bluuebunny/crossref_metadata_2025 huggingface dataset:
Small Area Estimation with Bivariate Hierarchical Bayes (HB) Approach to Estimate Monthly Average per Capita Expenditure of Food and Non-Food Commodities in Province of Bali
Authors: Purwa Taly , Rumiati Agnes Tuti , Zain Ismaini
Published: June 2019

Small Area Estimation (SAE) is an indirect method that has been widely used for estimating parameters in a small area or small domain by borrowing strength of predictor variables from census or registration. This study uses Hierarchical Bayes (HB) method under the univariate and bivariate Fay-Herriot (FH) model to estimate monthly average per capita expenditure of food and non-food commodities for each district level in Province of Bali in 2014. Then estimation results from both models will be compared. The bivariate FH model is expected to increase the accuracy of the results of estimation by taking into account correlation between two types of expenditure rather than perform univariate estimation separately. Thirteen predictor variables from the administrative record of village data (PODES 2014) are included in each model as factors that affect these two types of expenditure. From the result, there are three variables that have significant effect on food expenditure, both in univariate and bivariate FH model. While, for non-food expenditure both model show different result on significant variables. Based on the results of the performance comparison, the best model is bivariate FH model since it has smaller Mean Square Prediction Error (MSPE), Mean Absolute Percentage Error (MAPE) and Root Mean Square Error (RMSE) value than univariate FH models. In addition, the bivariate FH model produces shorter 95% credible interval of estimated values. These conditions indicate that jointly modeling can improve the accuracy of estimation. Bivariate FH also produces significant improvement in adjusted R
2 value. Finally, the mapping result shows the same pattern for two types of expenditure. The highest monthly average per capita expenditure is more localized in the southern districts of Bali. While the lowest expenditure is more localized in the eastern and western districts of Bali.
Standard Growth Chart of Weight for Height to Determine Wasting Nutritional Status in East Java Based on Semiparametric Least Square Spline Estimator
Authors: Ramadan W , Chamidah N , Zaman B , Muniroh L , Lestari B
Published: June 2019

Wasting is a condition of a children characterized by a lack of weight by measuring weight for height. Currently, to monitor the growth conditions for childrens in Indonesia, we use the Towards Healthy Card called as Kartu Menuju
Sehat (KMS) which is guided by WHO 2005. The samples used to design WHO-2005 standard charts are children from Brazil, Ghana, India, USA, Norway, and Oman that have different physical conditions from children in Indonesia. Therefore, the using of standards growth charts from other countries cause incompatibility with Indonesian’s children growth. To illustrate the growth patterns of children in East Java, we use the semiparametric least square spline estimator that gives more flexible pattern. In this study we used weight (kg) as a response variable, height (cm) as a predictor variable for nonparametric component, and gender as a predictor variable for parametric component. The results show the semiparametric least square spline estimator can explain the growth patterns of children well because it has determination coefficient (R2) of 99.78% and mean square error (MSE) of 0.0353. The standard chart of weight for height of boy is higher than that of girl and percentage of wasting nutritional status of girl greater than that of boy.
A Dynamics Behaviour of Two Predators and One Prey Interaction with Competition Between Predators
Authors: Savitri Dian , Suryanto Agus , Kusumawinahyu Wuryansari M , Abadi
Published: June 2019

This research focuses on the dynamical of a Leslie-Gower predator-prey model with competition on predator populations. The model represents an interaction between one prey and two predator populations. The analysis shows that there are four equilibrium points, namely the extinction of predator populations point, the extinction of the first predator population point, the extinction of the second predator and the interior point. The existence of the interior equilibrium point is investigated by using Cardan criteria. Local stability analysis shows that both predator populations have never been extinct together. The second and third equilibrium point is local asymptotically stable under some conditions. Numerical simulations are carried out to investigate the stability of the interior point as well as to show that more than one equilibrium point may be asymptotically stable together for a set of parameter.
Simulations Study Combined Estimator Fourier Series and Spline Truncated in Multivariable Nonparametric Regression
Authors: Wayan Sudiarsa I
Published: June 2019

The problems one of that appeared in everyday life is how to explain the shape of the relation pattern between a response with some predictor. Regression analysis is a statistical method used to estimate the relation pattern between response (y) with predictor (x). Development of nonparametric regression of Fourier series involving multiple predictor, has been more developed for predictors of the same pattern. We need to develop different estimator for different predictors of multivariable nonparametric regression. Theoretical research will be focused on estimator form, and applied to simulation data. The estimation of the combined regression function of the Fourier and spline truncated sequence is obtained through the optimization of penalized least square (PLS). Based on the simulation result obtained that the larger the sample size and the smaller the size of the variance, it will result in better estimation value of parameter and knot.
Food Security of Farmer Households in The Papua Border Region In The Era of Industrial Revolution 4.0: Ordinal Logit Regression Model
Authors: Widati Agatha W. , Darwanto Dwidjono H. , Masyhuri  , Waluyati Lestari R.
Published: June 2019

