bluuebunny/crossref_metadata_2025 huggingface dataset:
Stochastic Simulation of Yeast Cells and Its Colony Growth by Using Circular Granular Model for Cases of Growth and Birth Probabilities Depends on Position
Authors: Purwa Aji Dimas Praja , Aprianti Devi , Viridi Sparisoma
Published: October 2019

Until now, many studies were conducted on microorganisms in order to make the best use of them and prevent the loss. As a type of microorganism that is widely utilized by humans, the yeast has a simple single cell structure that can represent many other complex cell processes and generally has almost elliptical shapes making it easier to model for further investigation. In this study, we model yeast cells with two dimensional circular granular particles and the interaction between them are modeled by the force of gravity, normal force, and Stokes force. The growth and birth factor of yeast cells are modeled stochastic with the simulation is done by using javascript programming language. From the simulation results obtained, showing the growth of yeast cells in the colony has a behavior that is in accordance with the theory, which grows exponentially, as well as the growth of the size of the colony radius whose growth rate is half to the rate of growth of its number of cells.
Traffic flow simulation using agent-based model: A case of single lane with multiple traffic lights and input-output node
Authors: Viridi S , Dwitasari M , Takaendengan M , Sari KN , Pasaribu US
Published: October 2019

Vehicle is modeled as a point, which is moving along a closed trajectory. A small amount of time is defined as the time step, the smallest time difference, so that any time measurement is simply multiple of this value. Lowest positive velocity (but greater than zero) is where in the time step a vehicle advances its position for only a spatial step. Higher velocities and also the negative ones can be constructed from this value. Only a single lane is investigated in this work, where a vehicle must wait until there is an empy space in front of it before it can move forward. As pertubation several traffice lights are also installed in the trajectory. Number of vehicles stop at a stoplight or N
stop is observed.
Tortuosity and Percolation Probability on 3 Dimensional Rock Models with Different Model Sizes
Authors: Ramadhan FW , Fauzi U
Published: October 2019

Tortuosity, percolation probability and porosity are important rock parameters because all those things affect the fluid flow in rocks. In this study, 3-dimensional cube-shaped rock models were randomly generated with N × N × N size containing matrices and pores. Rock models were made with porosities ranging from 0.1 to 1 with increasing of value 0.1. The selected N is N = 5, 6, 7, 8, 9, 10, 25, 125 and for every N there are 10,000 random configurations. Then, tortuosity was calculated using a nearest-neighbor sites method with 6 neighboring sides. In addition, with the site percolation model, percolation probability was calculated by determining the comparison between the number of percolate configurations and the total number of configurations created. The results show that in large-size rock models, the average tortuosity will increase. Further, the percolation probability is zero at a small porosity and rises to 1 as the porosity increases. Moreover, the slope of the percolation probability curve will increase for the larger model. In other words, the larger the size of the model, the percolation threshold will become larger or more difficult to percolate for small porosity.
Report on Sky Brightness, Seeing, and Weather Measurements at Timau Observatory, East Nusa Tenggara
Authors: Akbar E I , Jatmiko A T P , Putra M , Nurzaman M Z , Mumpuni E S , Mandey D , Raharto M
Published: October 2019

In 2015, a joint collaboration project to build a new observatory in Mount Timau, East Nusa Tenggara was initiated between LAPAN, ITB, UNDANA, Kupang Regency and East Nusa Tenggara governments. The site selection is based on preliminary studies conducted on nearby location. This paper presents in situ measurements report on seeing, weather and sky brightness obtained on July 2018 using Differential Image Motion Monitor (DIMM) with 20 cm-telescope, Davis Vantage Vue automatic weather station, and Sky Quality Meter, respectively. Despite the high humidity and foggy condition on the afternoon, the site has good seeing condition with median of 0.93 arcsecond and sky brightness around 22.18 magnitude per arcsecond square after midnight.
In-Vitro Study of DNA Adduct 8-Hydroxy-2’-Deoxyguanosine Formation from 2’-Dexoyguanosine Exposure Against Benzo[a]pyrene and Ni(II) Compounds Through Fenton-Like Reactions
Authors: Farozy Ikko Haidar , Handayani Sri , Budiawan  , Dani Intan Cahaya
Published: October 2019

This research was performed to study the process of 8-hydroxy-2’-deoxyguanosine (8-OHdG) adduct formation as biomarker that used for early cancer detection in humans. This in-vitro study was conducted by reacting 2’-deoxyguanosine as one of the bases of DNA against benzo[a]pyrene (B[a]P) as xenobiotic, Ni(II), and H2O2, to study the effects of 2’- deoxyguanosine (2’-dG) exposure against xenobiotic through Fenton-like reaction. The reaction was incubated at 37°C for 18 hours in a shaker incubator. The reactions were varied at pH 7.4 and 8.4. The reaction products were then analyzed by using reverse phase HPLC with UV-Vis detector. The mobile phase used was a mixture of phosphate buffer and methanol with composition of 90:10. It was observed that exposure of 2’-dG against B[a]P and H2O2 and also B[a]P, Ni(II), and H2O2 both produced 8-OHdG. The higher 8-OHdG yield was obtained from the exposure of 2’-dG against B[a]P, Ni(II), and H2O2 compared to exposure against B[a]P and H2O2, which can be attributed to stronger effects from Fenton-like reaction. It was also observed that at similar exposure conditions, the 8-OHdG formation was higher at pH 7.4 compared to pH 8.4.
Synthesis of Fe3O4 nanoparticles for colour removal of printing ink solution
Authors: Jannah N R , Onggo D
Published: October 2019

