bluuebunny/crossref_metadata_2025_split huggingface dataset:
TK1 in Cancer Progression: elucidating its influence on cellular invasion and survival
Authors: Bitter Eliza E. , Townsend Michelle H. , Tsai Kary Y.F. , Allen Carolyn I. , Erickson Rachel I. , Pickett Brett E. , Arroyo Juan A. , O'Neill Kim 
Published: November 2019

Abstract
1. Background: The salvage pathway enzyme thymidine kinase 1 (TK1) is elevated in the serum of several different cancer types and higher expression is associated with more aggressive tumor grade. As a result, it has potential as a biomarker for diagnosis and prognosis. Recent studies indicate that TK1 may be involved in cancer pathogenesis; however, its direct involvement has not been identified. We propose to evaluate the effects of TK1 on cancer progression in vitro through measuring cellular invasion and survival of breast cancer cells.2.Methods: Breast cancer cells MDA-MB-231, HCC 1806, and MCF7 were cultured according to standard techniques. We employed the use of TK1 target siRNA and a CRISPR-Cas9 TK1 knockout plasmid to compare transfected cell lines to wild type cell lines. Protein factors in survival and invasive pathways were also tested for correlations to TK1 in BRCA RNA-seq patient data (n=1095) using the TIMER program. Cellular invasion was quantified in cell index (factor of impedance) over a 24-hour period. Cell survival was measured by apoptosis under metabolic and DNA stress using flow cytometry. All results were statistically assessed using an ANOVA or t-test in GraphPad PRISM®.3.Results: Cellular invasion assays assessing wild type and TK1 knockdown/knockout (TK1-/-) cell types showed TK1-/- cell lines had increased invasion potential (p= 0.0001). Bioinformatically, we saw a strong overall negative correlation between apoptotic factors and TK1 (p ≤ 0.05). When testing TK1 effects on cell survival we saw a protective affect under DNA stress (p ≤ 0.05), but not under metabolic stress (p= 0.0001).4.Conclusion From cell cycle analysis, we observed a shift towards S phase in TK1-/- cells. This shift to S phase would promote growth and account for the increased cellular invasion and decrease in metabolic induced stress in TK1-/- cells. We propose that cancer cells still may elicit a cancer progressive phenotype based on effects of TK1, but that a system which isolates TK1 is not effective to understand the effects. Instead, identifying protein networks inclusive of TK1 will help to elucidate its effects on cancer progression.
Transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.)
Authors: Zhang Huali , Zhang Shiya , Zhang Hua , Chen Xi , Liang Fang , Qin Heland , Zhang Yue , Cong Richen , Xin Haibo , Zhang Zhao 
Published: November 2019

Abstract
Background: Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. Results: To study the mechanism underlying marigold petal color, we performed a metabolomics analysis and de novo cDNA sequencing on the inbred line ‘V-01’ and its petal color mutant ‘V-01M’ at four flower developmental stages. A total of 49,217 unigenes were identified from 24 cDNA libraries. Based on our transcriptomic and metabolomic analyses, we present an overview of carotenoid biosynthesis, degradation, and accumulation in marigold flowers. The carotenoid content of the yellow mutant ‘V-01M’ was higher than that of the orange inbred line ‘V-01’, and the abundances of the yellow compounds lutein, neoxanthin, violaxanthin, zeaxanthin, and antheraxanthin were significantly higher in the mutant. During flower development, the carotenoid biosynthesis genes were upregulated in both ‘V-01’ and ‘V-01M’, with no significant differences between the two lines. By contrast, the carotenoid degradation genes were dramatically downregulated in the yellow mutant ‘V-01M’. Conclusions: We therefore speculate that the carotenoid degradation genes are the key factors regulating the carotenoid content of marigold flowers. Our research provides a large amount of transcriptomic data and insights into the marigold color metabolome.
PET is only moderately informative regarding theranostic Ttarget HIF-1α expression in solid tumors: A meta-analysis
Authors: Surov Alexey , Schmidt Stefan A. , Prasad Vikas , Beer Ambros J. , Wienke Andreas 
Published: November 2019

