bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening of tumor microenvironment-related prognostic genes in breast cancer by data mining
Authors: LI Yunhui , REN Na 
Published: February 2020

Abstract
Background Accumulating evidence has demonstrated that the components of tumor immune microenvironment (TME) play important roles in breast cancer (BC) initiation, progression and prognosis. Materials and methods We downloaded the TCGA, GSE12276, GSE58812 and GSE42568 datasets. We calculated the immune scores and tumor immune infiltrating cells (TIICs) of TCGA-BRCA and GEO datasets using ESTIMATE and CIBERSORT algorithm, respectively. Then, the overlapping immune-related differentially expressed genes (DEGs) were screened using R ‘limma ’ package between TCGA and GSE12276 datasets. The GO and KEGG enrichment analysis were used to predict the function and signaling pathways of common DEGs. Finally, we extracted a series of tumor immune microenvironment-related genes, and explore the relationship between these genes and clinical outcomes in TCGA, GSE58812 and GSE42568 datasets. Results Based on the ESTIMATE algorithm, the immune scores were significantly associated with cancer types, as well as overall survival in BC patients. The fractions of some TIICs, such asnaïve B cells, memory B cells, CD8 + T cells, resting CD4 + memory T cells, activated CD4 + memory T cells, resting NK cells, monocytes, macrophage M0, M1, M2, resting DCs, activated DCs and resting mast cells, were significantly different between low and high immune score groups (all P <0.05). The DEGs between low and high immune score groups were mainly involved in immune-related biological processes, including adaptive immune response, innate response and inflammatory response. Finally, we found that ACSL5, GIMAP2, HLA-DRA and CLEC10A were significantly associated with prognosis among TCGA, GASE58812 and GSE42568 datasets (all P <0.05). Conclusion These findings provide a more comprehensive understanding of immune cells and immune-related genes within TME as well as prognosis-related genes in BC. Future studies need to perform in vivo and in vitro experiments to clarify the mechanisms of these genes in TME and provide a comprehensive idea to immune therapy.
Helicobacter pylori genotypes, salt intake, and sociodemographic factors associated with premalignant gastric lesions in a Colombian population. A case control study.
Authors: Carlosama Yeison Harvey , Astaiza Claudia Patricia Acosta , Torres Carlos Hernan Sierra , Bravo Harold Bolaños 
Published: February 2020

Abstract
IntroductionGenetic variability of Helicobacter pylori is associated with various gastrointestinal diseases; however, little is known about its interaction with sociodemographic and dietary factors in the development of premalignant lesions.ObjectiveTo evaluate the association among Helicobacter genotypes, salt intake, and sociodemographic factors associated with precursor lesions of the stomachMaterials and MethodsAn analytical study was conducted including cases (patients with gastric atrophy, intestinal metaplasia, and gastric dysplasia) and controls (patients with nonatrophic gastritis). Sociodemographic information and information about salt intake were obtained using a questionnaire. Histopathological diagnosis was performed according to the Sydney System. The cagA and vacA genotypes were established using polymerase chain reaction in paraffin blocks. ANOVA was used for analyzing quantitative variables. Categorical variables are presented as proportions and absolute frequencies. The effect of each variable on the study outcome (premalignant lesion) is presented as odds ratio (OR) and 95% CI. A p-value of <0.05 was considered as statistically significant.ResultsThe vacA/s1m1 genotype increases the risk of developing precursor lesions of the stomach (OR: 3.82, 95% CI: 1.45–10.07, p = 0.007). Age and salt intake showed a positive interaction with the s1m1 genotype (adjusted OR: 5.19, 95% CI: 1.88–14.32, p = 0.001) and with bacterial coinfection (adjusted OR: 3.2, 95% CI: 1.06–9.59, p = 0.038). The cagA genotype was not correlated to the development of premalignant lesions of the stomach (OR: 1.21, 95% CI: 0.80–1.82, p = 0.361).ConclusionsThe vacA genotype, age, and salt intake are indicators of the risk of developing premalignant lesions of the stomach in the study population.
Application of Alphaviral Vectors for Immunomodulation in Cancer Therapy
Authors: Zajakina Anna , Spunde Karina , Lundstrom Kenneth 
Published: February 2020

Background:
The lack of specific and efficient cancer therapies has influenced the development of
novel approaches, such as immunotherapy, which from its original application of immunogenic protein delivery
has developed into the use of more sophisticated recombinant gene delivery methods to achieve better safety and
efficacy profiles. This approach involves viral and non-viral delivery systems.

