bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into IgM-mediated complement activation based on in situ structures of IgM-C1-C4b
Authors: Sharp Thomas H. , Boyle Aimee L. , Diebolder Christoph A. , Kros Alexander , Koster Abraham J. , Gros Piet
Published: May 2019

Antigen binding by serum Ig-M (IgM) protects against microbial infections and helps to prevent autoimmunity, but causes life-threatening diseases when mistargeted. How antigen-bound IgM activates complement-immune responses remains unclear. We present cryoelectron tomography structures of IgM, C1, and C4b complexes formed on antigen-bearing lipid membranes by normal human serum at 4 °C. The IgM-C1-C4b complexes revealed C4b product release as the temperature-limiting step in complement activation. Both IgM hexamers and pentamers adopted hexagonal, dome-shaped structures with Fab pairs, dimerized by hinge domains, bound to surface antigens that support a platform of Fc regions. C1 binds IgM through widely spread C1q-collagen helices, with C1r proteases pointing outward and C1s bending downward and interacting with surface-attached C4b, which further interacts with the adjacent IgM-Fab2and globular C1q-recognition unit. Based on these data, we present mechanistic models for antibody-mediated, C1q-transmitted activation of C1 and for C4b deposition, while further conformational rearrangements are required to form C3 convertases.
Primary structural differences at residue 226 of deer and elk PrP dictate selection of distinct CWD prion strains in gene-targeted mice
Authors: Bian Jifeng , Christiansen Jeffrey R. , Moreno Julie A. , Kane Sarah J. , Khaychuk Vadim , Gallegos Joseph , Kim Sehun , Telling Glenn C.
Published: May 2019

Significance

Our gene-targeting strategy addresses several critical issues relating to chronic wasting disease (CWD), a contagious, lethal neurodegenerative prion disease affecting wild as well as captive cervids, which poses an uncertain risk to humans. First, we show that residue 226, the sole primary structural difference between deer and elk prion protein, dictates the selection and propagation of different CWD strains. Because the strain properties of prions affect their host-range potential, these findings suggest that CWD from elk and deer pose distinct risks to humans and other species. Second, we show that these gene-targeted mice offer an unprecedented means to address distinctive aspects of CWD peripheral pathogenesis and horizontal transmission that are not afforded by previously generated transgenic mouse models.
Introduction.
Authors: Widodo P. , Nur F. , Nafisah E. , Forster B. P. , Hasibuan H. A.
Published: May 2019

A brief history of bunch analysis of the oil palm crop is provided. This includes bunch components (stalk, spikelets, fruits, mesocarp, nuts, shell and kernels) and oil yield analysis. These parameters are used by oil palm breeders to analyse the oil yield potentials (e.g. quantity and quality comparison of bunches, between bunches within an oil palm, between oil palms or between different progenies). Obtaining high fresh fruit bunch (FFB) production in oil palm plantations per hectare area per year, and high oil extraction rates from the bunch, are the main goals of growers to produce maximal oil yield. Oil extraction rates determined in the laboratory are useful in this respect, in monitoring and verifying extraction rates in oil mills.
Bunch sampling.
Authors: Widodo P. , Nur F. , Nafisah E. , Forster B. P. , Hasibuan H. A.
Published: May 2019

Bunch sampling is the harvesting of fresh fruit bunches (FFBs) from oil palm trees. This is done according to standard operating procedures (SOPs), with specific timed intervals between each round of harvesting. During bunch sampling, observations are conducted on the status of the bunches, e.g. fruit colour, number of loose fruits before and after harvesting on the ground, etc. These will correspond to the recoverable oil yield and quality - e.g. free fatty acid content. Good practices are essential to maximize and standardize data capture for oil yield and quality.
Recording, calculations and data checks.
Authors: Widodo P. , Nur F. , Nafisah E. , Forster B. P. , Hasibuan H. A.
Published: May 2019

The records of analyses in the previous chapters are calculated by defined formulae to obtain data on: bunch components; percentage of fertile fruits in the bunch (F/B); fruit set (FS); fruit weight (FWT); percentage of mesocarp in the fruits (M/F); percentage of mesocarp in the fruit check (M/FC); percentage of shell in the fruit (S/F); shell to kernel (S/K); percentage of kernel in the fruit (K/F); kernel to nut (K/N); percentage of kernel in the bunch (K/B); percentage of dry mesocarp to fruit (DM/F); dry mesocarp to wet mesocarp (DM/WM); percentage of oil in dry mesocarp (O/DM); percentage of oil in wet mesocarp (O/WM); and percentage of mesocarp oil in the bunch (O/B).
Meconium aspiration syndrome in mammals.
Authors: Martínez-Burnes J. , Mota-Rojas D. , Villanueva-García D. , Ibarra-Ríos D. , Lezama-García K. , Barrios-García H. , López-Mayagoitia A.
Published: May 2019

