bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated crystal structure analysis based on blackbox optimisation
Authors: Ozaki Yoshihiko , Suzuki Yuta , Hawai Takafumi , Saito Kotaro , Onishi Masaki , Ono Kanta 
Published: June 2020

AbstractIn the present study, we show that time-consuming manual tuning of parameters in the Rietveld method, one of the most frequently used crystal structure analysis methods in materials science, can be automated by considering the entire trial-and-error process as a blackbox optimisation problem. The automation is successfully achieved using Bayesian optimisation, which outperforms both a human expert and an expert-system type automation despite the absence of expertise. This approach stabilises the analysis quality by eliminating human-origin variance and bias, and can be applied to various analysis methods in other areas which also suffer from similar tiresome and unsystematic manual tuning of extrinsic parameters and human-origin variance and bias.
MutSpot: detection of non-coding mutation hotspots in cancer genomes
Authors: Guo Yu Amanda , Chang Mei Mei , Skanderup Anders Jacobsen 
Published: June 2020

AbstractRecurrence and clustering of somatic mutations (hotspots) in cancer genomes may indicate positive selection and involvement in tumorigenesis. MutSpot performs genome-wide inference of mutation hotspots in non-coding and regulatory DNA of cancer genomes. MutSpot performs feature selection across hundreds of epigenetic and sequence features followed by estimation of position- and patient-specific background somatic mutation probabilities. MutSpot is user-friendly, works on a standard workstation, and scales to thousands of cancer genomes.
Energy metabolism and mitochondrial defects in X-linked Charcot-Marie-Tooth (CMTX6) iPSC-derived motor neurons with the p.R158H PDK3 mutation
Authors: Perez-Siles G. , Cutrupi A. , Ellis M. , Screnci R. , Mao D. , Uesugi M. , Yiu Eppie M. , Ryan Monique M. , Choi B. O. , Nicholson G. , Kennerson M. L. 
Published: June 2020

AbstractCharcot-Marie-Tooth (CMT) is a group of inherited diseases clinically and genetically heterogenous, characterised by length dependent degeneration of axons of the peripheral nervous system. A missense mutation (p.R158H) in the pyruvate dehydrogenase kinase 3 gene (PDK3) has been identified as the genetic cause for an X-linked form of CMT (CMTX6) in two unrelated families. PDK3 is one of four PDK isoenzymes that regulate the activity of the pyruvate dehydrogenase complex (PDC). The balance between kinases (PDKs) and phosphatases (PDPs) determines the extend of oxidative decarboxylation of pyruvate to generate acetyl CoA, critically linking glycolysis and the energy producing Krebs cycle. We had shown the p.R158H mutation causes hyperactivity of PDK3 and CMTX6 fibroblasts show hyperphosphorylation of PDC, leading to reduced PDC activity and ATP production. In this manuscript we have generated induced pluripotent stem cells (iPSCs) by re-programming CMTX6 fibroblasts (iPSCCMTX6). We also have engineered an isogenic control (iPSCisogenic) and demonstrated that genetic correction of the p.R158H mutation reverses the CMTX6 phenotype. Patient-derived motor neurons (MNCMTX6) show increased phosphorylation of the PDC, energy metabolism defects and mitochondrial abnormalities, including reduced velocity of trafficking mitochondria in the affected axons. Treatment of the MNCMTX6 with a PDK inhibitor reverses PDC hyperphosphorylation and the associated functional deficits founds in the patient motor neurons, demonstrating that the MNCMTX6 and MNisogenic motor neurons provide an excellent neuronal system for compound screening approaches to identify drugs for the treatment of CMTX6.
Interplays between copper and Mycobacterium tuberculosis GroEL1
Authors: Yang Dong , Klebl David P , Zeng Sheng , Sobott Frank , Prévost Martine , Soumillion Patrice , Vandenbussche Guy , Fontaine Véronique 
Published: June 2020