Abstract
BACKGROUND: Hypoxia-inducible factor (HIF)-1α plays a key role in hypoxic adaptation of tumor cells. HIF-1α is overexpressed in solid tumor, directs the glucose metabolism pathway from oxidative to anaerobic pathway thereby reducing the oxygen consumption, decreases free radical level and thence prevents cancer cell death. 2-deoxy-2 [18F] fluoro-D-glucose (FDG) is taken up in solid tumors primarily regulated through glucose transporter 1 (GLUT-1) and hexokinase 2 which in turn are regulated by HIF-1α. Positron Emission Tomography (PET) with FDG allows semiquantitative delineation of GLUT-1 and Hexokinase 2 activity in tumor cells by standardized uptake value (SUV). There are inconsistent data about relationships between FDG-PET and HIF-1a. The purpose of the present analysis was to provide evidence regarding associations between FDG uptake measured as standardized uptake value (SUV) and HIF-1α expression in solid tumors.
METHODS: MEDLINE library, SCOPUS and EMBASE data bases were screened for relationships between SUVmax and HIF-1a up to August 2019. Overall, 21 studies with 1154 patients were identified. The following data were extracted from the literature: authors, year of publication, number of patients, and correlation coefficients.
RESULTS: Correlation coefficients between SUV and HIF-1α ranged from -0.51 to 0.71. The pooled correlation coefficient was 0.27, (95% CI = [0.14; 0.41]). Furthermore, correlation coefficients for specific tumor entities were calculated. For this sub-analysis, data for primary tumors with more than two reports were included. The calculated correlation coefficients in the analyzed subgroups were as follows: head and neck squamous cell carcinoma: ρ = 0.25 (95% CI = [0.07; 0.42]); non-small lung cell cancer: ρ = 0.27 (95% CI = [-0.14; 0.67]); uterine cervical cancer: ρ = -0.09 (95% CI = [- 0.89; 0.71]); thymic tumors: ρ = 0.39 (95% CI = [0.04; 0.58])
CONCLUSION: Published literature suggests wide heterogeneity and weak correlation between intensity of FDG uptake measured as SUVmax and expression of HIF-1a both in solid tumors in general and also in specific tumor subgroups. Because HIF-1α is a very important theranostic target, prospective state of the art studies are needed to elucidate the true potential of FDG PET in assessment of HIF-1α activity in solid tumors
BMP4-induced symmetry breaking in a 3D model of the human epiblast
Authors: Simunovic Mijo , Brivanlou Ali H. , Siggia Eric D. 
Published: November 2019

Abstract
We describe the protocol of generating a 3D stem-cell-based model of the human pre-gastrulation epiblast by culturing human embryonic stem cells in a mix of hydrogel and Matrigel. Much like the epiblast of an in vitro attached day-10 human embryo, this model is an epithelial sphere with a cavity at its center, it is expressing key pluripotency markers, and it displays apico-basal polarity. The 3D colonies can further be differentiated with morphogens and in the case of intermediate concentrations of BMP4, they break the anterior-posterior symmetry characterized by an asymmetric expression of a primitive streak marker and showing signs of epithelial to mesenchymal transition. The protocol described here is suitable for immunofluorescence staining and for live-cell imaging.
Gene Selection for the Discrimination of Colorectal Cancer
Authors: Wang Wenhui , Xie Guanglei , Ren Zhonglu , Xie Tingyan , Li Jinming 
Published: November 2019

Background:
Colorectal cancer (CRC) is the third most common cancer
worldwide. Cancer discrimination is a typical application of gene expression analysis
using a microarray technique. However, microarray data suffer from the curse of
dimensionality and usual imbalanced class distribution between the majority (tumor
samples) and minority (normal samples) classes. Feature gene selection is necessary
and important for cancer discrimination.

Objectives:
To select feature genes for the discrimination of CRC.

Methods:
We select out 16 single-gene feature sets for colorectal cancer discrimination
and 19 single-gene feature sets only for colon cancer discrimination.