This study aims to determine the factors that influence the food security of farmer households in the Papua border region. Twelve factors used in this study are maternal education, number of family members, price of rice, price of sweet potatoes, prices of cooking oil, prices of instant noodles, income, area of arable land, distance of buying food, share of food expenditure, reception of the rice for poor families (raskin), and farmer status (either local or transmigrant). This research uses primary data from direct interviews by asking a list of questions to farmer households in Jayapura City and Keerom District. The samples are randomly selected, and the total respondents are 160 farmer households, then the data analyzed by Ordinal Logit Regression. The results show that most of the household farmers classified as the food secure condition. Partially the number of family members, cultivated land area, the share of food expenditure and the price of sweet potato/cassava have a significant effect the probability of the occurrence of food security for farmer households significant at the 5% level of error, while dummy raskin significant at an error rate of 10%. The cultivated land area and dummy raskin have a positive effect on the food security of farmer households, while the number of family members, the price of sweet potato/cassava, and the share of food expenditure have a negative effect on farm household food security.
Identification of Epigenetic Regulation on The Expression of The Aberrant Gene of Kidney Renal Clear Cell Carcinoma Patients Observed in a Specific Race
Authors: Agustriawan David , Mulyono Hardi , Parikesit Arli Aditya , Nurdiansyah Rizky
Published: June 2019

Aberrant expression of genes in cancer is mainly caused by a mutation where there is a change in DNA sequences. However, the aberrant expression was also found without a change in the DNA sequences where epigenetic modification such as DNA methylation, histone modifications and microRNA become the main regulator in another layer of the cancer mechanism. The nature of epigenetic is heritable and reversible. It is important to search for the epigenetic mechanism in disease development in order to design epigenetic therapy and drugs. Methylation inhibitors and HDAC inhibitors drug already yielded seven FDA approved epigenetic drugs for myelodysplastic syndrome, cutaneous T-cell lymphoma, Multiple myelomas, peripheral T-cell lymphoma. This study search for the epigenetic mechanism in a kidney renal cell carcinoma patients in a white race. The dataset of transcriptome profiling and epigenetic was downloaded from The Cancer Genome Atlas (TCGA) database. Some programming languages such as R, Python, Matlab and MySQL database were used to pre-processing the datasets and correlation computation part. This study found 14 aberrant genes which significantly correlated with 19 aberrant methylation probes with the correlation score less than equal to -0.7 and p-value < 0.01. Some of those down-regulated genes such as ZNF542, ZFP28, TMEM25, STK33 are correlated with hypermethylation in more than one sites. It is suggested that those methylation sites can affect the down-regulation of their expression in cancer formation. Further study is needed to validate the results through wet lab analysis.
Submerged-Fermentation of Brassica oleracea L. capitata using Lactobacillus plantarum to Reduce Anti-Nutrient Compound
Authors: Fahmia Aulin Risyda , Srihardyastutie Arie , Prasetyawan Sasangka , Safitri Anna
Published: June 2019

Fermentation of cabbage (Brassica oleracea L. capitata) by Lactobacillus plantarumhas been successfully conducted using submerged-fermentation technique. The aims of this study is to determine the correlation between tannins and total sugar in the fermentation of cabbage. Fermentation process is proposed to reduce the concentration of tannins as anti-nutrient compound in cabbage. The tannin concentrations are determined using spectrophotometric method. Tannase enzyme produced by L. plantarum is hypothesised to be mainly responsible for the degradation of glucoside bonds, thus, reducing tannins contents. Total sugar contents were also investigated in this fermentation process. Fermentation process was carried out with variation of L. plantarum inoculum concentrations of 5%, 10%, 15%, and 20% (w/v). Results showed that the tannins value in cabbage raw materials was 290.877 mg/g FW. After fermentation process the optimal inoculum concentration reduced tannins concentration to 75.938 mg/g FW, at 5% inoculum concentration and pH 6for 96 h at 25 ºC. The correlation between tannins and total sugar in cabbage fermentation was found inversely proportional.
Actinodaphnine and Rutacridone as New T-Cell Protein Tyrosine Phosphatase Inhibitors for Drug Development of Obesity
Authors: Fitrianingrum Y , Indarto D , Kusumawati R , Suselo Y H
Published: June 2019

T-Cell Protein Tyrosine Phosphatase (TCPTP) is an obesogenic enzyme that inactivates a Signal Transducer and Activator Transcription 3 (STAT3) protein, leading to inhibition of leptin and insulin signalling. This protein can be a target for development of anti-obesity drugs. This study aimed to identify Indonesian phytochemicals as in silico TCPTP inhibitor. This bioinformatics study used a molecular docking method with AutoDock Vina software version 1.1.2. Three-dimensional structure of TCPTP protein and its Inhibitor (XIX, standard ligand) was obtained from Protein Data Bank (PDB) database with code 1L8K and PubChem database with code 9926586. Indonesian phytochemicals in this study were registered in the HerbalDB database and met criteria of Lipinski’s rule. The three-dimensional structure of phytochemicals was obtained from PubChem National Center for Biotechnology Information (NCBI). Binding affinity and molecular conformation of selected Indonesian phytochemicals were assessed and compared to the standard ligand. PyMol version 1.3 software was used to visualize molecular docking results. Inhibitor XIX interacted with TCPTP protein at Gln125 and Thr129 residues with -6.30 kcal/mol binding affinity. Actinodaphnine and Rutacridone had lower binding affinity (-6.40 kcal / mol) than the standard ligand. Actinodaphnine interacted with the TCPTP protein at Thr129 and Asp130 residues while Rutacridone had interaction at Thr129 only. However, both phytochemicals had different conformation from PTP inhibitor XIX. Actinodaphnine is more potential to become a TCPTP inhibitor in silico for treatment of obesity than Rutacridone. Further investigation is required to evaluate the inhibitory effect of both phytochemicals towards the TCPTP protein.
Synthesis of 3-(7-triphenylphosphonioheptyl)-2,6-dimethyl-1,4-benzoquinone) and The Activity Test Toward Glycogen Phosphorylase Enzyme: In silico Approach
Authors: Furoida Andriani , Ulfa Siti Mariyah
Published: June 2019