Meconium aspiration syndrome (MAS) is a common obstetric and paediatric problem and is one of the most common causes of neonatal respiratory distress. The pathophysiology of MAS is complex. The underlying mechanism of MAS is fetal hypoxia which causes redistribution of fetal blood, increased intestinal peristalsis and relaxation of the anal sphincter
in utero
, leading to the passage of meconium into the amniotic fluid. If hypoxia is severe and persistent, the fetus gasps for air, but instead aspirate amniotic fluid contaminated with meconium. Aspiration of meconium produces multiple physiological and structural changes in the neonatal lung which relates partially to the amount of aspirated meconium. The structural and functional sequels of MAS include airways obstruction, atelectasis, chemical pneumonitis, hypoxemia, acidosis, pulmonary hypertension and occasionally death. MAS survivors can develop airway hyperreactivity and nervous sequelae. The morbidity and mortality of human MAS have declined the last decades because of new therapies but remains a major paediatric problem. Although the prevalence and significance of MAS in veterinary medicine have been poorly investigated, there is ample evidence that intrapartum hypoxia in animals also causes meconium expulsion, amniotic staining and aspiration. The lungs of affected animals showed airway obstruction, focal atelectasis and alveolitis. Meconium staining of the skin and aspiration are indicators of fetal or perinatal hypoxia and postnatal respiratory distress in domestic animals. Experimental models have been developed to study the pathogenesis of MAS in laboratory animals. This review focuses on the current concepts of the pathophysiology of MAS in human and veterinary medicine.
New technologies available for livestock carcass classification and grading.
Authors: López-Campos Ó. , Prieto N. , Juárez M. , Aalhus J. L.
Published: May 2019

Livestock classification and grading systems are a key tool to evaluate carcass attributes and form the basis of trade amongst producers, packers and retailers. Also, these systems provide a better understanding of the products and market trends. One of the recurrent challenges in carcass classification and grading is the development of objective assessments for traits of economic value. Latest technology developments have improved the precision and accuracy of estimating carcass yields and predicting quality attributes and have the potential to be implemented as real-time management tools to optimize product fabrication and provide feedback to producers. This review outlines some of the most popular technologies available for classification and grading purposes in livestock, including those intended for carcass composition assessments, such as ultrasound, bioelectrical impedance analysis, optical probes, video image analysis, dual energy X-ray absorptiometry and computed tomography, and those for quality attributes evaluations, such as near infrared reflectance, hyperspectral imaging and Raman spectroscopy. The present review will also provide an overview of the recent research studies in the literature using these new technologies for carcass merit and quality assessments. Most of the technologies available are based on electromagnetic or mechanical energies that interact with the tissues at the atomic or molecular level, resulting in attenuated signals that can be detected and analysed quantitatively. Accuracy and repeatability along with cost, practicality and reliability will be important criteria in the successful uptake of these new technologies by the livestock industry. The complexity of the evaluations to place products in an optimum market pathway will eventually result in the deployment of a combination of technologies, working together to provide integral carcass attribute descriptions. Published reports and patents were also considered in the review process.
Transferring lessons learned from use of an ecosystem approach to restore degraded areas of North American Great Lakes to the Arabian Gulf
Authors: Hartig John H. , Munawar Mohiuddin , Hamza Waleed , Al-Yamani Faiza
Published: May 2019

Canada and USA have over a 100-year history of international cooperation on Great Lakes management. For over 30 years, federal, state, and provincial governments have successfully used locally-defined ecosystem approaches to develop and implement remedial action plans to restore beneficial uses impairments in 43 Great Lakes Areas of Concern. Each remedial action plan identifies use impairments/causes, remedial/preventive actions to restore uses, and implementation responsibilities and timeframes. Areas of concern are removed from the list when all uses are restored. Long-term efforts are needed to ensure sustainability through adaptive management. Shared resources, like the Arabian Gulf and Great Lakes, require collaboration among boundary countries to achieve common goals. A network of regional technical and governmental representatives could be established under or affiliated with the Regional Organization of Protecting Marine Environment to promote cleanup and ecosystem-based management of degraded areas of the Sea. It would have to be flexible, not prescriptive, science-based, action-oriented, and result in well recognized benefits to all partner countries. Workshops or conferences could be convened to address ecosystem issues. This network must be value-added and build capacity, and could eventually lead to use of locally-defined ecosystem approaches to develop cleanup plans for degraded areas of the Gulf, similar to Great Lakes Areas of Concern. Gulf countries, through the Regional Organization of Protecting Marine Environment and with support of a network, could then come together every three-five years to report on progress, identify research needs, celebrate successes, and establish next steps. Gulf I, II, and III conferences are building blocks for such a network. A logical next step would be to engage the Regional Organization of Protecting Marine Environment in the establishment of a network for ecosystem-based management and co-sponsorship of a Gulf IV Conference or other forum. In the spirit of cooperative learning, further exchanges of both scientific research and management practices would be beneficial between the Great Lakes and the Gulf.
A Three-Terminal Quantum Well Heat Engine with Heat Leakage*
Authors: Lin Ze-Bin , Li Wei , Fu Jing , Yang Yun-Yun , He Ji-Zhou
Published: May 2019