Fe3O4 nanoparticles can be used as an adsorbent for colour removal of printing ink which contribute as a pollutant in wastewater. Fe3O4 was synthesized by coprecipitation method using FeCl3.6H2O and (NH4)2Fe(SO4)2.6H2O precursors dissolved in distilled water in mol ratio of Fe3+: Fe2+ = 2:1. NaOH solution was added slowly into the iron solution with continuous stirring for 60 minutes in Argon gas atmosphere. After drying, Fe3O4 nanoparticle product is obtained as black crystalline powder with an average particle size about 34 nm. The Fe3O4 nanoparticles (0.1 g) were able to remove blue, red, and yellow colour with percentage of adsorption about 97%, 94%, and 62% for 40 minutes contact time and 100 rpm of stirring speed, respectively. Fe3O4 nanoparticle can be separated from the printing ink solution by an external magnetic field.
Bayesian Quantile Regression Method to Construct the Low Birth Weight Model
Authors: Yanuar Ferra , Zetra Aidinil , Muharisa Catrin , Devianto Dodi , Putri Arrival Rince , Asdi Yudiantri
Published: October 2019

This study aims to implement Bayesian quantile regression method in constructing the model of Low Birth Weight. The data of Low Birth Weight is violated of nonnormal assumption for error terms. This study considers quantile regression approach and use Gibbs sampling algorithm from Bayesian method for fitting the quantile regression model. This study explores the performance of the asymmetric Laplace distribution for working likelihood in posterior estimation process. This study also compare the result of variable selection in quantile regression and Bayesian quantile regression for Low Birth Weight model. This study. proved that Bayesan quantile method produced better model than just quantile approach. Bayesian quantile method proved that it can handle the nonnormal problem although using moderate size of data.
Optimal decision for two dimensional maintenance service contract involving three parties
Authors: Sa’idah Nur F , Cakravastia Andi , Pasaribu Udjianna S , Iskandar Bermawi P
Published: October 2019

A two-dimensional (i.e. time and use) maintenance service contract involving three parties i.e. manufacturer, agent and consumer are considered in this paper. The contract period by the manufacturer/agent begins since the warranty expires (W) until the lifetime of the equipment expires (L). The use of equipment by consumer is modeled with accelerated failure time (AFT) model. AFT model specifies the limit value of permitted equipment usage (Ul
). The contract time is limited to t = L, but equipment usage may exceed U

l
. High use of equipment will increase consumer revenue. However, the consumer will incur additional costs paid to the manufacturer/agent if the use of equipment exceeds U

l
. Therefore, consumers will seek the optimum value of use (U∗) that maximizes the profits. As with consumer, manufacturer and agent also want to maximize their profits. Decision problems in maintenance service contracts involving the three parties will be resolved consider the interaction of the manufacturer and the agent in carrying out maintenance action. One level optimization used if the manufacturer and agent compete with each other. However, if the manufacturer and agent interact in a cooperation, then optimization of the decision model becomes more difficult and should be done with bilevel optimization.
Probability of failure model in mechanical component because of fatigue
Authors: Mahdiyasa A W , Grahito A
Published: October 2019

Fatigue is one of the most common modes in the failure of a mechanical component. Fatigue experiment shows that the coefficient of variation of fatigue life data is ranging from 30% to 40%. High deviation of the data means the deterministic prediction of fatigue life may not be valid anymore, hence probability-based method to calculate the probability of failure due to fatigue damaged is conducted. The probability of failure prediction methodology is based on damage fraction concept. As the usage cycles increase, the damage fraction increases until it reaches critical damage point where a component fails. Damage fraction is a function of ultimate strength and fatigue limit, in which both are modelled as random variables with normal distribution. The validation is done by variating standard deviation of each random variables. The validation result shows that increasing standard deviation of both ultimate strength and fatigue limit will increase the probability of failure.
The comparative analysis of dependence for three-way contingency table using Burt matrix and Tucker3 in correspondence analysis
Authors: Lestari K E , Pasaribu U S , Indratno S W , Garminia H
Published: October 2019

In this paper, we confined our attention to compare two methods to obtain a graphical depiction of the association (dependency) between three categorical variables. We shall first describe how to recode a three-way contingency table by discussing the Burt matrix form of the data. This method is known as multiple correspondence analysis (MCA). Another method is to preserve a three-way contingency table form using Tucker3, it’s known as a three-way correspondence analysis (CA3). As a case study, we pay attention to analyze the association between race and gender in occupation field that may have contributes to differences in employment opportunity and the continuing increases in women’s educational attainment. The results show that CA3 is more simple in computation and provide the graphical depiction of three-way association simultaneously, while MCA’s plot can’t. Consider to the cumulative inertia on the two-dimensional plot, the percentage inertia of CA3’s plot is better than MCA’s plot.
Uniserial Dimensions of Finitely Generated Primary Modules Over A Discrete Valuation Domain
Authors: Arifin S , Garminia H , Astuti P
Published: October 2019