The synthesis of 3-(7-triphenylphosphonioheptyl)-2,6-dimethyl-1,4-benzoquinone) (TFH) is carried out by bromoalkylation and insertion of triphenylphosphonium moiety by refluxed of 2,3-dimethyl-1,4-benzoquinone using bromooctanoic acid triphenylphosphine. The alkylation gave 17.14% yield of 2-(7-bromoheptyl)-3,5-dimethyl-1,4-benzoquinone (C7) and 3-(7-triphenylphosphonioheptyl)-2,6-dimethyl-1,4-benzoquinone) (TFH) is obtained at 40.35% yield. Structure characterization of the synthesized product was performed mainly using UV-Vis, FT-IR, and 1H-NMR. UV-Vis characterization showed maximum wavelength of TFH at 198 nm, 226 nm, and 260 nm. FT-IR characterization showed sp3 character at 2930.43 cm−1 and the disappearance of C-Br peak at 687.37 cm−1, indicates the presence of long chain alkyl group and the replacement of Br with triphenylphosphonium. In silico investigation by using Glycogen Phosphorylase enzyme as molecular target estimated IC50 value of thymoquinone, C7, and TFH, that is, 16.14 ppm, 162.2 ppm, and 1.26 ppm, respectively. Thus, TFH has the smallest IC50 value suggested that most effective drug candidate compared with thymoquinone and C7.
Correlation and Meta-Analysis of HER2 in Each Stage of Breast Cancer
Authors: Ramanto K N , Agustriawan David , Parikesit A A , Nurdiansyah Rizky , Nasution Muhammad Z A
Published: June 2019

Human Epidermal growth Receptor 2 (HER2) plays an essential role in the pathogenesis of breast cancer. Previous studies have shown that HER 2 overexpression is associated with a higher histological tumor grade. Furthermore, the overexpression of HER 2 is associated with miRNAs expression. However, the interaction of HER2 and miRNAs in each stage of breast cancer remain unclear. The objective of this study is to identify the relationship between HER2 and miRNAs expression in each stage of breast cancer. Thirteen miRNAs were selected based on literature evidence that showed their interaction with the overexpression of HER 2. The correlation and meta-analysis were done by using the R programming language. The result of this study showed hsa-mir-10b has the highest correlation value in stage two and three breast cancer. On the other hand, hsa-let-7f-2 has the highest correlation value in stage one breast cancer. The result of meta-analysis also showed a significant level of p-value (0.007). These results indicate the downregulation miRNAs only occur in a specific stage of breast cancer.
Optimization of the Hermetia illucens Larvae Extraction Process with Response Surface Modelling and Its Amino Acid Profile and Antibacterial Activity
Authors: Sholikin Mohammad Miftakhus , Alifian Mochamad Dzaky , Jayanegara Anuraga , Nahrowi
Published: June 2019

Hermetia illucens Larvae (HiL) is a protein source that can replace soybean meal and act as functional feed in the poultry industry. This study aims to optimize the HiL extraction process and evaluate the amino acid profile and antibacterial activity. Response surface modelling (RSM) was used to optimize the HiL extraction process and yield assessment. RSM followed by three levels and three variables based on Box-Behnken design. The extraction method used alkali extraction procedure with three variables, e.g., X1: NaOH solvent, X2: HCl solvent, and X3: precipitation volume. Inhibitory zone assay used Staphylococcus aureus, Bacillus subtilis, Salmonella typhimurium and Escherichia coli. Model build by RSM has R2 = 0.9949 with significant value (P<0.01). The correlation plot of experimental yield versus predicted yield has R2 = 0.9974. Validation of the model has a lack of fit value (P>0.05) which indicate that the model is valid. The EAAI and BV value of HiL extract are 16.51 and 5.30%, respectively. HiL extract did not show antibacterial activity to inhibit gram-positive and gram-negative bacteria. The optimum yield (23.03%) was obtained by performing with NaOH 2.35 M, HCl 2.76 M, and precipitation volume 25.28 mL. EAAI of HiL extracts is slightly higher than that of dried HiL but lower than that of soybean meal.
The Potential of Bacillus cereus S1 as an Environmentally Friendly Bioaccumulator of Gold Nanoparticle Waste
Authors: Zulaika Enny , M. Andry P. Utomo , Fitria Avip N. , Prasetyo Endry Nugroho
Published: June 2019