We propose a model for a three-terminal quantum well heat engine with heat leakage. According to the Landauer formula, the expressions for the charge current, the heat current, the power output and the efficiency are derived in the linear-response regime. The curves of the power output and the efficiency versus the positions of energy levels and the bias voltage are plotted by numerical calculation. Moreover, we obtain the maximum power output and the corresponding efficiency, and analyze the influence of the heat leakage factor, the positions of energy levels and the bias voltage on these performance parameters.
Predictions of the Chou–Yang Model for p-p Scattering at

s=8

TeV
Authors: Zahra S. , Rashid H.
Published: May 2019

At low four-momentum transfer squared 0.02 < −t < 0.2 (GeV/c)2, we use the Chou–Yang model to predict the form factor of protons from proton–proton elastic scattering at center-of-mass energy

s

=
8

TeV. By fitting differential cross-sectional data from the TOTEM experiment to a single Gaussian, the form factor is extracted. We use this form factor to find the rms matter radius of the proton to be 0.88 fm, which is in good agreement with the experimental data and the theoretically predicted values of the rms radius.
Nucleonic 1S0 Superfluidity Induced by a Soft Pion in Neutron Star Matter with Antikaon Condensations*
Authors: Xu Yan , Zhi Qi-Jun , Wang Yi-Bo , Huang Xiu-Lin , Ding Wen-Bo , Yu Zi , Liu Cheng-Zhi
Published: May 2019

The nucleonic 1
S
0 superfluidity is investigated by solving the gap equation for the Reid soft-core potential as the nucleon–nucleon interaction in neutron star (NS) matter which is considered to be made up of n, p, e, μ and condensed antikaon matter. We mainly study the influence of the soft pion-induced potential on the nucleonic 1
S
0 pairing gaps in the above NS matter. It is found that the intensities of the nucleonic 1
S
0 pairing gaps including the soft pion-induced potential are smaller than those calculated in the case of not including the soft pion-induced potential. Furthermore, the nucleonic 1
S
0 pairing gaps with the soft pion-induced potential fall into decline with the deepening of the optical potential of antikaons in the above NS matter, whereas they increase with the parameter η for the fixed optical potential of antikaons. Due to the appearance of the soft pion-induced potential, the maximum values of nucleonic 1
S
0 pairing gaps at parameter η = 0.20, 0.55 are suppressed by 1.7%–6.8% with respect to the case without soft pion-induced potential in the above NS matter.
Angular Distribution of Production Planes in

J/ψ→ΛΛ¯

Decay*
Authors: Shen Qiaorong , Tong Xinyan , Long Yunfei , Mao Yajun
Published: May 2019

A new observable, the angle between Λ and

Λ
¯

decay planes, is proposed to test the theoretical predictions on the spin correlation. With 10 billion J/ψ events collected with the BESIII detector at the BEPCII e
+
e
− collider, the distribution of the angle could be measured to verify whether or not a correlation exists.
High-Power Continuous-Wave and Acousto-Optical Q-Switched Ho:(Sc0.5Y0.5)2SiO5 Laser Pumped by Laser Diode*
Authors: Duan Xiao-Ming , Chen Guang-Peng , Shen Ying-Jie , Zheng Li-He , Su Liang-Bi
Published: May 2019

We experimentally investigate the continuous-wave (cw) and acousto-optical (AO) Q-switched performance of a diode-pumped Ho:(Sc0.5Y0.5)2SiO5 (Ho:SYSO) laser. A fiber-coupled laser diode at 1.91 μm is employed as the pump source. The cw Ho:SYSO laser produces 13.0 W output power at 2097.9 nm and 56.0% slope efficiency with respect to the absorbed pump power. In the AO Q-switched regime, at a pulse repetition frequency of 5 kHz, the Ho:SYSO laser yields 2.1 mJ pulse energy and 21 ns pulse width, resulting in a calculated peak power of 100 kW. In addition, at the maximum output level, the beam quality factor of the Q-switched Ho:SYSO laser is measured to be about 1.6.
Tunable Bistability in the Goos–Hänchen Effect with Nonlinear Graphene*
Authors: Liu Binbin , Ma Pujuan , Yu Wenjing , Xu Yadong , Gao Lei
Published: May 2019

We present a planar model system of a silica covered with a monolayer of nonlinear graphene to achieve a tunable Goos–Hänchen (GH) shift in the terahertz range. It is theoretically found that the transition between a negative shift and a large positive one can be realized by altering the intensity of incident light. Moreover, by controlling the chemical potential of graphene and the incident angle of light, we can further control the tunable GH shift dynamically. Numerical simulations for GH shifts based on Gaussian waves are in good agreement with our theoretical calculations.
Negative Thermal Expansion of GaFe(CN)6 and Effect of Na Insertion by First-Principles Calculations*
Authors: Li Meng , Li Yuan , Wang Chun-Yan , Sun Qiang
Published: May 2019

We study the negative thermal expansion (NTE) properties and effect of Na insertion on the NTE of the framework material GaFe(CN)6 by first-principles calculations based on density functional theory within the quasi-harmonic approximation. The calculated results show that the material exhibits NTE due to the low transverse vibrational modes of the CN groups. The modes demonstrate larger negative values of the mode Grüneisen parameters. Once Na is introduced in the framework of the material, it prefers to locate at the center of the quadrates of the framework material and binds to the four N anions nearby. As a consequence, the transverse vibrational mode of the CN group is clearly hindered and the NTE of the material is weakened. Our theoretical calculations have clarified the mechanisms of NTE and the effect of the guest Na on the NTE of the framework material.
Negative Thermal Expansion of the Dy2Fe16Cr Compound*
Authors: Hao Li-Yu , Yang Tie , Wang Xiao-Tian , Tan Ming
Published: May 2019