Recently, the notion of the uniserial dimension of a module over a commutative ring that measures of how far the module deviates from being uniserial was introduced by Nazemian in 2014. In this article we give some methods to determine the uniserial dimension of a finitely generated primary module over a discrete valuation domain. It is well known that finitely generated primary modules over a discrete valuation domain can be decomposed as a direct sum of finite cyclic submodules where the orders of the cyclic generators are called the elementary divisors of the module. We show that the uniserial dimension of the module is a function of the elementary divisors of the module.
SPH simulation of surge waves generated by aerial and submarine landslides
Authors: Iryanto
Published: October 2019

Since the Indian Ocean Tsunami in 2004, there has been extensive research on tsunami modelling. Tsunami catastrophes were generally generated by earthquake fault plate or mass landslide. This article is focused on surge waves induced by mass landslides. Here we restrict to two dimensional study, in which a solid mass was sliding down over a sloping beach. Our approach is numerical simulation using the Smoothed Particle Hydrodynamics (SPH) method. The SPH method is a Lagrangian meshless method, commonly used to describe complex events. Here, the solid mass was modeled as a solid box with triangular-cross section. Its movement follows analytical solution derived by Watts in [1]. The SPH method was used to simulate surge waves induced by two types of landslides; aerial and submarine. Our results were validated using the experimental data of Heinrich [2]. It was shown that the resulting waves induced by aerial and submarine landslides as well as the solid box movement agree quite well with the experimental data. The Root Mean Square Error (RMSE) of free surface deformation in aerial simulation recorded at time t = 0.6, 1.0, 1.5 are 0.02053, 0.02342, 0.02221, respectively and in submarine simulation recorded at time t = 0.5, 1.0, 1.5, 2.0, 2.5, 3.0 are 0.02908, 0.04085, 0.03772, 0.03843, 0.03753, 0.02582, respectively. Whereas motion of the solid box in submarine simulation has better accuracy than in aerial simulation with RMSE 0.00799 and 0.03831, respectively.
Non-linearity analysis for cosmological inflation model with minimal and non-minimal coupling of scalar field from Horndeski theory
Authors: Hikmawan Getbogi , Suroso Agus , Zen Freddy P
Published: October 2019

In this work, we analyze the non-linearity aspect of perturbations generated in early times for cosmological inflation model with minimal and non-minimal couplings of scalar field from Horndeski theory. We study the spectral index of the perturbations and tensor-to-scalar ratio and can be seen as the evidence for inflation for some responsible coupling constant. We get the sign of non-linearity from the spectral index and tensor-to-scalar ratio for this model, and this result can be analyzed further to find non-Gaussianity.
Experimental data analysis of wave attenuation in mangroves
Authors: Abdullah F A R , Husrin S , Bachtiar H
Published: October 2019

The ability of mangrove forest to absorb wave energy was reported in several tsunami events. However, characteristics of mangrove trees that can often withstand the impact of tsunamis, as well as their ability to absorb wave energy, are still an interesting area of research. Based on the experiments conducted in a wave flume at Balai Penelitian dan Pengembangan Pantai, Buleleng, Bali, the effectiveness of mangrove swamps in reducing wave energy was studied. In the wave flume, paddles were put in motion in order to produce monochromatic wave influx. These waves propagate into the domain, then passing through mangrove forest, and further up till the wave was reflected back by the right hard wall boundary. In this article, the Mansard-Funke 3-point method was implemented to decompose the recorded wave signal into incident and reflection waves. Furthermore, the reflection and transmission coefficients were calculated. From sensitivity analysis of experimental data using various water depth and wave period, we found that in a 3 meter length of mangrove, the wave energy was dissipated up to 64%.
The mechanics of macro scale level plastic deformation localization
Authors: Zuev L B , Barannikova S A , Zharmukhambetova A M
Published: October 2019

The major salient features of plastic deformation localization, which are observed at the stage of linear work hardening for deforming metals and alloys, are considered. The dynamic and kinetic characteristics exhibited by the process of localization on transition to failure have been examined. The localization parameters have been related to the electronic properties of metals.
Observation of refraction-contrast effect in images obtained with microfocus bremsstrahlung gamma-rays generated in a narrow internal target of 18 MeV betatron
Authors: Rychkov M M , Kaplin V V , Smolyanskiy V A
Published: October 2019

The first results of experiments demonstrating refraction contrast in magnified (x2.5) images obtained using the Bremsstrahlung gamma radiation of 18 MeV betatron with a narrow tantalum (Ta) target inside are presented. The Ta foil-target with a thickness of 13 urn and a length of 4 mm along the electron beam was mounted in a goniometer inside the chamber of the betatron to guide her along the electron beam. In this case, a linear microfocus source of Bremsstrahlung gamma radiation with vertical and horizontal dimensions of 1.5 and 0.013 mm, respectively, is realized for direct-forward emission of radiation. The obtained magnified images of rectangular steel plates with thicknesses in the region of 15-0.3 mm and lead foils with thickness of 25 urn demonstrated a high resolution of their edges due to the refraction contrast effect, which is realized due to the refraction of microfocus gamma radiation on the surfaces of the lateral faces of the samples.
Geometric anisotropy of velocity of horizontally polarized shear wave in pipe
Authors: Myshkin Yu V , Muravieva O V , Yu Voronchikhin S , Samokrutov A A , Shevaldykin V G
Published: October 2019