Gold (Au) is one of the metals that is widely used for jewellery and electroplating. Although in the nanoparticle form, the waste that produced still has high economic value. Since its belong to heavy metals, gold nanoparticle waste need to be removed even in the very low concentration. One of the alternatives is utilized gold-resistant bacteria, namely Bacillus cereus S1. The purpose of our study was to determine the ability of B. cereus S1 to accumulates gold. Reconfirmation test of B. cereus S1 gold resistant ability was figured out using Minimal Salt Medium (MSM), 2% glucose and 0.1 ppm gold. The bioaccumulation process was used 1 ppm, 5 ppm, and 10 ppm concentration of gold; and the incubation periods were 6, 12, and 24 hours. Gold bioaccumulation performed by B. cereus S1 was measured using Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-EOS). The results showed that the longer incubation periods of B. cereus S1, the higher gold concentration will be accumulated at exposure concentration 1 ppm, 5 ppm and 10 ppm. B. cereus S1 showed good viability after 24 hours metal exposure.
Role of Clathrin Protein to Increase Electric Current on Dye-Sensitized Solar Cell (DSSC) Based Natural Dyes
Authors: Trihutomo Prihanto , Soeparman Sudjito , Widhiyanuriyawan Denny , Yuliati Lilis
Published: June 2019

Dye-Sensitized Solar Cell (DSSC) has the cost of fabrication is relatively cheap, easy to produce, work on the area of the visible light and environmentally friendly. The shortage of DSSC, namely the efficiency is still low compared with solar cells of silicon. In this study, have been successfully fabricated DSSC with clathrin protein deposited. The method used in this research is to deposit clathrin protein in porous TiO2 semiconductors with a concentration of 0%, 25%, 50%, and 75%. Tests carried out on the DSSC that has been made current testing electricity using a solar simulator to determine the changes in electrical current that occur in DSSC. The conclusion from this research is that with increasing concentration of the addition of the clathrin protein in the DSSC leads to an increase in the electric current generated by DSSC. From the results of testing using a solar simulator obtained the value of electric current is the highest, namely 5.247 mA with the addition of the concentration of the clathrin protein by 75%.
A Production Planning and Scheduling Method Based on Heuristic Rules for Forming-sintering Production System
Authors: Zhengmin Zhang , Zailin Guan , Lei Yue , Chuangjian Wang , Hao Wang
Published: June 2019

The forming-sintering process is the bottleneck of the magnetic material manufacturing system in general, which restricts the overall output of the workshop. It is hard to formulate a production plan due to the complex constraints in such production system. In current research, the production planning control framework integrated with DBR (Drum-Buffer-Rope) concept oriented for forming-sintering process is designed. Moreover, a heuristic method considering the constraints of the magnetic material production process is proposed, which standardize and optimize the preparation process of the forming-sintering production plan. The practical application indicates that the heuristic method greatly reduces the number of WIPs, shortens the order manufacturing cycle, and improves the on-time delivery rate and the utilization rate of the sintering furnace, as compared with the current planning method of the enterprise.
Collection and Storage of Assembly Quality Data of Complex Electromechanical Products
Authors: Liang Y , Zhang Q D , Zhao N , Duan H
Published: June 2019

In the context of made in China 2025 and intelligent manufacturing, “data-based decision” is one of the important concepts for quality management promotion, and data integrity and availability is an important aspect of data collection and data management. Combined with the characteristics of complex electromechanical products with complex structure, multiple development links and high quality requirements, this paper discusses the management category of quality big data from the perspective of manufacturing process operation management and product life cycle, studies the acquisition strategy by manual and automatic methods, acquisition process, the quality data modeling and expression specifications based on unified coding specifications and business flow and data flow framework and provides references for enterprises to carry out quality big data construction.
Research and Application of Bottleneck-based Planning and Scheduling Method for PCB Manufacturing System
Authors: Luo Dan , Guan Zailin , He Cong , Fang Weikang , Wang Chuangjian , Zeng Zhangyi
Published: June 2019

Researches on planning and scheduling of PCB production system are gaining more and more attention due to the complexity and uncertainty of it. Current research focused on the solving method how to make better schedule solution for PCB system based on a real case of PCB production enterprise. Firstly, for the bottleneck process of electroplating, a mixed integer programming model is proposed, moreover, a branch and bound method is employed to solve the problem. Secondly, for non-critical processes, the man-hour quota is predicted using the neural network model and the association rules, and then the data can be found using the association rules and be modified. Thirdly, the planning and scheduling method based on bottleneck is used for the order sequencing, and “pull-push” mechanism of Drum-Buffer-Rope are applied to generate the scheduling scheme for non-bottlenecks. In the end, the effectiveness of the proposed scheduling method is proved by computational experiments.
Research on Automatic Flow-shop Planning Problem Based on Data Driven Modelling Simulation and Optimization
Authors: Fang Weikang , Guan Zailin , Luo Dan , He Cong , Wang Hao , Wang Chuangjian
Published: June 2019

With the increasing demand for individualization, new smart manufacturing models are implemented in order to adapt to the market demands of high quality, multi-variety and fast delivery. However, new problems in production and operation are urgently needed for research. It is especially significant to study the automatic flow workshop planning based on data-driven modelling and simulation. Firstly, according to the rapid analysis of various data of the workshop, UML-based object-oriented data model is formulated. Then the application module of data-driven simulation modelling is established by using the simulation platform. The bottleneck recognition based simulation optimization module for the tabu search algorithm with guiding rules is designed. Data-driven modelling makes the model more flexible and reusable which can run a variety of different experiments by modifying the external data to drive simulation model. Finally, experiments are conducted to verify the effectiveness of the simulation optimization method proposed in current study. In addition an optimized production line configuration plan is provided.
Research on Pose Estimation of Mobile Robot Based on Convolutional Neural Network
Authors: Yue Min , Fu Guangyuan , Wu Ming
Published: June 2019