Structural, thermal expansion, and magnetic properties of the Dy2Fe16Cr compound are investigated by means of x-ray diffraction and magnetization measurements. The Dy2Fe16Cr compound has a hexagonal Th2Ni17-type structure. There exists a negative thermal expansion resulting from a strong spontaneous magnetostriction in the magnetic state of the Dy2Fe16Cr compound. The average thermal expansion coefficient is −0.794 × 10−5/K in the temperature range 292–407 K. The spontaneous magnetostrictive deformation and the Curie temperature are discussed.
Full-Quantum Simulation of Graphene Self-Switching Diodes
Authors: Horri Ashkan , Faez Rahim
Published: May 2019

We present a quantum study on the electrical behavior of the self-switching diode (SSD). Our simulation is based on non-equilibrium Green’s function formalism along with an atomistic tight-binding model. Using this method, electrical characteristics of devices, such as turn-on voltage, rectification ratio, and differential resistance, are investigated. Also, the effects of geometrical variations on the electrical parameters of SSDs are simulated. The carrier distribution inside the nano-channel is successfully simulated in a two-dimensional model under zero, reverse, and forward bias conditions. The results indicate that the turn-on voltage, rectification ratio, and differential resistance can be optimized by choosing appropriate geometrical parameters.
Silicon on Insulator with Highly Uniform Top Si Fabricated by H/He Coimplantation*
Authors: Su Xin , Gao Nan , Chen Meng , Xu Hong-Tao , Wei Xing , Di Zeng-Feng
Published: May 2019

Silicon on insulator with highly uniform top Si is fabricated by co-implantation of H+ and He+ ions. Compared with the conventional ion-slicing process with H implantation only, the co-implanted specimens whose He depth is deeper than H profile have the top Si layer with better uniformity after splitting. In addition, the splitting occurs at the position that the maximum concentration peak of H overlaps with the secondary concentration peak of He after annealing. It is suggested that the H/He co-implantation technology is a promising approach for fabricating fully depleted silicon on insulator.
Patterning of diamond with 10 nm resolution by electron-beam-induced etching
Authors: Dergianlis Vasilis , Geller Martin , Oing Dennis , Wöhrl Nicolas , Lorke Axel
Published: May 2019

We report on mask-less, high resolution etching of diamond surfaces, featuring sizes down to 10 nm. We use a scanning electron microscope (SEM) together with water vapor, which was injected by a needle directly onto the sample surface. Using this versatile and low-damage technique, trenches with different depths were etched. Cross sections of each trench were obtained by focused ion beam milling and used to calculate the achieved aspect ratios. The developed technique opens up the possibility of mask- and resist-less patterning of diamond for nano-optical and electronic applications.
Deep learning-based electroencephalography analysis: a systematic review
Authors: Roy Yannick , Banville Hubert , Albuquerque Isabela , Gramfort Alexandre , Falk Tiago H , Faubert Jocelyn
Published: May 2019

Context. Electroencephalography (EEG) is a complex signal and can require several years of training, as well as advanced signal processing and feature extraction methodologies to be correctly interpreted. Recently, deep learning (DL) has shown great promise in helping make sense of EEG signals due to its capacity to learn good feature representations from raw data. Whether DL truly presents advantages as compared to more traditional EEG processing approaches, however, remains an open question. Objective. In this work, we review 154 papers that apply DL to EEG, published between January 2010 and July 2018, and spanning different application domains such as epilepsy, sleep, brain–computer interfacing, and cognitive and affective monitoring. We extract trends and highlight interesting approaches from this large body of literature in order to inform future research and formulate recommendations. Methods. Major databases spanning the fields of science and engineering were queried to identify relevant studies published in scientific journals, conferences, and electronic preprint repositories. Various data items were extracted for each study pertaining to (1) the data, (2) the preprocessing methodology, (3) the DL design choices, (4) the results, and (5) the reproducibility of the experiments. These items were then analyzed one by one to uncover trends. Results. Our analysis reveals that the amount of EEG data used across studies varies from less than ten minutes to thousands of hours, while the number of samples seen during training by a network varies from a few dozens to several millions, depending on how epochs are extracted. Interestingly, we saw that more than half the studies used publicly available data and that there has also been a clear shift from intra-subject to inter-subject approaches over the last few years. About

of the studies used convolutional neural networks (CNNs), while

used recurrent neural networks (RNNs), most often with a total of 3–10 layers. Moreover, almost one-half of the studies trained their models on raw or preprocessed EEG time series. Finally, the median gain in accuracy of DL approaches over traditional baselines was

across all relevant studies. More importantly, however, we noticed studies often suffer from poor reproducibility: a majority of papers would be hard or impossible to reproduce given the unavailability of their data and code. Significance. To help the community progress and share work more effectively, we provide a list of recommendations for future studies and emphasize the need for more reproducible research. We also make our summary table of DL and EEG papers available and invite authors of published work to contribute to it directly. A planned follow-up to this work will be an online public benchmarking portal listing reproducible results.
Numerical analysis of blood flow in intracranial artery stenosis affected by ischemic stroke using Finite Element method
Authors: Fatahillah A , Setiawani S , Mandala A S , Suharto S , Murtikusuma R P , Safrida L N , Hussen S , Adawiyah R
Published: May 2019