Methods:
Expression vectors have been engineered for alphaviruses, including Semliki Forest virus, Sindbis virus
and Venezuelan equine encephalitis virus. For immunotherapeutic applications, recombinant particles, RNA
replicons and layered DNA vectors that express tumor-associated antigens (TAAs) and cytokines have been studied
in animal models and in a few clinical trials.

Results:
Immunization studies with TAAs and cytokines have elicited strong antibody responses and vaccination
has provided protection against challenges with tumor cells in mouse models. Furthermore, the combination of
TAAs and cytokines, antibodies and growth factors and the co-administration of chemotherapeutics and bacteriabased
adjuvants have enhanced immunogenicity. Intratumoral and systemic delivery of recombinant alphavirus
particles has demonstrated significant tumor regression and prolonged survival rates in rodent tumor models.

Conclusion:

Alphavirus-based immunotherapy represents a rapid and efficient method for prophylactic and
therapeutic applications in animal models.
Integrating Regulatory Drug Label Information to Facilitate Evaluation of Adverse Events in Pharmacovigilance
Authors: Hui Tom Z. 
Published: February 2020

Background:
Efficiency and accuracy for signal detection and evaluation activities are
integral components of routine Pharmacovigilance (PV) practices. However, an Individual Case
Safety Report (ICSR) may consist of a variety of confounders such as Concomitant Medications
(CM), Past Medical History (PMH), and concurrent medical conditions that influence a safety officer’s
evaluation of a potential Adverse Event (AE). Limited pharmacovigilance systems are currently available
as a tool designed to enhance the efficiency and accuracy of signal detection and management.

Objective:
To introduce a systemic approach to make critical safety information readily available
for users in order to discern possible interferences from CM and make informed decisions on the
signal evaluation process – saving time while improving quality.

Methods:
Oracle Empirica Signal software was utilized to extract cases with CM that are Known
Implicating Medications (KIM) for each AE according to public regulatory information from drug
labels – FDA Structured Product Labeling (SPL) or EMA Summary of Product Characteristics
(SPC). SAS Enterprise Guide was used to further process the data generated from Oracle Empirica
Signal software.

Results:
For any target drug being evaluated for safety purposes, a KIM reference table can be generated,
which summarizes all potential causality contributions from CMs.

Conclusion:
In addition to providing standalone KIM table as reference, adoption of this concept
and automation may also be fully integrated into commercial signal detection and management
software packages for easy use and accessibility and may even lead to reduced False Positive rate in
signal detection within the PV space.
Barriers and Facilitators in Conducting Clinical Trials in Inflammatory Bowel Disease: A Monocentric Italian Survey
Authors: Larussa Tiziana , Suraci Evelina , Marasco Raffaella , Imeneo Maria , Dumitrascu Dan L. , Abenavoli Ludovico , Luzza Francesco 
Published: February 2020

Background:
Clinical therapeutic trials are a fundamental tool for identifying and testing
new categories of drugs useful for ensuring clinical benefit in patients with Inflammatory Bowel
Diseases (IBD). A number of difficulties may affect the recruitment process in large clinical trials.

Objectives:
In order to increase the involvement of patients within clinical trials in IBD therapy, it is
necessary to identify which factors could facilitate or discourage participation. The aim of this study
was to evaluate the factors influencing the participation in clinical trials in a consecutive series of patients
with IBD from a single referral center from Southern Italy.