In this paper, we propose a new learning scheme for generating camera pose to be used for visual odometry. Pose estimation of mobile robot in unknown environment is formulated as a learning problem. We train a convolutional neural network end to end to compute the 6-dof pose of the robot from a series of images. The architecture is a kind of residual network with multiple attention resblocks, which can give features different weights in order to improve the accuracy of pose prediction. The network estimates ego-motion taking monocular image sequences as input instead of separate images. We call this novel network architecture Posenet. Compared to traditional methods, results are more accurate and in which we can see the potential of pose estimation methods with convolutional neural network.
Femtosecond Laser Double Pulses Nanofabrication on Silicon
Authors: Zhang Jin , Wang Sumei , Wang Mengmeng , Chu Zhuyuan
Published: June 2019

The temporal shaping femtosecond (fs) laser is realized by dividing a fs laser pulse into two identical sub-pulses. The double-pulse fs laser can be used to effectively control the initial free electron state such as electron temperature, capacity and density, etc. to improve the surface morphology quality. In this experiment, silicon was fabricated using the double-pulse fs laser. It was found that the average diameter of ablated micro-or nanoholes decreases with the increasing pulse delay (up to 1.5 ps) under the same laser fluence and the phenomenon was explained quantitatively by the plasma model. Furthermore, nanoholes were achieved using the double-pulse fs laser, which cannot be obtained by single pulse laser, and the processing size can be reduced to below 200 nm.
Newly redefined units come into force
Authors: Banks Michael
Published: June 2019

The redefinition of four base units of the International System of Units (SI) came into effect last month meaning that all seven units are now based on fundamental constants.
Rutherford's legacy
Authors: Campbell John
Published: June 2019

With the International Year of the Periodic Table of Elements in full swing, John Campbell celebrates the immense contribution of Ernest Rutherford, who first split the atom 100 years ago
Chartered status
Authors: Fletcher Anne
Published: June 2019

I am extremely concerned about the decision by the Institute of Physics (IOP) to remove Chartered Physicist (CPhys) and Chartered Engineer (CEng) status from any member of the IOP who can’t demonstrate they are carrying out the required amount of continuing professional development (CPD).
Listening for sharks
Authors: Murray Louise
Published: June 2019

Pelagic thresher sharks are a sight to behold, but their numbers are dwindling as a result of illegal hunting and fishing. Now, however, scientists are using acoustics to learn more about these animals’ behaviour and how they can be better protected. Louise Murray looks under the surface
A versatile technology
Authors: Zimmermann Julia , Photopoulos Julianna
Published: June 2019

Julia Zimmermann, co-founder of the German start-up firm Terraplasma, speaks to Julianna Photopoulos about how a desire to develop applications for cold atmospheric plasmas led her to co-found a family of companies
The functor of singular chains detects weak homotopy equivalences
Authors: Rivera Manuel , Wierstra Felix , Zeinalian Mahmoud
Published: June 2019

The normalized singular chains of a path connected pointed space

X
X

may be considered as a connected

E

∞

E_{\infty }

-coalgebra

C

∗

(
X
)

\mathbf {C}_*(X)

with the property that the

0
0

th homology of its cobar construction, which is naturally a cocommutative bialgebra, has an antipode; i.e., it is a cocommutative Hopf algebra. We prove that a continuous map of path connected pointed spaces

f
:
X
→
Y

f: X\to Y

is a weak homotopy equivalence if and only if
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="bold upper C Subscript asterisk Baseline left-parenthesis f right-parenthesis colon bold upper C Subscript asterisk Baseline left-parenthesis upper X right-parenthesis right-arrow bold upper C Subscript asterisk Baseline left-parenthesis upper Y right-parenthesis">

C

∗

(
f
)
:

C

∗

(
X
)
→

C

∗

(
Y
)

\mathbf {C}_*(f): \mathbf {C}_*(X)\to \mathbf {C}_*(Y)

is an

Ω

\mathbf {\Omega }

-quasi-isomorphism, i.e., a quasi-isomorphism of dg algebras after applying the cobar functor

Ω

\mathbf {\Omega }

to the underlying dg coassociative coalgebras. The proof is based on combining a classical theorem of Whitehead together with the observation that the fundamental group functor and the data of a local system over a space may be described functorially from the algebraic structure of the singular chains.
On some embeddings between the cyclotomic quiver Hecke algebras
Authors: Zhou Kai , Hu Jun
Published: June 2019

Let

I
I

be a finite index set and let

A
=
(

a

i
j

)

i
,
j
∈
I

A=(a_{ij})_{i,j\in I}

be an arbitrary indecomposable symmetrizable generalized Cartan matrix. Let

Q
+

Q^+

be the positive root lattice and

P
+

P^+

the set of dominant weights. For any

β
∈

Q
+

\beta \in Q^+

and

Λ
∈

P
+

\Lambda \in P^+

, let

R

β

Λ

\mathscr {R}_{\beta }^{\Lambda }

be the corresponding cyclotomic quiver Hecke algebra over a field

K
K

. For each

i
∈
I

i\in I

, there is a natural unital algebra homomorphism

ι

β
,
i

\iota _{\beta ,i}

from

R

β

Λ

\mathscr {R}_{\beta }^{\Lambda }

to

e
(
β
,
i
)

R

β
+

α
i

Λ

e
(
β
,
i
)

e(\beta ,i)\mathscr {R}_{\beta +\alpha _i}^{\Lambda }e(\beta ,i)