Results:
In summary, we find a series of high potential candidate biomarkers or
signatures, which can discriminate either or both of colon cancer and rectal cancer with
high sensitivity and specificity.
Neuropharmacological and Neurogenetic Correlates of Opioid Use Disorder (OUD) As a Function of Ethnicity: Relevance to Precision Addiction Medicine
Authors: Abijo Tomilowo , Blum Kenneth , Gondré-Lewis Marjorie C. 
Published: November 2019

Background:
Over 100 people die daily from opioid overdose and $78.5B per year is
spent on treatment efforts, however, the real societal cost is multifold greater. Alternative strategies
to eradicate/manage drug misuse and addiction need consideration. The perception of opioid addiction
as a social/criminal problem has evolved to evidence-based considerations of them as clinical
disorders with a genetic basis. We present evaluations of the genetics of addiction with ancestryspecific
risk profiles for consideration.

Objective:
Studies of gene variants associated with predisposition to substance use disorders
(SUDs) are monolithic, and exclude many ethnic groups, especially Hispanics and African Americans.
We evaluate gene polymorphisms that impact brain reward and predispose individuals to
opioid addictions, with a focus on the disparity of research which includes individuals of African
and Hispanic descent.

Methodology:
PubMed and Google Scholar were searched for: Opioid Use Disorder (OUD), Genome-
wide association studies (GWAS); genetic variants; polymorphisms, restriction fragment
length polymorphisms (RFLP); genomics, epigenetics, race, ethnic group, ethnicity, ancestry, Caucasian/
White, African American/Black, Hispanic, Asian, addictive behaviors, reward deficiency
syndrome (RDS), mutation, insertion/deletion, and promotor region.

Results:
Many studies exclude non-White individuals. Studies that include diverse populations
report ethnicity-specific frequencies of risk genes, with certain polymorphisms specifically associated
with Caucasian and not African-American or Hispanic susceptibility to OUD or SUDs, and vice versa.

Conclusion:
To adapt precision medicine-based addiction management in a blended society, we
propose that ethnicity/ancestry-informed genetic variations must be analyzed to provide real precision-
guided therapeutics with the intent to attenuate this uncontrollable fatal epidemic.
Isoniazid-functionalized Fe3O4 Magnetic Nanoparticles as a Green and Efficient Catalyst for the Synthesis of 3, 4-dihydropyrimidin-2(1H)-ones and their Sulfur Derivatives
Authors: Moradi Farzaneh , Abdoli-Senejani Masumeh , Ramezani Majid 
Published: November 2019

Background:
A wide variety of dihydropyrimidins (DHPMs) exhibit pharmacological and
biological activities. Herein, an efficient one-pot synthesis of some 3, 4-dihydropyrimidin-2(1H)-one
derivatives is reported using Fe3O4 @SiO2–Pr-INH.

Objective:
Recently, several catalysts have been used to improve the Biginellis-reaction. However, some of
these catalysts have imperfections. Herein, a convenient method for the synthesis of 3, 4-dihydropyrimidin-
2(1H)-ones and their sulfur derivatives using Fe3O4 @SiO2–Pr-INH is reported.

Materials and Methods:
Firstly, the catalyst was synthesized through a simple four-step method. The Fe3O4
MNPs were synthesized using the chemical co-precipitation method, coated with a layer of silica using TEOS,
and then functionalized with CPTMS. Subsequently, a nucleophilic substitution of Cl by isoniazid resulted in
the formation of the magnetic Fe3O4@SiO2–Pr-INH. After the preparation and characterization of
Fe3O4@SiO2–Pr-INH, its catalytic activity was studied in the synthesis of 3, 4-dihydropyrimidin-2(1H)-one
derivatives. Following the optimization of the reaction conditions, several 3, 4-dihydropyrimidin-2(1H)-one
derivatives were synthesized by the reaction of ethyl acetoacetate or acetylacetone, thiourea or urea and
aromatic aldehydes at 80 °C under solvent-free conditions.

Results:
Isoniazid-functionalized Fe3O4 magnetic nanoparticles (Fe3O4@SiO2–Pr-INH) were prepared using
Fe3O4 with silica layer and their surface was modified with isoniazid. They were characterized successfully by
infrared spectroscopy, powder X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray
spectroscopy and were used for the synthesis of some 3, 4-dihydropyrimidin-2(1H)-one derivatives as
catalysts. Aromatic aldehydes with electron-donating or electron-withdrawing groups afforded 3, 4-
dihydropyrimidin-2(1H)-ones and their sulfur derivatives in good to excellent yields in short reaction times.

