosclerosis was assessed using computed tomographic angiography. Among PWH, a 10-fold decrease in IL-10 was associated with a 2.6-fold increase in the odds of coronary plaque (P = .01), after controlling for traditional and nontraditional cardiovascular risk factors. IL-10 was also inversely associated with total coronary plaque (ρ = −0.19; P = .02) and noncalcified coronary plaque (ρ = −0.24; P = .004). Our findings suggest a role for IL-10 in mitigating atherosclerosis in PWH.

Clinical Trials Registration. NCT00455793
BEEF SPECIES–RUMINANT NUTRITION CACTUS BEEF SYMPOSIUM: Energy and roughage levels in cattle receiving diets and impacts on health, performance, and immune responses1
Authors: Richeson John T , Samuelson Kendall L , Tomczak Dexter J
Published: May 2019

Transition of newly received feedlot cattle from a forage- to grain-based diet is challenging, and the appropriate roughage level in receiving diets is debatable. Nutritionists must consider the paradox of dietary transition and roughage level to mitigate ruminal acidosis, yet concomitantly low feed intake presents difficulty in achieving nutrient requirements when metabolic demand is increased due to inherent stress and disease challenge during the receiving period. Previous research suggests that performance is improved at the expense of increased morbidity for newly received cattle consuming diets with less roughage and greater starch concentration. The clinical signs of bovine respiratory disease (BRD) and acute acidosis are analogous; therefore, it is probable that acidotic cattle are incorrectly diagnosed with BRD in both research and production settings. Additional research efforts have attempted to elucidate alterations in microbial populations and digestion, physiological response to inflammatory challenge, and immunological response to infectious bovine rhinotracheitis virus challenge in cattle consuming diets of various roughage levels. Furthermore, our understanding of the rumen microbiome is improving rapidly with culture-independent assays, products such as direct-fed microbials are available, and increased availability and use of fibrous byproduct ingredients requires further attention. Beef cattle nutritionists and producers should consider that the health benefit of receiving diets containing greater levels of roughage and lower energy may not compensate for the reduction in performance compared with feeding receiving diets with lower roughage and greater energy.
Sublethal Effects of Four Insecticides on the Seven-Spotted Lady Beetle (Coleoptera: Coccinellidae)
Authors: Tengfei Liu , Yao Wang , Lixia Zhang , Yongyu Xu , Zhengqun Zhang , Wei Mu
Published: May 2019

To further develop integrated pest management (IPM) strategies against two sucking insect pests, Aleurocanthus spiniferus (Quaintanca) (Hemiptera: Aleyrodidae) and Toxoptera aurantii Boyer (Hemiptera: Aphididae), in Chinese tea plantations, it is important to evaluate the effects of insecticides on biological control agents, such as the seven-spot lady beetle, Coccinella septempunctata L. (Coleoptera: Coccinellidae). Therefore, we tested the toxicity and sublethal effects of spirotetramat, clothianidin, lambda-cyhalothrin, and bifenthrin on C. septempunctata. The side effects of the active ingredients of the insecticides were evaluated with residual contact tests on the larvae of C. septempunctata in the laboratory. Spirotetramat and clothianidin exhibited lower lethality to C. septempunctata as shown by the higher LC50 values and had higher selectivity for A. spiniferus and T. aurantii based on the selective toxicity ratios being superior to other tested insecticides. Spirotetramat also did not affect survival, longevity, fecundity, and egg hatching of C. septempunctata. Clothianidin and bifenthrin prolonged the duration of larval development stages of C. septempunctata obviously. Clothianidin at >2.5 mg/liter, lambda-cyhalothrin at >0.03 mg/liter, and bifenthrin at >0.125 mg/liter significantly reduced the survival and pupation rates of C. septempunctata larvae. Furthermore, spirotetramat at 3.125 mg/liter was harmless (IOBC class 1) to larvae of this coccinellid species. Based on the results, spirotetramat was innocuous to C. septempunctata larvae compared with clothianidin, lambda-cyhalothrin, and bifenthrin. Therefore, spirotetramat might be incorporated into IPM programs in combination with C. septempunctata for control of A. spiniferus and T. aurantii in the tea plantations.