Abstract
The recalcitrance of pathogenic Mycobacterium tuberculosis, the agent of tuberculosis, to eradication is due to various factors allowing bacteria to escape from stress situations. The mycobacterial chaperone GroEL1, overproduced after macrophage entry and under oxidative stress, could be one of these key players. We previously reported that GroEL1 is necessary for the biosynthesis of phthiocerol dimycocerosate, a virulence-associated lipid and for reducing antibiotic susceptibility. In the present study, we showed that GroEL1, bearing a unique C-terminal histidine-rich region, is required for copper tolerance during Mycobacterium bovis BCG biofilm growth. Mass spectrometry analysis demonstrated that GroEL1 displays high affinity for copper ions, especially at its C-terminal histidine-rich region. Furthermore, the binding of copper protects GroEL1 from destabilization and increases GroEL1 ATPase activity. Altogether, these findings suggest that GroEL1 could counteract copper toxicity, notably in the macrophage phagosome, and further emphasizes that M. tuberculosis GroEL1 could be an interesting antitubercular target.
Cytotoxic, Anti-bacterial, and Wound-healing Activity of Prenylated Phenols from the Kurdish Traditional Medicinal Plant Onobrychis Carduchorum (Fabaceae)
Authors: Clericuzio Marco , Hussain Faiq H. S. , Amin Hawraz Ibrahim M. , Bona Elisa , Gamalero Elisa , Giorgia Novello , Lappano Rosamaria , Talia Marianna , Maggiolini Marcello , Bazzicalupo Miriam , Cornara Laura 
Published: June 2020

AbstractOnobrychis carduchorum (Fabaceae) is a plant widely employed in Kurdish traditional medicine to cure wounds, inflammations, and other skin diseases. We could isolate ten different polyphenols from the acetone extract of this plant: 1–4 are isoflavones, having a genistein skeleton; 5–7 are flavanones, having a naringenin skeleton; and 8–10 are prenylated dihydro-stilbenes. In particular, 8–10 have been isolated, so far, only from Glycyrrhiza glabra (liquorice). Many of the above prenylated phenols showed significant toxicity on some human breast cancer cell lines, and a relevant growth inhibition of Staphylococcus aureus strains. In addition, 9 and 10 had marked wound healing activity. It is suggested that these bioactivities are responsible, at least partly, for the plant’s traditional use.
Artificial intelligence-based diagnostic system classifying gastric cancers and ulcers: comparison between the original and newly developed systems
Authors: Namikawa Ken , Hirasawa Toshiaki , Nakano Kaoru , Ikenoyama Yohei , Ishioka Mitsuaki , Shiroma Sho , Tokai Yoshitaka , Yoshimizu Shoichi , Horiuchi Yusuke , Ishiyama Akiyoshi , Yoshio Toshiyuki , Tsuchida Tomohiro , Fujisaki Junko , Tada Tomohiro 
Published: June 2020

Abstract
Background We previously reported for the first time the usefulness of artificial intelligence (AI) systems in detecting gastric cancers. However, the “original convolutional neural network (O-CNN)” employed in the previous study had a relatively low positive predictive value (PPV). Therefore, we aimed to develop an advanced AI-based diagnostic system and evaluate its applicability for the classification of gastric cancers and gastric ulcers.
Methods We constructed an “advanced CNN” (A-CNN) by adding a new training dataset (4453 gastric ulcer images from 1172 lesions) to the O-CNN, which had been trained using 13 584 gastric cancer and 373 gastric ulcer images. The diagnostic performance of the A-CNN in terms of classifying gastric cancers and ulcers was retrospectively evaluated using an independent validation dataset (739 images from 100 early gastric cancers and 720 images from 120 gastric ulcers) and compared with that of the O-CNN by estimating the overall classification accuracy.
Results The sensitivity, specificity, and PPV of the A-CNN in classifying gastric cancer at the lesion level were 99.0 % (95 % confidence interval [CI] 94.6 %−100 %), 93.3 % (95 %CI 87.3 %−97.1 %), and 92.5 % (95 %CI 85.8 %−96.7 %), respectively, and for classifying gastric ulcers were 93.3 % (95 %CI 87.3 %−97.1 %), 99.0 % (95 %CI 94.6 %−100 %), and 99.1 % (95 %CI 95.2 %−100 %), respectively. At the lesion level, the overall accuracies of the O- and A-CNN for classifying gastric cancers and gastric ulcers were 45.9 % (gastric cancers 100 %, gastric ulcers 0.8 %) and 95.9 % (gastric cancers 99.0 %, gastric ulcers 93.3 %), respectively.
Conclusion The newly developed AI-based diagnostic system can effectively classify gastric cancers and gastric ulcers.
Spherical and cylindrical shocks in a non-ideal dusty gas with magnetic field under the action of heat conduction and radiation heat flux
Authors: Sahu P. K. 
Published: June 2020

