bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selecting optimal reference genes for breast cancer research
Authors: Song Qiang , Huang Man , Wu Guicheng , Dou Lu , Zhang Wenjin , Peng Yang , Wang Jiangen , Wang Chaoyi , Zhao Qiurong , Wu Shaobo , Luo Xiaohe , Zhang Jipan , Wang Mengyuan 
Published: October 2020

Abstract
Background Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes (RGs) is critical for normalizing and evaluating changes in the expression of target genes. However, uniform and reliable RGs for breast cancer research have not been identified, limiting the value of target gene expression studies. Here, we provide a novel approach for mining RGs by using the RNA-seq dataset to identify reliable and accurate RGs that can be applied to different types of breast cancer tissues and cell lines. Methods First, we compiled the transcriptome profiling data from the TCGA database involving 1217 samples to identify novel RGs and then ten genes (SF1, TARDBP, THRAP3, QRICH1, TRA2B, SRSF3, YY1, DNAJC8, RNF10, and RHOA) with relatively stable expression levels were chosen as novel candidate RGs. Additionally, six conventional RGs (ACTB, TUBA1A, RPL13A, B2M, GAPDH, and GUSB) were also selected. To determine and validate the optimal RGs we performed qRT-PCR experiments on 87 samples from 5 types of surgically excised breast tumor specimens including HR+HER2-, HR+HER2+, HR-HER2-, HR-HER2+, breast cancer after neoadjuvant chemotherapy (NAC) and their matched para-carcinoma tissues, furthermore, we also included a benign breast tumor sample. Six biological replicates were included for each tissue. Moreover, we assessed 7 breast cancer cell lines (MCF-10A, MCF-7, T-47D, MDA-MB-231, MDA-MB-468, as well as MDA-MB-231 with either CNR2 knockdown or overexpression; 3 biological replicates for each line). Five statistical algorithms (geNorm, NormFinder, ΔCt method, BestKeeper, and ComprFinder) were used to assess the stability of expression of each RG across all breast cancer tissues and cell lines. Results Our results show that RG combinations SF1+TRA2B+THRAP3 and THRAP3+RHOA+QRICH1 showed stable expression in breast cancer tissues and cell lines, respectively, and that these two combinations displayed good interchangeability. Therefore, we propose that the above two combinations are optimal triplet RGs for breast cancer research. Conclusions In summary, we identified novel and reliable RG combinations for breast cancer research based on a public RNA-seq dataset which lays a solid foundation for accurate normalization of qRT-PCR results across different breast cancer tissues and cells.
Prediction of Immune-Checkpoint Blockade Monotherapy Response in Patients with Melanoma Based on Easily Accessible Clinical Indicators
Authors: Byun Hwa Kyung , Chang Jeesuk , Jung Minkyu , Koom Woong Sub , Chung Kee Yang , Oh Byung Ho , Roh Mi Ryung , Kim Kyung Hwan , Lee Choong-Kun , Shin Sang Joon 
Published: October 2020