Methods:
Consecutive patients with Crohn´s Disease (CD) and Ulcerative Colitis (UC) were recruited
to complete a questionnaire dealing with their knowledge about clinical trials and attitudes towards
participation. Patients also completed the Short Inflammatory Bowel Disease Questionnaire
(S-IBDQ) to investigate their Quality of Life (QoL). Demographic and clinical data were recorded.

Results:
Of the 145 consecutive patients invited to the survey, 132 completed the survey (91%
response rate). Of them, 67% claimed their willingness to take part in a clinical therapeutic trial for
IBD. Multivariate analysis showed a significant positive association between interest in clinical trials
and previous experience (p = 0.014), high education (p < 0.001), poor QoL (p = 0.016), money
retributions (p = 0.03) and informative materials (p = 0.02). On the other hand, a long-standing
disease (p = 0.017), the possibility of receiving a placebo (p = 0.04) and the frequent colonoscopies
required by the study protocol (p = 0.04) were significantly associated with the lack of interest in
clinical trials.

Conclusion:
In a native local resident series of IBD patients, the majority of the patients were willing
to participate in a clinical therapeutic trial. A long-standing disease, placebo and invasive procedures
represented a barrier to enrollment while previous experience, high education, monetary compensation
and adequate information could be facilitative. Knowing barriers and facilitators affecting participation
in IBD clinical trials is of fundamental importance in order to increase the involvement of patients
in research and explore new treatment opportunities.
Classification of Chromosomal DNA Sequences Using Hybrid Deep Learning Architectures
Authors: Du Zhihua , Xiao Xiangdong , Uversky Vladimir N. 
Published: February 2020

Background:
Chromosomal DNA contains most of the genetic information of
eukaryotes and plays an important role in the growth, development and reproduction of living
organisms. Most chromosomal DNA sequences are known to wrap around histones, and
distinguishing these DNA sequences from ordinary DNA sequences is important for understanding
the genetic code of life. The main difficulty behind this problem is the feature selection process.
DNA sequences have no explicit features, and the common representation methods, such as onehot
coding, introduced the major drawback of high dimensionality. Recently, deep learning models
have been proved to be able to automatically extract useful features from input patterns.

Objective:
We aim to investigate which deep learning networks could achieve notable
improvements in the field of DNA sequence classification using only sequence information.

Methods:
In this paper, we present four different deep learning architectures using convolutional
neural networks and long short-term memory networks for the purpose of chromosomal DNA
sequence classification. Natural language model Word2vec was used to generate word embedding
of sequence and learn features from it by deep learning.

Results:
The comparison of these four architectures is carried out on 10 chromosomal DNA
datasets. The results show that the architecture of convolutional neural networks combined with
long short-term memory networks is superior to other methods with regards to the accuracy of
chromosomal DNA prediction.

Conclusion:
In this study, four deep learning models were compared for an automatic classification
of chromosomal DNA sequences with no steps of sequence preprocessing. In particular, we have
regarded DNA sequences as natural language and extracted word embedding with Word2Vec to
represent DNA sequences. Results show a superiority of the CNN+LSTM model in the ten
classification tasks. The reason for this success is that the CNN module captures the regulatory
motifs, while the following LSTM layer captures the long-term dependencies between them.
Corynebacterium Striatum, an Emerging Nosocomial Pathogen: Case Reports
Authors: Datta Priya , Gupta Varsha , Gupta Menal , Pal Kritika , Chander Jagdish 
Published: February 2020

Background::
Corynebacterium striatum is an emerging nosocomial pathogen, capable
of causing a variety of infections in immunocompromised and hospitalized patients.

Case Presentation:
We describe three cases of infection by C. striatum that were initially considered
as contamination. Clinical suspicion in the wake of predisposing factors and accurate identification,
using the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
(MALDI-TOF MS), were key to implicate this commensal bacterium as a cause of infection.
New Generalized Intuitionistic Fuzzy Divergence Measure with Applications to Multi-Attribute Decision Making and Pattern Recognition
Authors: Umar Adeeba , Saraswat Ram N. 
Published: February 2020

Background:
The notion of fuzzy set was introduced by Zadeh. After that, many researchers
extended the concept of fuzzy sets in different ways. Atanassov introduced the concept
of intuitionistic fuzzy sets as an extension of fuzzy sets. This concept is applied in many fields such
as bio-informatics, image processing, decision making, feature selection, pattern recognition, etc.