In this article, the propagation of spherical or cylindrical shock waves in a mixture of small solid particles of microsize and a non-ideal gas with conductive as well as radiative heat fluxes are studied under the influence of an azimuthal or axial magnetic field. The solid particles are uniformly distributed in the mixture, and the shock wave is assumed to be driven by a piston. It is assumed that the equilibrium flow conditions are maintained and the moving piston continuously supplies the variable energy input. The density of the undisturbed medium is assumed to be constant in order to obtain the self-similar solutions. Heat conduction is expressed in terms of Fourier’s law, and the radiation is considered to be of diffusion type for an optically thick gray gas model. The thermal conductivity and the absorption coefficient are assumed to vary with temperature and density. Numerical calculations have been performed to obtain the flow profiles of variables. The effects of different values of the non-idealness parameter, the strength of the magnetic field, the mass concentration, the ratio of the density of solid particles to the initial density of the gas, the piston velocity index, and the adiabatic index are shown in detail. It is interesting to note that in the presence of an azimuthal magnetic field, the pressure and density vanish at the piston, and hence, a vacuum is formed at the center of symmetry, which is in excellent agreement with the laboratory condition to produce the shock wave.
The author of the article agrees to the retraction of the article effective AUGUST 20, 2021.
The novel combinations of CTB, CpG, and aluminum hydroxide significantly enhanced the immunogenicity of clumping factor A 221-550 ofStaphylococcus aureus
Authors: Ma Jinzhu , Wang Beiyan , Yu Liquan , Song Baifen , Yu Yongzhong , Wu Shuangshuang , Dong Yazun , Zhu Zhanbo , Cui Yudong 
Published: June 2020

AbstractHere, we prepared the novel combined adjuvants, CTB as intra-molecular adjuvant, CpG and aluminum hydroxide (Alum) to strengthen the immunogenicity of clumping factor A221-550 of Staphylococcus aureus (S. aureus). The protein-immunoactive results showed CTB-ClfA221-550 elicited the strong immune responses to serum from mice immunized with CTB and ClfA221-550, respectively. The mice immunized with CTB-ClfA221-550 plus CpG and Alum adjuvant exhibited significantly stronger CD4+ T cell responses for IFN-γ, IL-2, IL-4, and IL-17 and displayed the higher proliferation response of splenic lymphocytes than the control groups, in addition, these mice generated the strongest humoral immune response against ClfA221-550 among all groups. Our results also showed CTB-ClfA221-550 plus CpG and Alum adjuvant obviously increased the survival percentage of the mice challenged by S. aureus. These data suggested that the novel combined adjuvants, CTB, CpG, and Alum, significantly enhance the immune responses triggered with ClfA221-550, and could provide a new approach against infection of S. aureus.AbbreviationsCTB: Cholera Toxin B; CpG: Cytosine preceding Guanosine; ODN: Oligodeoxynucleotides; Alum: Aluminum hydroxide; TRAP: Target of RNAIII-activating Protein; TLR9: Toll-like Receptor 9; TMB: 3, 3ʹ, 5, 5ʹ-tetramethylbenzidine; mAbs: Monoclonal Antibodies; OD: Optical Densities; S. aureus: Staphylococcus aureus; ClfA: Clumping factor A; FnBPA: Fibronection-binding protein A; IsdB: Iron-regulated surface determinant B; SasA: Staphylococcus aureus Surface Protein A; GapC: Glycer-aldehyde-3-phosphate dehydrogenase-C
Regional income management information system with Enterprise Architecture Planning Approach (EAP): a case study in BPKPD Klungkung Regency
Authors: Darmita I B G A , Dantes G R , Candiasa I M 
Published: June 2020