Conclusion:
Isoniazid-functionalized Fe3O4 magnetic nanoparticles (Fe3O4@SiO2–Pr-INH) were used as an
efficient catalyst for Biginelli-type synthesis of 3, 4-dihydropyrimidin-2(1H)-ones and 3, 4-dihydropyrimidin-
2(1H)-thiones in good to excellent yields and short reaction times. It is noteworthy that this method has several
advantages such as simple experimental procedures, the absence of solvent, environmentally benign process,
stability and reusability of the catalyst.
POCl3 Mediated Syntheses, Pharmacological Evaluation and Molecular Docking Studies of Some Novel Benzofused Thiazole Derivatives as a Potential Antioxidant and Anti-inflammatory Agents
Authors: Raut Dattatraya G. , Patil Sandeep B. , Choudhari Prafulla B. , Kadu Vikas D. , Lawand Anjana S. , Hublikar Mahesh G. , Bhosale Raghunath B. 
Published: November 2019

Background:
The present research work is focused on the development of alternative
antioxidant and anti-inflammatory agents. The review of the literature reveals that many
benzofused thiazole analogues have been used as lead molecules for the design and development
of therapeutic agent, including anticancer, anti-inflammatory, antioxidant and antiviral.
The synthesized benzofused thiazole derivatives are evaluated for in vitro antioxidant,
anti-inflammatory activities and molecular docking study. Thus, the present research work
aims to synthesize benzofused thiazole derivatives and to test their antioxidant and antiinflammatory
activities.

Objective:
To design and synthesize an alternative antioxidant and anti-inflammatory agents.

Methods:
The substituted benzofused thiazoles 3a-g were prepared by cyclocondensation reaction
of appropriate carboxylic acid with 2-aminothiophenol in POCl3 and heated for about
2-3 h to offer benzofused thiazole derivatives 3a-g. All the newly synthesized compounds
were in vitro screened for their anti-inflammatory and antioxidant activities by using a
known literature method.

Results:
At the outset, the study of in vitro indicated that the compounds code 3c, 3d and 3e
possessed distinct anti-inflammatory activity as compared to a standard reference. All the
tested compounds show potential antioxidant activity against one or more reactive (H2O2,
DPPH, SO and NO) radical scavenging species. Additionally, docking simulation is further
performed to the position of compounds 3d & 3e into the anti-inflammatory active site to determine
the probable binding model.

Conclusion:
New anti-inflammatory and antioxidant agents were needed; it has been proved
that benzofused thiazole derivatives were 3c, 3d and 3e constituted as an interesting template
for the evaluation of new anti-inflammatory agents and an antioxidant’s work also may provide
an interesting template for further development.
Ионно-пучковые и рентгеновские методы элементной диагностики тонкопленочных покрытий
Authors: Егоров В.К. , Егоров Е.В. , Афанасьев М.С. 
Published: November 2019

Abstract We show how the combined use of the methods of Rutherford backscattering of ions and X-ray fluorescence analysis under conditions of total external reflection of the flow of exciting hard X-ray radiation and registration of the X-ray radiation output during ion excitation allows to effectively diagnose the elemental composition of thin-film coatings and films of dry residues of liquids. These methods and the features of their experimental application are briefly described. Examples of the complex methodological analysis of real objects are given. The possibility of increasing the efficiency of the methods of X-ray fluorescence analysis of materials due to the inclusion in the X-ray optical schemes of experimental measurements of flat X-ray waveguide resonators is indicated.
Zonasi Daerah Rawan Longsor Menggunakan Analisis Sistem Informasi Geografis Berdasarkan Metode AHP Pada Daerah Gunung Kidul Yogyakarta
Authors: Haris Bahrudin Muhammad Joko Umbaran 
Published: November 2019