Objectives:
The prime objective of this paper is to introduce a new generalized intuitionistic fuzzy divergence measure with proof of its validity and discussions on its elegant properties. Applications of the proposed divergence measure in multi-attribute decision making and pattern recognition are also discussed with some numerical illustrations. Further, the proposed divergence measure is compared with other methods for solving MADM and pattern recognition problems which exist in the literature.

Methods:
The divergence measure method is used to measure the divergence between two given
sets. In addition, the results of the other existing measures are also given to compare with the proposed
measure.

Results:
It was observed that the proposed divergence measure found much better results in comparison
with the other existing methods.

Conclusion:
A new divergence measure for intuitionistic fuzzy sets is introduced with some of its
properties. Applications of the proposed divergence measure to pattern recognition and MADM are
illustrated through examples. The comparison of the proposed method with the existing methods
shows the legacy of the results of the proposed method. It is concluded that the proposed divergence
measure is effective for solving real-world problems related to MADM and pattern recognition.
Hubungan pola asuh orang tua dengan kemandirian anak
Authors: Lestari Mira 
Published: February 2020

Penelitian ini bertujuan untuk mengetahui hubungan pola asuh orang tua dengan kemandirian anak kelompok B di gugus VIII Kasihan, Bantul. Penelitian ini merupakan penelitian kuantitatif dengan metode korelasi. Populasi penelitian ini adalah anak kelompok B di gugus VIII Kasihan. Teknik sampling yang digunakan adalah random sampling dengan jumlah 106 anak. Metode pengumpulan data menggunakan kuesioner dan lembar observasi. Metode analisis yang digunakan yaitu analisis diskriptif dan analisis statisik nonparametik dengan teknik chi square. Berdasarkan hasil penelitian diperoleh sebanyak 34,9% anak memiliki tingkat kemandirian rendah dan 65,1% memiliki tingkat kemandirian tinggi. Sebanyak 15,1% orang tua menggunakan pola asuh autoritarian dan 84,9% menggunakan pola asuh autoritative. Pola asuh dengan kemandirian anak memiliki hubungan yang signifikan dengan nilai X2 sebesar 11,335. Pola asuh autoritaive memiliki kontribusi lebih dalam menumbuhkan kamendirian anak daripada pola asuh autoritarian. AbstractThe objective of this study is to determine relationship of parenting with independence of children in gruob B at gugus VIII Kasihan, Bantul. This study a quantitative research with correlation method. The pupulation of this study were children in groub B at gugus VIII Kasihan.. The sampling technique used was random sampling with total of 106 children. Methods of collecting data using questionnaries and observation sheets. The analytical methods used is descriptive analysis and nonparametic static analysis with the chi square technique. Based on the results of the study, 34,9 % of children had a low level of independence and 65,1% high. A total of 15,1% of parents use authoritarian parenting and 84,9% of parents use democratic parenting. Parenting with the independance of children has a significant relationship with the resuls X2 of 11,335. Authoritative parenting have more contributes to develop children independence than authoritarian parenting.
Utilization of indonesian megabiodiversity for integrated science learning with nationalism values to develop concepts understanding and soft security among students of border areas
Authors: Sukardiyono Sukardiyono , Rosana Dadan 
Published: February 2020