. In this paper we show that the homomorphism
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="iota Subscript beta Baseline colon equals circled-plus Underscript i element-of upper I Endscripts iota Subscript beta comma i Baseline colon script upper R Subscript beta Superscript normal upper Lamda Baseline right-arrow circled-plus Underscript i element-of upper I Endscripts e left-parenthesis beta comma i right-parenthesis script upper R Subscript beta plus alpha Sub Subscript i Subscript Superscript normal upper Lamda Baseline e left-parenthesis beta comma i right-parenthesis">

ι
β

:=

⨁

i
∈
I

ι

β
,
i

:

R

β

Λ

→

⨁

i
∈
I

e
(
β
,
i
)

R

β
+

α
i

Λ

e
(
β
,
i
)

\iota _\beta :=\bigoplus _{i\in I}\iota _{\beta ,i}: \mathscr {R}_{\beta }^{\Lambda }\rightarrow \bigoplus _{i\in I}e(\beta ,i)\mathscr {R}_{\beta +\alpha _i}^{\Lambda }e(\beta ,i)

is always injective unless

β
=
0

\beta =0

and

ℓ
(
Λ
)
=
0

\ell (\Lambda )=0

or

A
A

is of finite type and

β
=
Λ
−

w
0

Λ

\beta =\Lambda -w_0\Lambda

, where

w
0

w_0

is the unique longest element in the finite Weyl group associated to the finite Cartan matrix

A
A

, and

ℓ
(
Λ
)

\ell (\Lambda )

is the level of

Λ
\Lambda

.
Uniform approximation of Abhyankar valuation ideals in function fields of prime characteristic
Authors: Datta Rankeya
Published: June 2019

We prove the prime characteristic analogue of a characteristic

0
0

result of Ein, Lazarsfeld, and Smith on uniform approximation of valuation ideals associated with real-valued Abhyankar valuations centered on regular varieties.
Volumes of 3-ball quotients as intersection numbers
Authors: Deraux Martin
Published: June 2019

We give an explicit description of the 3-ball quotients constructed by Couwenberg-Heckman-Looijenga and deduce the value of their orbifold Euler characteristics. For each lattice, we also give a presentation in terms of generators and relations.
Comparison and pure infiniteness of crossed products
Authors: Ma Xin
Published: June 2019

Let

α
:
G
↷
X

\alpha : G\curvearrowright X

be a continuous action of an infinite countable group on a compact Hausdorff space. We show that, under the hypothesis that the action

α
\alpha

is topologically free and has no

G
G

-invariant regular Borel probability measure on

X
X

, dynamical comparison implies that the reduced crossed product of

α
\alpha

is purely infinite and simple. This result, as an application, shows a dichotomy between stable finiteness and pure infiniteness for reduced crossed products arising from actions satisfying dynamical comparison. We also introduce the concepts of paradoxical comparison and the uniform tower property. Under the hypothesis that the action

α
\alpha

is exact and essentially free, we show that paradoxical comparison together with the uniform tower property implies that the reduced crossed product of

α
\alpha

is purely infinite. As applications, we provide new results on pure infiniteness of reduced crossed products in which the underlying spaces are not necessarily zero dimensional. Finally, we study the type semigroups of actions on the Cantor set in order to establish the equivalence of almost unperforation of the type semigroup and comparison. This sheds light on a question arising in a paper of Rørdam and Sierakowski.
Actin assembly produces sufficient forces for endocytosis in yeast
Authors: Nickaeen Masoud , Berro Julien , Pollard Thomas D. , Slepchenko Boris M.
Published: June 2019

We formulated a spatially resolved model to estimate forces exerted by a polymerizing actin meshwork on an invagination of the plasma membrane during endocytosis in yeast cells. The model, which approximates the actin meshwork as a visco-active gel exerting forces on a rigid spherocylinder representing the endocytic invagination, is tightly constrained by experimental data. Simulations of the model produce forces that can overcome resistance of turgor pressure in yeast cells. Strong forces emerge due to the high density of polymerized actin in the vicinity of the invagination and because of entanglement of the meshwork due to its dendritic structure and cross-linking. The model predicts forces orthogonal to the invagination that are consistent with formation of a flask shape, which would diminish the net force due to turgor pressure. Simulations of the model with either two rings of nucleation-promoting factors (NPFs) as in fission yeast or a single ring of NPFs as in budding yeast produce enough force to elongate the invagination against the turgor pressure.
Breast Implant Prevalence in the Dutch Female Population Assessed by Chest Radiographs
Authors: de Boer Mintsje , van Middelkoop Michele , Hauptmann Michael , van der Bijl Noortje , Bosmans Jorn A W , Hendriks-Brouwer Narda , Schop Sijmen J , de Boer Jan Paul , Hijmering Nathalie J , Overbeek Lucy I H , Lobbes Marc B I , Klazen Caroline A H , de Jong Daphne , Rakhorst Hinne A , van der Hulst René R W J , van Leeuwen Flora E
Published: June 2019

Background

Breast implant-related health problems are a subject of fierce debate. Reliable population-based estimates of implant prevalence rates are not available, however, due to a lack of historical registries and incomplete sales data, precluding absolute risk assessments.

Objectives

This study aimed to describe the methodology of a novel procedure to determine Dutch breast implant prevalence based on the evaluation of routine chest radiographs.