<p class="E-TPABSTRACTTITINDO">Abstract</p><p class="E-TPABSTRACTINDO"> </p>Data from the Yogyakarta Regional National Survey and Mapping Coordinating Board (Bakosurtanal), disasters that often occur in Yogyakarta are landslides, droughts, tornadoes.In this study, the modeling of potential landslides in the Gunung Kidul area of Yogyakarta has been carried out using GIS analysis and scoring and weighting methods with reference to PU Candy No. 22 /PRT /M /2007 concerning the Guidelines for Landslide Disaster Prone Areas and the Analytical Hierarchy Process (AHP) method. The results were in the form of Three Zoning landslide prone areas, namely high potential found in three Hamlets namely Kacangan Hamlet Hargomulyo Village located at N 42º E, Kedok Ploso N 186º E Hamlet, and Kembang Village Nglegi Hamlet N 160º E based on vulnerability maps landslides processed based on Permen PU No. 22 / PRT / M / 2007. While the Medium Zone is located in Karangduwet Hamlet, Ngalang Village N 95º E. The low vulnerability zone is located in Duwet Hamlet, Ngalang Village N 4º E. Criteria in the study area include lithology: 0,250, slope: 0,053, groundwater condition 0,304, soil structure: 0,161 , land cover: 0.102 and relative reief: 0.131 all criteria determination is based on landscape hazard evaluation factor (LHEF) which is processed based on AHP method and map overlay technique.
Inuit Early Child Care Centres
Authors: Pearson Landon 
Published: November 2019

The wisdom of the Inuit people (IQ) is a great resource to draw on for designing early childhood centres for all Indigenous children as well as for others in our increasingly diverse society. Respecting their rights, as the two settings described in this article do, can lighten the burden of trauma carried by so many children and, by building trust , release their humanity to the benefit of us all.
“Help Them Back Home”: Italian Fantasies of (Neoliberal) Inclusion from Buona Scuola to Salvini’s Government
Authors: Migliarini Valentina 
Published: November 2019

This paper explores how inclusive education in the Italian context has shifted from the Marxist model based on the solidarity of Integrazione Scolastica (see D’Alessio, 2011) to a neoliberal approach which targets Black migrant and forced-migrant children. The introduction of Renzi’s policy reform, Buona Scuola, marked this shift towards neoliberal inclusion, and the current far-right government, led by Salvini, adds a populist character to it, evident in his mantra of “helping them back home”. Drawing from Butler’s (1997) notions of subjectivation and referring to Tomlinson’s (1982) concept of benevolent humanitarianism, the paper analyzes how Italian educators conceptualize the inclusion of migrants and refugees through neoliberal fantasies. However, the space of neoliberal inclusion is ableist, racist, and exclusionary. Ultimately, the paper advances the intersectional approach of Disability Critical Race Theory (DisCrit) to (re)frame educational and social inclusion in Italy and to refute a neoliberal model that perpetuates racial disparities (Annamma, Connor, Ferri, 2013; 2016).
The Research Data Centre of the German Federal Employment Agency at the Institute for Employment Research (RDC-IAB)
Authors: Antoni Manfred , Schmucker Alexandra 
Published: November 2019

Background and data portfolioSince 2004, the Research Data Centre of the German Federal Employment Agency at the Institute for Employment Research (RDC-IAB) has been offering comprehensive individual data on employees, unemployed persons, job seekers and participants in active labour market policy programmes for scientific labour market research. For this purpose, data from employer notifications and from different administrative processes in the labour market administration are linked. These administrative data are also combined with survey data. In addition, linked employer-employee data allow simultaneous analyses of the supply and demand sides of the labour market.
Data linkageThe data can be linked using unique identifiers, such as social insurance numbers, client numbers from local employment agencies, or establishment numbers. Since the foundation of the German Record Linkage Center (GRLC) in 2011, the RDC-IAB also applies methods for linking with non-unique and error-prone linkage identifiers like names, addresses and birth dates.
Data accessGerman data protection law classifies the data offered by the RDC-IAB as highly sensitive and strictly regulates their use by external researchers. The RDC-IAB has therefore established various data access modes. Although data can be transferred directly to research institutions in anonymised form, this procedure is generally not effective for linked data, as the loss of information due to the necessary anonymisation would be too great. For this reason, the RDC-IAB focuses on the access modes on-site use and remote data execution. In cooperation with other data centres, RDC-IAB has therefore established on-site data access at currently 16 locations worldwide.