Abstract
Background: Immune checkpoint blocker (ICB) has shown significant clinical activity in melanoma. However, there are no clinically approved biomarkers to aid patient selection. We aimed to identify patients with advanced or metastatic melanoma who are likely to benefit from ICB monotherapy using easily accessible clinical indicators. Methods: We retrospectively reviewed the records of 134 patients with advanced or metastatic melanoma who received ICB monotherapy between 2014 and 2018. Prognostic factors of overall survival (OS) and progression-free survival (PFS) were determined using Cox regression analysis. Results: During the median follow-up of 13.7 months, the median OS and PFS were 18.4 and 3.4 months, respectively. Visceral/central nervous system (CNS) metastasis (OS: adjusted hazards ratio [HR], 1.82; p=.014; PFS: HR, 1.59; p=.024), lymphopenia (<1000 cells/µL) within 3 months (OS: HR, 1.89, p=.006; PFS: HR, 1.70; p=.010), and elevated baseline lactate dehydrogenase (LDH) level (OS: HR, 2.61; p<.001; PFS: HR, 2.66; p<.001) were independent prognostic factors for both poor OS and PFS. Development of immune-related adverse events (irAE; e.g., hypothyroidism or vitiligo) within 6 months showed a trend toward better OS in multivariate analysis (HR, 0.37; p=.058). Patients with normal LDH levels and no visceral/CNS metastasis had a substantially better OS than the others (median, 40.4 vs. 13.6 months; p<.001). Among others, patients who developed irAE within 6 months achieved long-term OS (median, 43.6 vs. 13.1 months; p=.008). A decision tree was suggested using four risk factors, and the risk stratification provided significant distinction between the survival curves. Conclusion: The four easily accessible clinical indicators associated with better treatment outcomes after ICB monotherapy in patients with advanced or metastatic melanoma were LDH level, the extent of disease, lymphopenia, and irAE. The combined use of these indicators can be clinically useful in improving risk stratification of patients treated with ICB monotherapy.
Accuracy of p16/Ki-67 dual staining for improved cervical cancer risk stratification in women aged ≤30 years with hr-HPV positive
Authors: Wang Xingmin , Wang Xindan , Wu Ping , Fu Jinjian , Yi Guixian , Xu Jianhua 
Published: October 2020

Abstract
Background: Cervical cancer (CC) is the most common malignancy inwomen on the earth. Cervical cancer usually develops from cervical intraepithelial neoplasia (CIN) grade 1 or above. Early detection of CIN1 or above precancerous lesion can effective control of cervical cancer incidence. The goal of this study was to evaluate the accuracy of p16/Ki67 dual staining in triaging hr-HPV positive population aged ≤ 30 years. Methods: A total of 336 women with an average age of 27.8 years old were included in this study. Liquid based cytology (LBC) samples were detected by p16/Ki67 immunocytochemical dual staining, liquid-based cytology, high-risk human papillomavirus (hr-HPV) and HPV 16/18 test. Diagnosis of each method was verified by histopathological test. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and AUC (area under the receiver operating characteristic curve, ROC curve) was obtained. Results: All assays had a high sensitivity for the detection of CIN2+. p16/Ki67 dual staining had similar sensitivity with hr-HPV test for CIN2+ detection (89.9% vs 93.9%, P = 0.781), and had similar sensitivity with LBC test (89.9% vs 82.7%, P=0.588). However, p16/Ki67 dual staining had higher specificity than that of both hr-HPV test (70.1% vs 25.5%, P<0.001) and LBC test (70.1% vs 38.9%, P=0.002) for CIN2+ detection. p16/Ki67 dual staining had bigger AUC (0.80) than that of hr-HPV test (0.60) and LBC test (0.61), the P value was 0.002, 0.003, respectively. The specificity of dual staining for CIN2+ detection in hr-HPV positive women was 70.1%, which was higher than that of LBC test (41.9%, P=0.020). Colposcopy referral rate of p16/Ki67 was lower than that of both hr-HPV and LBC (P=0.002, <0.001, respectively). HPV infection was significantly associated with p16/Ki67 expression in all patients. p16/Ki67 expression in HPV16/18 and other 15 types of hr-HPV infection was significantly higher than negative hr-HPV infection, odds ratio (OR) was 12.16 (95% confidence interval, 95% CI = 5.82-25.41) and 2.65 (95% CI = 1.27-5.51), respectively. Conclusions: p16/Ki67 dual staining has a good specificity of high-grade cervical lesions detection and is a promising tool in triage of CIN2+ and hr-HPV positive population and avoid over diagnosis and treatment.
Gastric Cancer Stem Cells Survive in Stress Environments via Their Autophagy System
Authors: Togano Shingo , Yashiro Masakazu , Masuda Go , Sugimoto Atsushi , Miki Yuichiro , Yamamoto Yurie , Sera Tomohiro , Kushiyama Shuhei , Nishimura Sadaaki , Kuroda Kenji , Okuno Tomohisa , Ohira Masaichi 
Published: October 2020