Abstract
Financial and Revenue Management Agency (BPKPD) Klungkung is a type of agency that carries out financial support functions to assist the Regent of Klungkung in administering regional autonomy. Although the regional revenue is in considerable amount, BPKPD Klungkung has no guidance in developing a regional revenue management information system in Klungkung. Thus, a good, efficient, effective, and accountable local revenue management procedure becomes essential. One of the options is to employ information systems and information technology (SI/IT) through the implementation of applications in various organizational functions. Enterprise Architecture Planning (EAP) is a method or frame of reference in building an information architecture that focuses on business needs that consist of data architecture, applications, and technology as well as the implementation plan of architecture created to support business activities to achieve the organization objectives. The result of the research using EAP showed that data architecture methodology was first to be defined so as to produce 19 data entities, defining the application architecture and technology. Based on application portfolio, there were 6 key operational applications 2 strategic applications, 2 high potential applications, and 1 supporting application displayed. It was expected that the regional revenue of Klungkung will be optimized through the strategic information system planning using EAP.
Comparison of microcontroller-based and mechanically controlled water rate control systems in solar energy water distillation
Authors: Parikesit E , Sambada F R 
Published: June 2020

Abstract
The current problem of solar energy water distillation is in its low efficiency. The commonly used mechanical control system still has weaknesses such as the instability of the water entering the absorber. This causes less effective evaporation of water so that the resulting distillation efficiency is not optimal. The microcontroller-based input water rate control system allows the rate of input water with a small but continuous flow rate so that the water evaporation process can be more effective. This study aimed at comparing the stability of the flow rate of water in the distillation device using a microcontroller flow regulator compared to the mechanical flow regulator. The stability of the flow was measured by changes in the rate of inflow of water to the initial rate of water flow. The research was carried out by the experimental method. The results of this study indicated that regulating the flow of water in a distillation device with a peristaltic flow control produced a more constant flow than a mechanical regulator. The change in the flow rate of inflow to the smallest initial flow rate with a peristaltic regulator was 0.2% at the variation of the initial flow rate of 1.2 liters/hour. The change in the mechanical regulating flow rate at a variation of the 1.2 liter/hour flow rate was 20%. From the results of this study, it can also be concluded that microcontroller based water rate controller is more stable than mechanical water flow control, especially in small flow.
Comparative study of classification method on diagnosis of plasmodium phase
Authors: Maysanjaya I M D 
Published: June 2020

Abstract
Malaria is a plague in humans induced by the Plasmodium parasitoid transferred through a single bite of female Anopheles mosquitoes. Once reaching human blood passage, this parasitoid bears asexual proliferation which is classified toward three phases (trophozoite, schizont, and gametocyte). To discover the phases, the paramedic will analyse the blood specimen of the subject within the microscope. However, the aforementioned approach has the potential to misdiagnosis. Many CAD-based investigations have been carried out to reduce the diagnosis errors that have formed. This research sought to develop a CAD-based design that can help paramedics in diagnosing the parasitoid Plasmodium, including trying to get a classification algorithm that is able to analyze the Plasmodium phase precisely. Based on the experiment outcome, Naïve Bayes was mostly useful applied as a classifier that attained the accuracy of 97.29%, the sensitivity, and specificity of 97.30% toward the P.vivax case. In the case of P.falciparum, it emerged in the accuracy, sensitivity, and specificity of 98.36%, 98.40%, and 98.40% apiece. Meantime, Perceptron was a useless algorithm applied as a classifier that realized the accuracy up to 81.08%, sensitivity and specificity of 93.80% on each. In the case of P.vivax, the accuracy, sensitivity, and specificity realized were 80.33%, 92.50%, and 92.50% respectively.
Balinese glyph recognition with gabor filters
Authors: Kesiman M W A , Pradnyana G A , Maysanjaya I M D 
Published: June 2020

Abstract
Recognizing Balinese glyphs from the Balinese script on palm leaf manuscripts is not trivial. In Balinese script, there are more than a hundred glyphs which represent basic syllables and compound syllables, and also some punctuation marks. They naturally share a strong interclass similarity between each other related to the form of their writing curves. The degraded image of textured palm leaf manuscript also offer some challenging parts in recognizing the Balinese glyph. In this paper, we investigated the use of Gabor filter bank as the feature extraction method to recognize the Balinese glyphs. By using Gabor filter, we can detect many texture variations with different orientations and frequencies. In our experiments, the published dataset of AMADI_LontarSet for glyph recognition was used. It showed a very promising result by using a single hidden layer Neural Network as the classifier. Gabor filters with Zoning method achieved a high enough recognition rate. For future works, Gabor filters will be analyzed in combination with the Histogram of Gradient, Neighborhood Pixel Weight and Kirsch Edges features.
Melajah pupuh BALI application “anggita” as a medium of learning in multimedia
Authors: Aditama P W , Aditya I N A F , Radhitya M L , Ningsih K A A 
Published: June 2020