Intracranial stenosis is a narrowing an artery inside the brain. This causes reduced blood flow to the cerebrum and damaged neurons in a short span of time due to reduced oxygenation. Intracranial stenosis can cause ischemic stroke due to a plaque occlusion. This research uses a mathematical model that expresses the velocity of arterial flow of an intracranial stenosis causing ischemic stroke that is expressed by the momentum equation and solved using the finite element method. The analysis of blood velocity is simulated using MATLAB and FLUENT software. This study looks at the effect of plaque thickness and initial speed of blood flow during an intracranial stenosis. The results shows that the larger the plaque thickness, the smaller the area reduction, so the greater the increases blood velocity and the higher the initial velocity of blood that given, the greater the increase of the initial velocity of blood in the artery Intracranial stenosis. According to the MATLAB simulation, blood velocity with 80% plaque thickness increases blood velocity to 1.8665 m/sec at rest and 1.8825 m/sec at exercises. When the initial velocity of blood was 0.2 m/sec, it increases to 0.5712 m/sec at rest and 0.70058 m/sec at exercises.
Ultradiscrete Lotka-Volterra system computes tropical eigenvalue of symmetric tridiagonal matrices
Authors: Fukuda Akiko , Watanabe Sennosuke , Hanaoka Ayumi , Iwasaki Masashi
Published: May 2019

Some of authors’ recent study shows that the time evolution of the integrable ultradiscrete Toda equation computes eigenvalue of tridiagonal matrices over min-plus algebra, where min-plus algebra is a semiring with two binary operations: ⊕ : = min and ⊗ : = +. In this paper, we rst present a Backlund transformation between the ultradiscrete Toda equation and the ultradiscrete Lotka-Volterra system. Using the Backlund transformation, we show that the ultradiscrete Lotka-Volterra system can also compute eigenvalue of symmetric tridiagonal matrices over min-plus algebra.
Numerical simulation of tsunami propagation with Finite Difference Method and Runge Kutta 4th Order Method (study case : south coast of Java island)
Authors: Priyatno Putra Firdaus , Nurul Fajar Shaffiani , Aditya Prima , Apriliani Erna , Sadjidon  , Khusnul Arif Didik
Published: May 2019

Tsunamis are disasters that cause so much damage. In the history of the tsunami, Indonesia has been hit by tsunami several times, based on data from the National Disaster Management Agency (BNBP), as of 1629 - 2007, Indonesia was recorded 184 times affected by large and small tsunami disasters. Based on these data, it is very important for Indonesia to increase security against the tsunami disaster. Also, the tsunami in Indonesia occurred due to earthquakes, volcanic eruptions, and landslides in the sea. This study discussed about to the tsunami with a location located in the southern of Java, precisely in the area of Central Java, considering that in 2017 there was friction between the Indies and Eurasian plates which caused an earthquake measuring 6.9 magnitude, but did not cause a tsunami. In this study, a tsunami wave propagation simulation was carried out with the aim of knowing how long it would take the waves to the shoreline and how high the waves would be when they were on the shoreline. The model used is a tsunami model created by Imamura by solving differential equations using finite difference and Runge-Kutta 4th order. Based on the simulation results with the initial determination of a 5 m tsunami wave centered at a distance of 25 km from the shoreline, Tsunami waves with a height of 8.7 m will arrive at the shoreline at 140 seconds. With wave height is 8.7 m at the shoreline, the water will enter the land or can also be called the tsunami disaster. At that time, residents are expected to have been evacuated from the coastal area. In addition, based on numerical simulations that have been carried out, information is obtained that the computation time of the method is faster than the computation time of the Runge-Kutta method with differences in altitude results that are quite small and can be tolerated. This shows that the Finite Difference method can be applied to tsunami disaster mitigation software because it has a fairly fast computing time compared to the Runge-Kutta 4th order method.
The commutative ring for prime near-rings by involving derivation
Authors: Reza Habibi Mochammad , Winda Setyawati Dian , Baihaqi Komar
Published: May 2019

A near-ring is an extension of the ring without having to fulfill the commutative of the sum and left distributive of the addition and multiplication operations. This paper shows that a prime and zero symmetric near-ring with derivation on near-ring satisfies proposed conditions is a commutative ring.
Clustering the basic human category indicator levels in Banten region
Authors: Asri Y , Palupiningsih P , Haryono  , Reviansya R M
Published: May 2019

Indonesia has an inequality in human development, education provides the highest inequality. Loss that occurs in the education category reaches 20.8 percent. In the categories of decent living standards reaches 17.3 percent, and in the health category 16.5 percent. Most volunteers and the society take responsive action after getting information from the media or from the local communities. Therefore, this study aims to find out which areas have problems on indicators of basic human categories in a certain year. Regions will be grouped into three cluster groups, regions with low values, regions with medium values, and regions with high values. K-Means is an algorithm used to classify regions. The results of this study are, knowing the areas that have the lowest, medium, and highest values based on indicators of basic human categories in 2013 to 2017. Pandeglang and Serang Regencies are the lowest indicators such as life expectancy with a center point of 62.928 in 2013 and up to 64.03 in 2017, mean years of school is 6.299 to 6.666, per capita expenditure is 8411.72 to 9065.33. The cities of South Jakarta, East Jakarta, and Central Jakarta, areas that are at the highest indicators such as life expectancy with a center point of 72.938 to 73.107, expected years of school is 12.673 to 13.438, mean years of school is 10.469 to 10.851, and per capita expenditure with a center point of 17942.57 up to 18856.4.
Model reduction analysis using Hankel Norm Approximation on discrete-time linear system with the special shape of matrix A
Authors: Khusnul Arif Didik , Adzkiya Dieky , Khoirul Roziq Mohammad , Aditya Prima , Nur Fadhilah Helisyah
Published: May 2019