A finite element model has been developed to study the propagation velocity of a horizontally polarized shear waves (SH-waves) in pipes of different diameters depending on geometrical parameters, excitation parameters, physical and elastic properties of the pipe material. The results of studies of the geometric anisotropy of the group and phase velocities of the SH-wave for a pipe with a diameter of 1020 mm with a wall thickness of 16 mm are presented. It has been established that in the case of isotropic properties of the pipe material, the velocity on the outer cylindrical surface in the direction of the envelope is 50 m/s more than on the generatrix. The radiation patterns of the SH-wave are given for the studied pipe size with radiation along the generatrix and envelope of the pipe. The results of experimental studies are in satisfactory agreement with the results of modeling.
Advanced features of ECG mapping
Authors: Avdeeva D K , Yuzhakov M M , Ivanov M L , Turushev N V , Maksimov I V , Kodermyatov R E , Mazikov S V , Wenjia Guo , Zimin I A
Published: October 2019

Cardiovascular diseases are the leading cause of death worldwide. A great number of methods have been developed to monitor the state of the heart, each of which has its own advantages and limitations. One of the most promising method is surface mapping. To improve reliability and informativity of this method, researchers of Medical Engineering Laboratory of TPU developed nanosensors with unique metrological characteristics for non-invasive measurement of ECG signals of microvolt and nanovolt levels. The results of previous studies showed that metrological characteristics of the developed nanosensors significantly exceed those of conventional electrodes. Based on this, nanosensors used for surface ECG mapping will enable qualitative improvement of data obtained and diagnostic capabilities of this method.
Wearable nanosensor-based hardware and software complex for dynamic cardiac monitoring
Authors: Ivanov M L , Enshin S I , Avdeeva D K , Yuzhakov M M , Kodermyatov R E , Tsoi E I
Published: October 2019

To date, continuous dynamic monitoring of the cardiovascular system is relevant for improvement of the quality of diagnosis of cardiac diseases. The equipment available for continuous cardiac monitoring operates in the standard frequency range, has a low resolution, and contains filters that limit signals in low and high frequencies. The development of wearable devices and high-resolution methods for dynamic cardiac monitoring to record signals in the range from 0 to 3500 Hz without filtering and averaging is of high priority. In addition, this will allow us to obtain new data on the atria and ventricles of the heart and to detect cardiovascular diseases at an early stage. A wearable hardware and software complex based on nanosensors was developed, and preliminary technical tests of the complex were carried out. An algorithm and a program were developed to detect micropotentials over the entire duration of the ECG signal except for the waves of cardiac pulses and sharp peaks in signal processing. Histograms were built for quantitative evaluation of micropotentials, and the total energy of micropotentials was calculated. Preliminary medical studies were carried out on volunteers.
Digital device for thermophysical measurements by wire probe
Authors: Starostin A , Luk’yanov K , Kotov A , Skripov P , Volosnikov D
Published: October 2019

The paper is devoted to development of a digital device for rapid measurements over a wide temperature range, including superheated states of a substance. The design of the device enables automation of the measurement procedure with a minimum number of preset settings and real-time output of information. Single- and double-pulse heating modes are discussed.
Capturing and tracing an object with the indoor IR positioning system
Authors: Khmelev V L , Zavyalova K V
Published: October 2019

This paper presents a method of “capturing” an object and reconstruction trajectory. It based on digital processing of a stream of optical images and depth maps from an RGB-D camera. This method relies on statistical processing and it possible to capture any objects, not only some type as neuro-algorithms. Reconstructed of trajectory performs in the field of view of RGB-D camera. Such video systems can be used for implementation to a covert scanning scheme of movement person. It will focusing radio wave or optical thermal sensors on the surface of a moving person’s body. The result of the algorithm is an object depth map, which represents the distance to each point of the visible surface of object.
Low-temperature monoclinic layer stacking in atomically thin CrI3 crystals
Authors: Ubrig Nicolas , Wang Zhe , Teyssier Jérémie , Taniguchi Takashi , Watanabe Kenji , Giannini Enrico , Morpurgo Alberto F , Gibertini Marco
Published: October 2019

Chromium triiodide, CrI3, is emerging as a promising magnetic two-dimensional semiconductor where spins are ferromagnetically aligned within a single layer. Potential applications in spintronics arise from an antiferromagnetic ordering between adjacent layers that gives rise to spin filtering and a large magnetoresistance in tunnelling devices. This key feature appears only in thin multilayers and it is not inherited from bulk crystals, where instead neighbouring layers share the same ferromagnetic spin orientation. This discrepancy between bulk and thin samples is unexpected, as magnetic ordering between layers arises from exchange interactions that are local in nature and should not depend strongly on thickness. Here we solve this controversy and show through polarization resolved Raman spectroscopy that thin multilayers do not undergo a structural phase transition typical of bulk crystals. As a consequence, a different stacking pattern is present in thin and bulk samples at the temperatures at which magnetism sets in and, according to previous first-principles simulations, this results in a different interlayer magnetic ordering. Our experimental findings provide evidence for the strong interplay between stacking order and magnetism in CrI3, opening interesting perspectives to design the magnetic state of van der Waals multilayers.
Menger fractal structure with negative refraction and sound tunnelling properties
Authors: Liu Yu , Xu Wenshuai , Chen Meng , Pei Dongliang , Yang Tao , Jiang Heng , Wang Yuren
Published: October 2019