Methods

The validity of the new method was first examined in a separate study. Eight reviewers examined a series of 180 chest radiographs with (n = 60) or without (n = 120) a breast implant confirmed by a computed tomography or magnetic resonance imaging scan. After a consensus meeting with best-performing expert reviewers, we reviewed 3000 chest radiographs of women aged 20 to 70 years in 2 large regional hospitals in the Netherlands in 2015. To calculate the national breast implant prevalence, regional prevalence variations were corrected utilizing the National Breast Cancer Screening Program.

Results

Eight reviewers scored with a median sensitivity of 71.7% (range, 41.7%-85.0%) and a median specificity of 94.6% (range, 73.4%-97.5%). After a consensus meeting and a reevaluation by best-performing expert reviewers, sensitivity was 79.9% and specificity was 99.2%. The estimated national prevalence of breast implants among women between 20 and 70 years was 3.0%, ranging from 1.7% at 21 to 30 years to 3.9% between 51 and 60 years.

Conclusions

The novel method in this study was validated with a high sensitivity and specificity, resulting in accurate prevalence estimates and providing the opportunity to conduct absolute risk assessment studies on the health consequences of breast implants.

Level of Evidence: 2
Sub-dominant principal components inform new vaccine targets for HIV Gag
Authors: Ahmed Syed Faraz , Quadeer Ahmed A , Morales-Jimenez David , McKay Matthew R
Published: June 2019

Motivation

Patterns of mutational correlations, learnt from patient-derived sequences of human immunodeficiency virus (HIV) proteins, are informative of biochemically linked networks of interacting sites that may enable viral escape from the host immune system. Accurate identification of these networks is important for rationally designing vaccines which can effectively block immune escape pathways. Previous computational methods have partly identified such networks by examining the principal components (PCs) of the mutational correlation matrix of HIV Gag proteins. However, driven by a conservative approach, these methods analyze the few dominant (strongest) PCs, potentially missing information embedded within the sub-dominant (relatively weaker) ones that may be important for vaccine design.

Results

By using sequence data for HIV Gag, complemented by model-based simulations, we revealed that certain networks of interacting sites that appear important for vaccine design purposes are not accurately reflected by the dominant PCs. Rather, these networks are encoded jointly by both dominant and sub-dominant PCs. By incorporating information from the sub-dominant PCs, we identified a network of interacting sites of HIV Gag that associated very strongly with viral control. Based on this network, we propose several new candidates for a potent T-cell-based HIV vaccine.

Availability and implementation

Accession numbers of all sequences used and the source code scripts for all analysis and figures reported in this work are available online at https://github.com/faraz107/HIV-Gag-Immunogens.

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimating Long-term Tuberculosis Reactivation Rates in Australian Migrants
Authors: Dale Katie D , Trauer James M , Dodd Peter J , Houben Rein M G J , Denholm Justin T
Published: June 2019

Background

The risk of progression to tuberculosis (TB) disease is greatest soon after infection, yet disease may occur many years or decades later. However, rates of TB reactivation long after infection remain poorly quantified. Australia has a low incidence of TB and most cases occur among migrants. We explored how TB rates in Australian migrants varied with time from migration, age, and gender.

Methods

We combined TB notifications in census years 2006, 2011, and 2016 with time- and country-specific estimates of latent TB prevalences in migrant cohorts to quantify postmigration reactivation rates.

Results

During the census years, 3246 TB cases occurred among an estimated 2 084 000 migrants with latent TB. There were consistent trends in postmigration reactivation rates, which appeared to be dependent on both time from migration and age. Rates were lower in cohorts with increasing time, until at least 20 years from migration, and on this background there also appeared to be increasing rates during youth (15–24 years of age) and in those aged 70 years and above. Within 5 years of migration, annual reactivation rates were approximately 400 per 100 000 (uncertainty interval [UI] 320–480), dropping to 170 (UI 130–220) from 5 to 10 years and 110 (UI 70–160) from 10 to 20 years, then sustaining at 60–70 per 100 000 up to 60 years from migration. Rates varied depending on age at migration.

Conclusions

Postmigration reactivation rates appeared to show dependency on both time from migration and age. This approach to quantifying reactivation risks will enable evaluations of the potential impacts of TB control and elimination strategies.
Pyronaridine-artesunate Efficacy and Safety in Uncomplicated Plasmodium falciparum Malaria in Areas of Artemisinin-resistant Falciparum in Viet Nam (2017–2018)
Authors: Quang Bui Phuc , Hong Huynh Quang , Thanh Tran Duong , Thanh Le Dong , Quang Nguyen Thieu , Van Truong Hanh , Khim Nimol , Witkowski Benoit , Cong Tran Dai , Bustos Maria Dorina , Ringwald Pascal , Thi Ta Tinh
Published: June 2019

Background

Multidrug-resistant Plasmodium falciparum undermines the efficacy of currently deployed antimalarial therapies in southern Viet Nam.

Methods

Between May 2017 and December 2018, this prospective, open-label, single-arm, observational clinical trial, conducted in Binh Phuoc, Dak Nong, Gia Lai, Khanh Hoa, and Ninh Thuan provinces, evaluated the safety and efficacy of oral pyronaridine-artesunate once daily for 3 consecutive days in adults and children with microscopically confirmed P. falciparum malaria. Patients were treated as inpatients for Days 0–3, with follow-up visits on Days 7, 14, 21, 28, 35, and 42. The primary outcome was the proportion of polymerase chain reaction (PCR)-adjusted adequate clinical and parasitological response (ACPR) at Day 42.