A system can describe real problems that occur in the environment. The system is the result of modeling of real problems. Based on the results of real problem modeling, it often produces a linear system with a special shape of matrix A. In general, to represent the actual conditions of the real problem accurately, a system with a large order is required. While on the other hand, in terms of analysis and computation of the system, it is not desired to have a system with a large order. Therefore, we propose to use a model reduction that produces a system with small orders but without significant errors. One of the commonly used model reduction methods is Hankel Norm Approximation (HNA). In this research, we analyze the process of model reduction with the HNA method in the discrete-time linear system which has special forms of the matrix A. The process of reduction of this model begins with the formulation of the initial system with a special shaped matrix A. Next, we analyze the nature of stability, controllability and observability of the initial system. Then a balanced system is formed and followed by model reduction using HNA. Based on the results of the model reduction simulation using HNA, it was found that the reduced system with HNA has the same performance and properties as the initial system, which is stable, controllable, and observable. Besides that, HNA model reduction is suitable for use at high frequencies and has a fast computation time.
An object-based classification of mangrove land cover using Support Vector Machine Algorithm
Authors: Rosmasita  , Siregar Vincentius P , Agus Syamsul B , Jhonnerie Romie
Published: May 2019

Accurate mapping of mangrove is necessary for effective planning and management of ecosystem and resources, due to the function of mangrove as a provider of natural products The use of satellite remote sensing to map mangrove has become widespread as it can provide accurate, effecient, and repeatable assessments. The type of remote sensing that is based on imaging using the pixel method sometimes results in the misclassification of the imaging due to the “salt and pepper effects”. The aim of this study to use approach support vector machine (SVM) algorithm to classification mangrove land cover using sentinel-2B and Landsat 8 OLI imagery based on object-based classification method (OBIA). The field observation was done using Unmanned Aerial Vehicle (UAV) at Liong River, Bengkalis, Riau Province. The result by show overall accuracy classification using Sentinel-2B was better than Landsat 8 OLI imagery the value of 78.7% versus 62.7% and them were different significantly 7.23%.
Monitoring long-term shoreline changes along the coast of Semarang
Authors: Dewi Ratna S
Published: May 2019

Shoreline is defined as the intersection of land and water which provides economic and social security to coastal communities. Semarang is having approximately 20 km shorelines. It faces multiple threats as a result of for instance urban development, industrialization, land reclamation, land subsidence and erosion. In the present study, an attempt was made to monitor the accretion and erosion processes from multi-temporal images from 1988 up to 2017. Fuzzy approach and OTSU method were made to extract the shoreline and DSAS (Digital Shoreline Analysis System) was used to analyse the changes and estimated the shoreline change rate. From change detection results, a general trend of continuous changes of shoreline can be detected representing a vulnerable shoreline affected by human activities. The results of this study can be used to prioritize action and to develop a suitable adaptation measure.
Printculture of Surgical Pathology and Autopsy Specimens
Authors: McMullen Phillip D , Tesic Vera , Pytel Peter
Published: May 2019

Objectives

Printculture is a method of microbiologic assessment previously described for use in the autopsy setting. We sought to compare printculture of surgical and autopsy pathology specimens to standard microbiology culture using matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF)–based colony identification.

Methods

Printculture was performed on 18 frozen samples with corresponding standard culture results. The results of MALDI-TOF identification of colonies recovered by printculture were compared with standard cultures, and percent concordance was calculated.

Results

There was 95.8% concordance to standard culture methods for cases with infections and 100% concordance for cases without infection. The pattern of growth was found to aid in the distinction between contamination and true infection.

Conclusions

Printculture allows the identification of microorganisms from routinely frozen tissues and provides a bridge between microbiology and histomorphology through the identification of associated histologic features of infection. This technique can be successfully integrated into autopsy and surgical pathology workup of potentially infected tissues.
The Triple Plane, the Bra-Flap, and the Inverted Bra-Flap Modified Dual Plane Techniques for Breast Augmentation
Authors: Bracaglia Roberto , Servillo Maria , Fortunato Regina , Gentileschi Stefano
Published: May 2019

Background

Breast augmentation (BA) is a very common procedure performed for a wide range of indications. The short-term and long-term outcomes are strongly correlated with the choice of the correct implant pocket, which should be tailored to the anatomic features of the breast.

Objectives

The aim of this study was to report the safety and efficacy of the triple-plane technique and Bra-flap modified dual-plane techniques for BA.

Methods

From January 1995 to January 2016, 605 patients underwent BA procedures that utilized the triple-plane technique or Bra-flap modified dual-plane techniques. Patient evaluation was performed preoperatively and postoperatively at 6 and 12 months and every 5 years thereafter. The occurrence of ptosis and implant malposition, as well as breast animation deformity, were assessed. Patient satisfaction was evaluated with the BREAST-Q Augmentation Module.