We construct new quasi-three-dimensional fractal acoustic metamaterials based on adoption of the Menger structure, which offers extraordinary parameters such as double-negative properties and a near-zero density. The resulting metamaterials can thus achieve negative refraction, acoustic focusing and sound tunneling. Using the finite element method and the S-parameter retrieval method, the band structures and the effective parameters of these acoustic metamaterials are researched, respectively. The negative refraction property is numerically simulated using a Gaussian beam passing through a double negative prism. A plate lens with a refractive index of n = −1 is constructed to achieve acoustic focusing and the sound tunnelling ability is verified using the near-zero-density metamaterial. The results show that the Menger fractal structures have excellent acoustic properties and are promising for acoustic applications.
Random generation of the special linear group
Authors: Eberhard Sean , Virchow Stefan-C.
Published: October 2019

It is well known that the proportion of pairs of elements of

SL
⁡
(
n
,
q
)

\operatorname {SL}(n,q)

which generate the group tends to

1
1

as

q
n

→
∞

q^n\to \infty

. This was proved by Kantor and Lubotzky using the classification of finite simple groups. We give a proof of this theorem which does not depend on the classification.

An essential step in our proof is an estimate for the average of

(
ord
⁡
g

)

−
1

(\operatorname {ord} g)^{-1}

when

g
g

ranges over

GL
⁡
(
n
,
q
)

\operatorname {GL} (n,q)

, which may be of independent interest. We prove that this average is
\[

exp
⁡
(
−
(
2
−
o
(
1
)
)

n
log
⁡
n
log
⁡
q

)
.

\exp (-(2-o(1)) \sqrt {n \log n \log q}).

\]
Constant Gauss curvature foliations of AdS spacetimes with particles
Authors: Chen Qiyu , Schlenker Jean-Marc
Published: October 2019

We prove that for any convex globally hyperbolic compact maximal (GHCM) anti-de Sitter (AdS) 3-dimensional spacetime

N
N

with particles (cone singularities of angles less than

π
\pi

along time-like lines), the complement of the convex core in

N
N

admits a unique foliation by constant Gauss curvature surfaces. This extends and provides a new proof of a result of Barbot, Béguin, and Zeghib. We also describe a parametrization of the space of convex GHCM AdS metrics on a given manifold, with particles of given angles, by the product of two copies of the Teichmüller space of hyperbolic metrics with cone singularities of fixed angles. Finally, we use the results on

K
K

-surfaces to extend to hyperbolic surfaces with cone singularities of angles less than

π
\pi

a number of results concerning landslides, which are smoother analogs of earthquakes sharing some of their key properties.
Malignant Mesothelioma Among Employees of a Connecticut Factory That Manufactured Friction Materials Using Chrysotile Asbestos: An Update
Authors: Finkelstein Murray M , Meisenkothen Christopher
Published: October 2019

There is an ongoing argument about the potency of chrysotile asbestos to cause malignant mesothelioma. Authors of chrysotile risk assessments have relied upon the results of an epidemiologic study, published in 1984, to state that there were no mesotheliomas found among workers at a Connecticut friction products plant. McDonald reported the first two cases in 1986. In 2010, we reported the work histories and pathologic reports of five individuals from the Connecticut plant who were diagnosed with mesothelioma. Despite this, a review of the health effects of chrysotile published in 2018 continued to state that there were no cases of mesothelioma from this plant. We report here two new cases that were diagnosed after the publication of our previous report, bringing the current total to nine cases. We also discuss the results of previously unpublished air sampling data from the plant. Chrysotile, mainly from Canada, was the only asbestos fiber type used until 1957 when some anthophyllite was added in making paper discs and bands. Beyond this original description of the anthophyllite usage from McDonald, there is a dearth of information about the amount of anthophyllite used in the plant, the frequency of its use, and the specific departments where it was used. For over 30 years in the published literature, this factory has alternatively been described as a ‘chrysotile’ or ‘predominantly chrysotile’ factory. While it is clear that some anthophyllite was used in the factory (in addition to 400 pounds of crocidolite in the laboratory), given the volume, frequency, and processes using chrysotile, it still seems satisfactory to describe this cohort as a predominantly, but not exclusively, chrysotile-exposed cohort.
GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
Authors: Strauss Magdalena E , Kirk Paul D W , Reid John E , Wernisch Lorenz
Published: October 2019

Motivation

Many methods have been developed to cluster genes on the basis of their changes in mRNA expression over time, using bulk RNA-seq or microarray data. However, single-cell data may present a particular challenge for these algorithms, since the temporal ordering of cells is not directly observed. One way to address this is to first use pseudotime methods to order the cells, and then apply clustering techniques for time course data. However, pseudotime estimates are subject to high levels of uncertainty, and failing to account for this uncertainty is liable to lead to erroneous and/or over-confident gene clusters.