Abstract
With the industrial revolution 4.0, technology is important to be utilized in various fields. Technology is a medium to support education especially at elementary school level. Technology in the cultural sphere is an important thing in the current era, such as the use of software application for preserving Balinese culture. This application teaches how to sing the Balinese poems correctly for beginners. There are three buttons that go into pupuh Ginada, Ginanti, Pucung and are supported by video. As sustainable development, the role of the AngGita application is relevant to be applied in the field of multimedia learning, because it increases the effectiveness of delivering information to students. Since, this application was published on July 6, 2019, it ranked 4.6 within 5 months and has been downloaded more than 100 downloads with the Android version 8.1. Conceptually, this application is in line with governor regulation number 80 of 2018.
Improving self-efficacy in the teaching of prospective mathematics teachers by involving them in the online teacher community
Authors: Mertasari N M S , Candiasa I M 
Published: June 2020

Abstract
Self-efficacy in teaching is very important for prospective teachers. Prospective teachers who have good self-efficacy inteaching can carry out the profession as a teacher well in the future. This study aims to improve the self-efficacy in teaching of prospective mathematics teachers by involving them in the online teacher community. A total of 58 prospective mathematics teachers were included as samples. They were divided into two groups. The experimental group attended micro teaching courses while involved in the online teacher community, on the other hand the control group attended a micro teaching course while assisting the model teacher. Self-efficacy in teaching was measured by a questionnaire at the beginning of the semester as a pre-test and at the end of the semester as a post-test. The results showed that prospective mathematics teacher who took micro teaching courses while involved in the online teacher community experienced a higher increase in self-efficacy compared to those who attended micro teaching courses while assisting the model teacher. These results indicate that the association of prospective mathematics teachers in the online teacher community has a positive effect on increasing their self-efficacy in teaching. In-depth interviews indicate that a combination of synchronous and asynchronous communication plays a role in increasing their self-efficacy. Computer-mediated communication that is context-free and not too bound by social conventions greatly helps increase the self-efficacy of prospective teachers.
A practical method of accurate troubleshooting mechanism in the decision objective teaching type on the integrated landing system
Authors: Ema  , Hendrarini N 
Published: June 2020

Abstract
An aircraft is a transportation system that works in conditions according to the standards. When an aircraft technician is aware of a system failure or damage, he must make the right decision to overcome the problems that occur. A relatively high level of accuracy decision making based is a necessary treat. This condition must be anticipated in aircraft vocational education. An integrated landing system is one of the subsystems on an aircraft that requires quick and precise handling if there are problems. A practical method that accommodates various concepts in troubleshooting is proposed to facilitate aircraft technicians’ competence. This method performs standardization of troubleshooting steps in a particular algorithm so that it is more systematic. The appropriate validation and verification steps follow this troubleshooting mechanism to ensure that the system is up to standard.
Development of TRIZ based competency test material and its influence on improving problem solving skills
Authors: Cahyono E A B , Artanto D , Arbiyanti P , Heliarko G 
Published: June 2020

Abstract
Vocational education provides necessary education and skills, which is directed at the mastery of certain expertise. As the learning outcome of this education, the graduates of Politeknik Mekatronika Sanata Dharma have been able to solve engineering problems in terms of maintenance and repair, operation, and assembly of industrial automation machines. For this reason, problem solving skills are important to learn. This paper presents a research on the effect of developing TRIZ-based competency test material on improving problem solving skills. The subjects of this study were 60 students of Politeknik Mekatronika Sanata Dharma. After several TRIZ-based competency tests, the results revealed that the problem solving skills of students on the basis of a systematic approach have increased, while problem solving on the basis of intuition (trial and error) have decreased.
Revisiting assessment of heat and mass transfer in contact apparatus for steam treatment of air
Authors: Averkin A G , Eremkin A I , Greysukh G I , Averkin Y A 
Published: June 2020

Abstract
Modified methods are proposed for determining the surface area of heat and mass transfer in the contact apparatus in the humidification, cooling, dehumidification of air with water, as well as dehumidification of air with solid drying agent, based on the number of transfer units. The number of transfer units is determined by the method of graphical integration using I-d-diagram of humid air to evaluate both heat and mass transfer process.