Results

The average patient age was 39.3 years. The follow-up period ranged from 24 months to 20 years. The triple-plane technique was performed in 450 patients, the Bra-flap modified dual-plane technique in 97, and the inverted Bra-flap modified dual-plane technique in 58. No cases of double-bubble deformity or implant bottoming-out were observed. Regarding animation deformity, 209 patients presented with mild to moderate distortion, whereas no patients presented with severe distortion. The BREAST-Q questionnaire reported significant postoperative improvements in all scales.

Conclusions

In over 20 years of experience, the triple-plane technique has proven to be a reliable procedure that offers natural and long-lasting results. The Bra-flap and inverted Bra-flap modified dual-plane techniques are efficient options to expand the range of breast conditions treated.

Level of Evidence: 4
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods
Authors: Ebrahimpoor Mitra , Spitali Pietro , Hettne Kristina , Tsonaka Roula , Goeman Jelle
Published: May 2019

Studying sets of genomic features is increasingly popular in genomics, proteomics and metabolomics since analyzing at set level not only creates a natural connection to biological knowledge but also offers more statistical power. Currently, there are two gene-set testing approaches, self-contained and competitive, both of which have their advantages and disadvantages, but neither offers the final solution. We introduce simultaneous enrichment analysis (SEA), a new approach for analysis of feature sets in genomics and other omics based on a new unified null hypothesis, which includes the self-contained and competitive null hypotheses as special cases. We employ closed testing using Simes tests to test this new hypothesis. For every feature set, the proportion of active features is estimated, and a confidence bound is provided. Also, for every unified null hypotheses, a $P$-value is calculated, which is adjusted for family-wise error rate. SEA does not need to assume that the features are independent. Moreover, users are allowed to choose the feature set(s) of interest after observing the data. We develop a novel pipeline and apply it on RNA-seq data of dystrophin-deficient mdx mice, showcasing the flexibility of the method. Finally, the power properties of the method are evaluated through simulation studies.
New algorithms for detecting multi-effect and multi-way epistatic interactions
Authors: Ansarifar Javad , Wang Lizhi
Published: May 2019

Motivation

Epistasis, which is the phenomenon of genetic interactions, plays a central role in many scientific discoveries. However, due to the combinatorial nature of the problem, it is extremely challenging to decipher the exact combinations of genes that trigger the epistatic effects. Many existing methods only focus on two-way interactions. Some of the most effective methods used machine learning techniques, but many were designed for special case-and-control studies or suffer from overfitting. We propose three new algorithms for multi-effect and multi-way epistases detection, with one guaranteeing global optimality and the other two being local optimization oriented heuristics.

Results

The computational performance of the proposed heuristic algorithm was compared with several state-of-the-art methods using a yeast dataset. Results suggested that searching for the global optimal solution could be extremely time consuming, but the proposed heuristic algorithm was much more effective and efficient than others at finding a close-to-optimal solution. Moreover, it was able to provide biological insight on the exact configurations of epistases, besides achieving a higher prediction accuracy than the state-of-the-art methods.

Availability and implementation

Data source was publicly available and details are provided in the text.
Fitting the US National Park Service for Change
Authors: Schwartz Mark W , Redford Kent H , Leslie Elaine F
Published: May 2019

The US National Park Service (NPS), which manages over 85 million acres and over 400 units, contends with myriad external drivers of ecosystem change that threaten parks. Stressors such as invasive species, habitat fragmentation, warming climates and rising sea level, raise the potential that parks will not attain or sustain their congressionally designated missions. Using invasive animals as a focal example of such changes, we suggest the NPS consider increasing active management of resources, participating in cooperative ecoregional management, increasing the use of public participation, and using formal decision support tools. We illustrate how these management approaches are currently underused. Acknowledging that invasive species are but one of a suite of problems that are threatening to overwhelm park management capacity we believe that the approaches we outline generalize to myriad problems facing the NPS.
Parkin interacting substrate zinc finger protein 746 is a pathological mediator in Parkinson’s disease
Authors: Brahmachari Saurav , Lee Saebom , Kim Sangjune , Yuan Changqing , Karuppagounder Senthilkumar S , Ge Preston , Shi Rosa , Kim Esther J , Liu Alex , Kim Donghoon , Quintin Stephan , Jiang Haisong , Kumar Manoj , Yun Seung Pil , Kam Tae-In , Mao Xiaobo , Lee Yunjong , Swing Deborah A , Tessarollo Lino , Ko Han Seok , Dawson Valina L , Dawson Ted M
Published: May 2019

α-Synuclein misfolding and aggregation plays a major role in the pathogenesis of Parkinson’s disease. Although loss of function mutations in the ubiquitin ligase, parkin, cause autosomal recessive Parkinson’s disease, there is evidence that parkin is inactivated in sporadic Parkinson’s disease. Whether parkin inactivation is a driver of neurodegeneration in sporadic Parkinson’s disease or a mere spectator is unknown. Here we show that parkin in inactivated through c-Abelson kinase phosphorylation of parkin in three α-synuclein-induced models of neurodegeneration. This results in the accumulation of parkin interacting substrate protein (zinc finger protein 746) and aminoacyl tRNA synthetase complex interacting multifunctional protein 2 with increased parkin interacting substrate protein levels playing a critical role in α-synuclein-induced neurodegeneration, since knockout of parkin interacting substrate protein attenuates the degenerative process. Thus, accumulation of parkin interacting substrate protein links parkin inactivation and α-synuclein in a common pathogenic neurodegenerative pathway relevant to both sporadic and familial forms Parkinson’s disease. Thus, suppression of parkin interacting substrate protein could be a potential therapeutic strategy to halt the progression of Parkinson’s disease and related α-synucleinopathies.
One-year Mortality Outcomes From the Advancing Cryptococcal Meningitis Treatment for Africa Trial of Cryptococcal Meningitis Treatment in Malawi
Authors: Kanyama Cecilia , Molloy Síle F , Chan Adrienne K , Lupiya Duncan , Chawinga Chimwemwe , Adams Jack , Bright Philip , Lalloo David G , Heyderman Robert S , Lortholary Olivier , Jaffar Shabbar , Loyse Angela , van Oosterhout Joep J , Hosseinipour Mina C , Harrison Thomas S
Published: May 2019