Results

The proposed method, GPseudoClust, is a novel approach that jointly infers pseudotemporal ordering and gene clusters, and quantifies the uncertainty in both. GPseudoClust combines a recent method for pseudotime inference with non-parametric Bayesian clustering methods, efficient Markov Chain Monte Carlo sampling and novel subsampling strategies which aid computation. We consider a broad array of simulated and experimental datasets to demonstrate the effectiveness of GPseudoClust in a range of settings.

Availability and implementation

An implementation is available on GitHub: https://github.com/magStra/nonparametricSummaryPSM and https://github.com/magStra/GPseudoClust.

Supplementary information

Supplementary data are available at Bioinformatics online.
Postsurgical residual lung complications following left upper trisegmentectomy
Authors: Koike Yutaro , Hattori Aritoshi , Matsunaga Takeshi , Takamochi Kazuya , Oh Shiaki , Suzuki Kenji
Published: October 2019

OBJECTIVES

Segmentectomy has become an increasingly popular surgical procedure for small-sized lung lesions. Left upper trisegmentectomy (LUTS) is one of the most common segmentectomies performed because of its relative ease and simplicity; however, limited information is currently available on the specific postoperative complications associated with this procedure.

METHODS

Among 2060 surgically resected cases in our institute between 2009 and 2016, 129 (6.2%) underwent LUTS. Postoperative chest X-rays and/or thoracic computed tomography (CT) scans were retrospectively assessed for all cases to assess postsurgical residual lung complications following LUTS. We categorized cases into 4 groups: type A (atelectasis of the lingular segment), type B (lung torsion of the lingular segment), type C (necrosis of the ‘isolated segment’) and type D (haematoma along stapling lines).

RESULTS

Postsurgical lung complications following LUTS were observed in 17 (13.1%) patients (type A: n = 7, type B: n = 1, type C: n = 4 and type D: n = 5). Three patients (2.3%) required surgical intervention because of type B (n = 1) and type C (n = 2), namely, decreased permeability and remaining ground glass opacities in the residual lung, showing an exacerbated systemic inflammatory response. In contrast, type A and D cases were successfully observed by chest CT without any surgical intervention, and patients recovered within a few months of surgery.

CONCLUSIONS

We identified several postoperative residual lung complications following LUTS. Lung torsion or necrosis of the residual segment may require intensive care, including reoperation. Potentially serious complications always need to be ruled out after LUTS when radiological consolidation is detected postoperatively.
Modulation of Neural and Muscular Adaptation Processes During Resistance Training by Fish Protein Ingestions in Older Adults
Authors: Watanabe Kohei , Holobar Aleš , Mita Yukiko , Tomita Aya , Yoshiko Akito , Kouzaki Motoki , Uchida Kenji , Moritani Toshio
Published: October 2019

Assessments of both neural and muscular adaptations during interventions would provide valuable information for developing countermeasures to age-related muscle dysfunctions. We investigated the effect of fish protein ingestion on training-induced neural and muscular adaptations in older adults. Twenty older adults participated 8 weeks of isometric knee extension training intervention. The participants were divided into two groups who took fish protein (n = 10, Alaska pollack protein, APP) or casein (n = 10, CAS). Maximal muscle strength during knee extension, lower extremity muscle mass (body impedance method), and motor unit firing pattern of knee extensor muscle (high-density surface electromyography) were measured before, during, and after the intervention. Muscle strength were significantly increased in both CAS (124.7 ± 5.8%) and APP (117.1 ± 4.4%) after intervention (p < .05), but no significant differences between the groups were observed (p > .05). Significant increases in lower extremity muscle mass from 0 to 8 weeks were demonstrated only for APP (102.0 ± 3.2, p < .05). Greater changes in motor unit firing pattern following intervention were represented in CAS more than in APP. These results suggest that nutritional supplementations could modulate neural and muscular adaptations following resistance training and fish protein ingestion preferentially induces muscular adaptation without the detectable neural adaptation in older adults.
Impact of relebactam-mediated inhibition of Mycobacterium abscessus BlaMab β-lactamase on the in vitro and intracellular efficacy of imipenem
Authors: Le Run Eva , Atze Heiner , Arthur Michel , Mainardi Jean-Luc
Published: October 2019

Objectives

Imipenem is one of the recommended β-lactams for the treatment of Mycobacterium abscessus pulmonary infections in spite of the production of BlaMab β-lactamase. Avibactam, a second-generation β-lactamase inhibitor, was previously shown to inactivate BlaMab, but its partner drug, ceftazidime, is devoid of any antibacterial activity against M. abscessus. Here, we investigate whether relebactam, a novel second-generation inhibitor developed in combination with imipenem, improves the activity of this carbapenem against M. abscessus.

Methods

The impact of BlaMab inhibition by relebactam was evaluated by determining MICs, time–kill curves and M. abscessus intracellular proliferation in human macrophages. Kinetic parameters for the inhibition of BlaMab by relebactam were determined by spectrophotometry using nitrocefin as the substrate. The data were compared with those obtained with avibactam.