This research aimed at (1) producing Subject Specific Pedagogic (SSP) of integrated science learning with nationalism values by utilizing Indonesian megabiodiversity which is valid and practical for the students of border areas, (2) obtaining empirical test results on the effectiveness of SSP integrated science learning with nationalism values by utilizing Indonesian megabiodiversity to improve the quality of students’ learning outcomes and soft security in border area. The SSP was prepared through a research design referring to "Prototypal Studies" as put forward by Akker (1999) and Plomp (2001). The important thing that needs to be considered in the development research is the quality of the produced learning tools (product). Plomp (2001) has pointed out the product quality criteria, namely: valid (reflects state-of-the-art knowledge and internal consistency), added value, practical, and effective. This research is intended to solve the problems of junior high schools in the region of (1) Atambua, Belu Regency, East Nusa Tenggara Province, and (2) Entikong, Sanggau Regency, West Kalimantan Province. The reserach results showed that SSP science learning integrating Indonesian megabiodiversity utilization with nationalism values was valid, practical and effective to develop concepts understanding and soft security among students in border areas schools.
Models and a Tecnique for Determining the Speech Activity of a User of a Socio-Cyberphysical System
Authors: Usina E. E. , Shabanova A. R. , Lebedev I. V. 
Published: February 2020

Purpose of reseach. The article presents the development of the model-algorithmic support for the process of determining the speech activity of a user of a socio-cyberphysical system. A topological model of a distributed subsystem of audio recordings implemented in limited physical spaces (rooms) is proposed; the model makes it possible to assess the quality of perceived audio signals for the case of distribution of microphones in such a room. Based on this model, a technique for determining the speech activity of a user of a socio-cyberphysical system, which maximizes the quality of perceived audio signals when a user moves in a room by means of determining the installation coordinates of microphones has been developed. Methods. The mathematical tools of graph theory and set theory was used for the most complete analysis and formal description of the distributed subsystem of the audiorecording. In order to determine the coordinates of the placement of microphones in one room, a relevant technique was developed; it involves performing such operations as emitting a speech signal in a room using acoustic equipment and measuring signal levels using a noise meter in the places intended for installing microphones. Results. The dependences of the correlation coefficient of the combined signal and the initial test signal on the distance to the signal source were calculated for a different number of microphones. The obtained dependences allow us to determine the minimum required number of spaced microphones to ensure high-quality recording of the user’s speech. The results of testing the developed technique for determining speech activity in a particular room indicate the possibility and high efficiency of determining the speech activity of a user of a socio-cyberphysical system. Conclusion. Application of the proposed technique for determining the speech activity of a user of a sociocyberphysical system will improve the recording quality of the audio signal and, as a consequence, its subsequent processing, taking into account the possible movement of a user.
Study of the Effectiveness of the Application of Information Technology in the Technosphere Safety Management System
Authors: Popov V. M. , Yushin V. V. , Iordanova A. V. , Trifonov A. P. 
Published: February 2020

Purpose of research. The purpose of this study is to assess the potential of applying information technology, in particular mobile multifunction devices, as an additional type of control of harmful production factors in the field of labour protection.Methods. One of the main techniques used in this study is an experiment involving laboratory measurements of the level of artificially created production noise using a mobile multifunction device (smartphone) with pre-installed utilities and a calibrated device ‒ noise meter, and subsequent comparison of the results. The measurements were carried out in accordance with the methodological guidelines developed specially for mobile multifunction devices (MMFDs) by the authors. Results. An analysis of the results obtained made it possible to assess the possibility of applying mobile multifunction devices in monitoring harmful factors in the work environment. While conducting the research, it was found that it is possible to use MMFDs in the occupational safety management system of the enterprise, since the deviations of the obtained values from the values of the calibrated noise meter adopted as the standard are insignificant. According to the results of the study, a flow diagram for the use of mobile multifunctional devices in occupational safety management systems of an enterprise was developed. Conclusion. Thus, the use of MMFDs as an additional means of controlling the parameters of the production environment from the theoretical point of view is possible. It should be noted that in practice, application of MMFDs in the occupational safety management system will be challenging from legal and methodological viewpoints. The most basic problem is that MMFDs are not registered in the State Register of Measuring Equipment as measuring tools, which does not allow the official use of the data obtained. However, application of mobile multifunctional devices in the field of labour protection will ensure rapid collection of information on changes in indicators of harmful factors in the work environment, and as a result, will make it possible to quickly respond to these changes, which will significantly reduce the risk of accidents and occupational diseases.