In Malawi, 236 participants from the Advancing Cryptococcal Meningitis Treatment for Africa trial were followed for 12 months. The trial outcomes reported at 10 weeks were sustained to 1 year. One-week amphotericin B plus flucytosine was associated with the lowest 1 year mortality (27.5% [95% confidence interval, 16.3 to 44.1]).
Declines in Pneumonia and Meningitis Hospitalizations in Children Under 5 Years of Age After Introduction of 10-Valent Pneumococcal Conjugate Vaccine in Zambia, 2010–2016
Authors: Mpabalwani Evans M , Lukwesa-Musyani Chileshe , Imamba Akakambama , Nakazwe Ruth , Matapo Belem , Muzongwe Chilweza M , Mufune Trust , Soda Elizabeth , Mwenda Jason M , Lutz Chelsea S , Pondo Tracy , Lessa Fernanda C
Published: May 2019

Background

Pneumococcus is a leading cause of pneumonia and meningitis. Zambia introduced a 10-valent pneumococcal conjugate vaccine (PCV10) in July 2013 using a 3-dose primary series at ages 6, 10, and 14 weeks with no booster. We evaluated the impact of PCV10 on meningitis and pneumonia hospitalizations.

Methods

Using hospitalization data from first-level care hospitals, available at the Ministry of Health, and from the largest pediatric referral hospital in Lusaka, we identified children aged <5 years who were hospitalized with pneumonia or meningitis from January 2010–December 2016. We used time-series analyses to measure the effect of PCV10 on monthly case counts by outcome and age group (<1 year, 1–4 years), accounting for seasonality. We defined the pre- and post-PCV10 periods as January 2010–June 2013 and July 2014–December 2016, respectively.

Results

At first-level care hospitals, pneumonia and meningitis hospitalizations among children aged <5 years accounted for 108 884 and 1742 admissions in the 42 months pre-PCV10, respectively, and 44 715 and 646 admissions in the 30 months post-PCV10, respectively. Pneumonia hospitalizations declined by 37.8% (95% confidence interval [CI] 21.4–50.3%) and 28.8% (95% CI 17.7–38.7%) among children aged <1 year and 1–4 years, respectively, while meningitis hospitalizations declined by 72.1% (95% CI 63.2–79.0%) and 61.6% (95% CI 50.4–70.8%), respectively, in these age groups. In contrast, at the referral hospital, pneumonia hospitalizations remained stable and a smaller but significant decline in meningitis was observed among children aged 1–4 years (39.3%, 95% CI 16.2–57.5%).

Conclusions

PCV10 introduction was associated with declines in meningitis and pneumonia hospitalizations in Zambia, especially in first-level care hospitals.
Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand
Authors: Rawlence Nicolas J , Rayner Matt J , Lovegrove Tim G , Stoddart Debbie , Vermeulen Melanie , Easton Luke J , Tennyson Alan J D , Scofield R Paul , Kennedy Martyn , Spencer Hamish , Waters Jonathan M
Published: May 2019

Genetic data are increasingly being used to prioritize species conservation in a fiscally constrained age of seemingly boundless conservation crises. Such data can also reveal previously cryptic biodiversity requiring further revision of conservation management guidelines. Using a combination of mitochondrial (control region) and nuclear (beta fibrinogen intron 7) DNA, and morphology, we reveal that the endemic New Zealand Spotted Shag (Phalacrocorax punctatus) complex exhibits phylogenetic structure that is decoupled from previously recorded qualitative morphological variation. Crucially, the most genetically distinct populations within P. punctatus are from northern New Zealand; recent surveys show that these populations, which house important genetic diversity within Spotted Shags, are in danger of being extirpated. In contrast, we find the previously phenotypically differentiated nominate (P. punctatus punctatus) and Blue (P. punctatus oliveri) Shag subspecies show no genetic and morphological separation, and are of least conservation concern.
Learning and Mechanism Design: An Experimental Test of School Matching Mechanisms with Intergenerational Advice
Authors: Ding Tingting , Schotter Andrew
Published: May 2019

While the mechanisms that economists design are typically static, one-shot games, in the real world, mechanisms are used repeatedly by generations of agents who engage in them for a short period of time and then pass on advice to their successors. Hence, behaviour evolves via social learning and may diverge dramatically from that envisioned by the designer. We demonstrate that this is true of school matching mechanisms—even those for which truth-telling is a dominant strategy. Our results indicate that experience with an incentive-compatible mechanism may not foster truthful revelation if that experience is achieved via social learning.