Results

Combination of relebactam (4 mg/L) with β-lactams led to >128- and 2-fold decreases in the MICs of amoxicillin (from >4096 to 32 mg/L) and imipenem (from 8 to 4 mg/L). In vitro, M. abscessus was not killed by the imipenem/relebactam combination. In contrast, relebactam increased the intracellular activity of imipenem, leading to 88% killing. Relebactam and avibactam similarly potentiated the antibacterial activities of β-lactams although BlaMab was inactivated 150-fold less effectively by relebactam than by avibactam.

Conclusions

Inhibition of BlaMab by relebactam improves the efficacy of imipenem against M. abscessus in macrophages, indicating that the imipenem/relebactam combination should be clinically considered for the treatment of infections due to M. abscessus.
A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients
Authors: Pishvaian Michael J , Blais Edik M , Bender R Joseph , Rao Shruti , Boca Simina M , Chung Vincent , Hendifar Andrew E , Mikhail Sam , Sohal Davendra P S , Pohlmann Paula R , Moore Kathleen N , He Kai , Monk Bradley J , Coleman Robert L , Herzog Thomas J , Halverson David D , DeArbeloa Patricia , Petricoin Emanuel F , Madhavan Subha
Published: October 2019

Objectives

Scalable informatics solutions that provide molecularly tailored treatment recommendations to clinicians are needed to streamline precision oncology in care settings.

Materials and Methods

We developed a cloud-based virtual molecular tumor board (VMTB) platform that included a knowledgebase, scoring model, rules engine, an asynchronous virtual chat room and a reporting tool that generated a treatment plan for each of the 1725 patients based on their molecular profile, previous treatment history, structured trial eligibility criteria, clinically relevant cancer gene-variant assertions, biomarker-treatment associations, and current treatment guidelines. The VMTB systematically allows clinician users to combine expert-curated data and structured data from clinical charts along with molecular testing data to develop consensus on treatments, especially those that require off-label and clinical trial considerations.

Results

The VMTB was used as part of the cancer care process for a focused subset of 1725 patients referred by advocacy organizations wherein resultant personalized reports were successfully delivered to treating oncologists. Median turnaround time from data receipt to report delivery decreased from 14 days to 4 days over 4 years while the volume of cases increased nearly 2-fold each year. Using a novel scoring model for ranking therapy options, oncologists chose to implement the VMTB-derived therapies over others, except when pursuing immunotherapy options without molecular support.

Discussion

VMTBs will play an increasingly critical role in precision oncology as the compendium of biomarkers and associated therapy options available to a patient continues to expand.

Conclusion

Further development of such clinical augmentation tools that systematically combine patient-derived molecular data, real-world evidence from electronic health records and expert curated knowledgebases on biomarkers with computational tools for ranking best treatments can support care pathways at point of care.
Idiosyncrasies in cities: evaluating patterns and drivers of ant biodiversity along urbanization gradients
Authors: Perez Abe , Diamond Sarah E
Published: October 2019

Urbanization is expected to reduce biodiversity. However, an increasing number of studies report urban biodiversity comparable to that of surrounding nonurban areas, leaving open the question: what maintains biodiversity in cities? We characterized patterns of ant biodiversity across urbanization gradients of three major cities in the Midwestern United States and evaluated the support for two mechanisms underlying the maintenance of biodiversity in cities, specifically via introduced non-native species and differential phenology of communities along each urbanization gradient. We observed idiosyncrasies in ant species diversity such that each city displayed either increased, decreased or no change in biodiversity across the urbanization gradient. We found partial support (one of the three cities) for the hypothesis that non-native species can contribute positively to overall species diversity in cities, though even with introduced species removed from consideration, native ant biodiversity was maintained along the urbanization gradient. We found no support for systematic differential phenology across urbanization gradients, although species diversity did vary over time across all sites. Our results further challenge the assumption of biodiversity loss in cities, as two of our three cities exhibited maintained species diversity along the urbanization gradient. Most importantly, our study demonstrates that urban biodiversity can be maintained entirely by native communities.
Kerosene Nights: Light and Enlightenment in Late Ottoman Jerusalem*
Authors: Wishnitzer Avner
Published: October 2019

Street lighting was first introduced into Ottoman cities in the second half of the nineteenth century. However, unlike in larger Ottoman cities, where coal gas was used, in Jerusalem it was kerosene that served as burning material, creating the distinct nocturnal reality that is here called the ‘kerosene night’. This reality was the result and, simultaneously, one of the most glaring manifestations of Jerusalem’s economic, administrative and infrastructural peripherality. Between the early 1890s and the First World War, kerosene allowed the Jerusalem municipality an affordable means to respond to inhabitants’ expectations for more light. Both public expectations and municipal action were fanned by a discourse that associated street lighting with Enlightenment, order and progress. Yet, kerosene illumination also set the limits of nocturnal conviviality and frustrated the very expectations it kindled. Measured against larger metropoles, the relative darkness of Jerusalem heightened among residents feelings of provinciality and governmental neglect — feelings that the kerosene lamps, paradoxically, brought to light.
The Infant Cuddler Study: Evaluating the effectiveness of volunteer cuddling in infants with neonatal abstinence syndrome
Authors: Hignell Amanda , Carlyle Karen , Bishop Catherine , Murphy Mary , Valenzano Teresa , Turner Suzanne , Sgro Michael
Published: October 2019

Objectives

St. Michael’s Hospital launched a volunteer cuddling program for all infants admitted into the neonatal intensive care unit in October 2015. The program utilizes trained volunteers to cuddle infants when caregivers are not available. This was a pilot study to assess the impact of a volunteer cuddle program on length of stay (LOS) and feasibility of implementation of the program.