Results

The cumulative incidence of PCR-adjusted ACPR at Day 42 was 96.1% (95% confidence interval [CI] 91.4–98.2; Kaplan–Meier). In the per-protocol analysis, the proportion of patients with Day 42 PCR-adjusted ACPR was 96.1% (147/153; 95% CI 91.7–98.5). The proportion of patients with parasitemia at Day 3 was 24.0% (40/167; 95% CI 17.7–31.2). The prevalences of the Kelch13 (C580Y) mutation were: in Binh Phuoc, 97.7% (43/44); in Dak Nong, 96.2% (25/26); in Gia Lai, 57.8% (37/64); in Khanh Hoa, 66.6% (6/9); and in Ninh Thuan, 3.6% (1/28). The majority of artemisinin-resistant isolates also had increased plasmepsin2 copy number (75.9%; 85/112). There was 1 isolate (Binh Phuoc) that had Kelch13 (C580Y) plus increased plasmepsin2 and Pfmdr1 copy numbers. Asymptomatic transient increases in alanine transaminase and aspartate transaminase were observed at Day 7, resolving by Day 28.

Conclusions

Pyronaridine-artesunate can be used to diversify antimalarial therapy in areas of artemisinin-resistant P. falciparum in Viet Nam.

Clinical Trials Registration

ACTRN12618001274268.
Natural Clostridioides difficile Toxin Immunization in Colonized Infants
Authors: Kociolek Larry K , Espinosa Robyn O , Gerding Dale N , Hauser Alan R , Ozer Egon A , Budz Maria , Balaji Aakash , Chen Xinhua , Tanz Robert R , Yalcinkaya Nazli , Conner Margaret E , Savidge Tor , Kelly Ciaran P
Published: June 2019

Background

Clostridioides (Clostridium) difficile colonization is common among infants. Serological sequelae of infant C. difficile colonization are poorly understood.

Methods

In this prospective cohort study of healthy infants, stools serially collected between ages 1-2 and 9-12 months were tested for non-toxigenic and toxigenic C. difficile (TCD). Cultured isolates underwent whole-genome sequencing. Serum collected at 9–12 months underwent measurement of IgA, IgG, and IgM against TCD toxins A and B and neutralizing antibody (NAb) titers against toxin B. For comparison, antitoxin IgG and NAb were measured in cord blood from 50 mothers unrelated to study infants.

Results

Among 32 infants, 16 (50%) were colonized with TCD; 12 were first colonized >1 month before serology measurements. A variety of sequence types were identified, and there was evidence of putative in-home (enrolled siblings) and outpatient clinic transmission. Infants first colonized with TCD >1 month prior had significantly greater serum antitoxin IgA and IgG against toxins A (P = .02 for both) and B (P = .009 and .008, respectively) compared with non–TCD-colonized infants, and greater IgG compared with unrelated cord blood (P = .005). Five of 12 (42%) colonized infants had detectable NAb titers compared with zero non–TCD-colonized infants (P = .02). Breastfeeding was not associated with differences in serological measurements.

Conclusions

TCD colonization is associated with a humoral immune response against toxins A and B, with evidence of toxin B neutralization in vitro. The extent and duration of protection against CDI later in life afforded by natural C. difficile immunization events require further investigation.
Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis)
Authors: Shirasawa Kenta , Esumi Tomoya , Hirakawa Hideki , Tanaka Hideyuki , Itai Akihiro , Ghelfi Andrea , Nagasaki Hideki , Isobe Sachiko
Published: June 2019

We report the phased genome sequence of an interspecific hybrid, the flowering cherry ‘Somei-Yoshino’ (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that ‘Somei-Yoshino’ might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.
Lead extraction for cardiac implantable electronic device infection: comparable complication rates with or without abandoned leads
Authors: Bracke Frank , Verberkmoes Niels , van 't Veer Marcel , van Gelder Berry
Published: June 2019

Aims

Abandoned leads are often linked to complications during lead extraction, prompting pre-emptive extraction if leads become non-functional. We examined their influence on complications when extracted for device-related infection.

Methods and results

All patients undergoing lead extraction for device-related infection from 2006 to 2017 in our hospital were included. The primary endpoint was major complications. Out of 500 patients, 141 had abandoned leads, of whom 75% had only one abandoned lead. Median cumulative implant times were 24.2 (interquartile range 15.6–38.2) and 11.6 (5.6–17.4), respectively years with or without abandoned leads. All leads were extracted only with a femoral approach in 50.4% of patients. Mechanical rotational tools were introduced in 2014 and used in 22.2% of cases and replacing laser sheaths that were used in 5% of patients. Major complications occurred in 0.7% of patients with abandoned leads compared with 1.7% of patients with only active leads (P = 0.679). Failure to completely remove all leads was 14.9% and 6.4%, respectively with or without abandoned leads (P = 0.003), and clinical failure was 6.4% and 2.2% (P = 0.028), respectively. Procedural failure dropped to 9.2% and 5.7% (P = 0.37), respectively after the introduction of mechanical rotational tools. The only independent predictor of procedural and clinical failure in multivariate analysis was the cumulative implant duration.

Conclusion

Despite longer implant times, patients with abandoned leads did not have more major complications during lead extraction. Therefore, preventive extraction of non-functional leads to avoid complications at a later stage is not warranted.