Methods

A mixed methods approach was utilized to measure both quantitative and qualitative impact. A pilot cohort study with a retrospective control group assessed the feasibility of implementing a volunteer cuddling program for infants with neonatal abstinence syndrome (NAS). Length of stay was used as a surrogate marker to measure the impact of cuddling on infants being treated for Neonatal Abstinence Syndrome. Focus groups using semi-structured interviews were conducted with volunteers and nurses at the end of the pilot study.

Results

LOS was reduced by 6.36 days (U=34, P=0.072) for infants with NAS in the volunteer cuddling program. Focus groups with both bedside nurses and program volunteers described a positive impact of cuddling programs on infants, families, staff, and volunteers alike.

Conclusions

The study results suggest that the volunteer cuddling program may reduce LOS in infants with NAS and have potential economic savings on hospital resources. However, larger prospective cohort studies are needed to confirm these results.
In situ sol-gel synthesis of hyaluronan derivatives bio-nanocomposite hydrogels
Authors: D’Amora U , Ronca A , Raucci M G , Dozio S M , Lin H , Fan Y , Zhang X , Ambrosio L
Published: October 2019

The main driving idea of the present study was the comparison between two different chemical modifications of hyaluronic acid (HA) followed by the development of nanocomposite hydrogels directly in situ by biomineralization of photocrosslinkable HA polymers through sol-gel synthesis. In this way, it has been possible to overcome some limitations due to classical approaches based on the physical blending of inorganic fillers into polymer matrix. To this aim, methacrylated and maleated HA, synthesized with similar degree of substitution (DS) were compared in terms of mechanical and physico-chemical properties. The success of in situ biomineralization was highlighted by reflect Fourier transform infrared spectroscopy and thermogravimetric analysis. Furthermore, mechanical characterization demonstrated the reinforcing effect of inorganic fillers evidencing a strong correlation with DS. The swelling behavior resulted to be correlated with filler concentration. Finally, the cytotoxicity tests revealed the absence of toxic components and an increase of cell proliferation over culture time was observed, highlighting these bio-nanocomposite hyaluronan derivatives as biocompatible hydrogel with tunable properties.
Physician Behavior Change: A Systematic Review
Authors: Cunningham Brian P. , Bakker Caitlin J. , Parikh Harsh R. , Johal Herman , Swiontkowski Marc F.
Published: October 2019

Evidence-based medicine (EBM) has been advocated as one of the central dogmas of health care since the late 20th century. EBM provides health care entities the prospect to revolutionize health care practices and improve the standard of health care for everyone. Therefore, the potential benefits for adopting EBM practices cannot be overlooked. However, physicians face an increasingly difficult challenge, both personal and professional, when adopting EBM practices. Therefore, knowledge of effective strategies for driving physician behavioral is necessary. To this effort, this systematic review is tasked to compile and analyze the literature focused on physician behavior change. After a review of 1970 studies, 29 different studies were meticulously evaluated by 2 separate reviewers. Studies were then categorized into 5 broad distinctions based on their assessed outcomes: (1) physician knowledge; (2) ordering of tests; (3) compliance with protocols; (4) prescription of medications; and (5) complication rates. The testing group was focused on osteoporosis screening, using educational interventions. Protocol compliance studies were heterogeneous, ranging from diagnosing supracondylar fractures in pediatric patients to antimicrobial administration. Prescription pattern studies were primarily focused around the management of osteoporosis. Multimodal interventions seemed to be more effective when producing change. However, due to the variability in intervention type and outcomes assessment, it is difficult to conclude the most effective intervention for driving physician behavioral change. Physician behavior and specifically surgeon behavior are disproportionately influenced by mentors, fellowship training, and memories of excellent or catastrophic outcomes much more so than literature and data. Adopting evidence-based practices (EBM) and value centric care may provide an opportunity for physicians to improve personal performance.
ClustR: A Space–Time Cluster Analysis R Package for Individual-level Data
Authors: Enders Catherine , Hyde Rebecca J. , Selvin Steve , Metayer Catherine , Francis Stephen Starko
Published: October 2019

Background:

Until recently, large individual-level longitudinal data were unavailable to investigate clusters of disease, driving a need for suitable statistical tools. We introduce a robust, efficient, intuitive R package, ClustR, for space–time cluster analysis of individual-level data.

Methods:

We developed ClustR and evaluated the tool using a simulated dataset mirroring the population of California with constructed clusters. We assessed Cluster’s performance under various conditions and compared it with another space–time clustering algorithm: SaTScan.

Results:

ClustR mostly exhibited high sensitivity for urban clusters and low sensitivity for rural clusters. Specificity was generally high. Compared with SaTScan, ClustR ran faster and demonstrated similar sensitivity, but had lower specificity. Select cluster types were detected better by ClustR than SaTScan and vice versa.

Conclusion:

ClustR is a user-friendly, publicly available tool designed to perform efficient cluster analysis on individual-level data, filling a gap among current tools. ClustR and SaTScan exhibited different strengths and may be useful in conjunction.