Abstract
Background: It has been reported that cancer stem cells (CSCs) play an important role in the progression of carcinoma and have a high potential for survival in various stress environments such as starvation and hypoxia. However, the mechanisms responsible for the capacity of CSCs to survive under stresses have been unclear. The aim of this study was to clarify the significance of the autophagy systems of CSCs under stress environments.Methods: Four human gastric cancer cell line, OCUM-12, OCUM-2MD3, MKN-45 and MKN-74 were used. Side population (SP) cells were sorted from the parent OCUM-12 and OCUM-2MD3, as CSC rich cells. The expression of stem cell markers was examined by RT-PCR. The viability of cancer cells under starvation and hypoxia (1%O2) was evaluated by MTT assay with or without the autophagy inhibitor, chloroquine. The expression level of the autophagy molecule LC3-II was examined by western blot. The numbers of autophagosomes and autolysosomes were counted by electron microscope.Results: SP cells of OCUM-12 showed a higher expression of stem cell markers and higher viability in starvation and hypoxia. Western blot and electron microscope examinations indicated that the autophagy was more induced in SP cells than in parent cells. The autophagy inhibitor significantly decreased the viability and the proportion of SP cells under the stress environments.Conclusions: Cancer stem cells of gastric cancer might maintain their viability under stress environments of starvation and hypoxia via the autophagy system. Autophagy inhibitors might be a promising therapeutic agent for gastric cancer.
Data science in economics: comprehensive review of advanced machine learning and deep learning methods
Authors: Nosratabadi Saeed , Mosavi Amir , Duan Puhong , Ghamisi Pedram , Ferdinand Filip , Band Shahab S. , Reuter Uwe , Gama Joao , Gandomi Amir H. 
Published: October 2020

Abstract
This paper provides the state of the art of data science in economics. Through a novel taxonomy of applications and methods advances in data science are investigated. The data science advances are investigated in three individual classes of deep learning models, ensemble models, and hybrid models. Application domains include stock market, marketing, E-commerce, corporate banking, and cryptocurrency. Prisma method, a systematic literature review methodology is used to ensure the quality of the survey. The findings revealed that the trends are on advancement of hybrid models as more than 51% of the reviewed articles applied hybrid model. On the other hand, it is found that based on the RMSE accuracy metric, hybrid models had higher prediction accuracy than other algorithms. While it is expected the trends go toward the advancements of deep learning models.
Smart Governance of City’s Culture: Theoretical and Empirical Aspects
Authors: Milkintas Rytis 
Published: October 2020

The goal of the research is to prepare a theoretical model of smart cultural governance and to evaluate the smart cultural management of Šiauliai city according to it. The background of creating a smart culture governance model is to define the theoretical constructs of smart city and smart culture management by looking for correlations between these concepts in order to closely link cultural management with the implementation of cultural policy in city management processes and to highlight the specifics of smart cultural management. A systematic model of a smart city is formed and presented, of which cultural management is an integral part. The model highlights the links between cultural management and other dimensions of the smart city. The theoretical model of smart culture management, which was adapted to investigate the expression of smart culture management in Šiauliai city, is presented. This kind of research has not been done so far in analyzing smart culture management in Šiauliai city. The need for the research was inspired by culture specialists of Šiauliai City Municipality Administration and heads of cultural institutions. The qualitative content analysis of theoretical sources of foreign countries and Lithuania was conducted as well as in-depth interviews to collect information that was processed through qualitative content analysis and systematized using matrices. The assessment of model expression based on the informants’ attitudes enabled the researcher to draw substantive conclusions.
The research is relevant to Šiauliai city culture field institutions (private, subordinate municipality, subordinate to the Ministry of Culture of the Republic of Lithuania), Šiauliai city culture field policymakers. In a broader sense, the improvement in the quality of the intelligent social system highlighted in the study will significantly contribute to the general level of culture in Šiauliai. These positive changes will be experienced by the recipients of cultural services.
Further research in the field of smart city cultural management is planned to analyze not only the situation of Šiauliai city but also the cultural field of Lithuania as a whole, in connection with the practices of the international cultural field. It is planned to study the smoothness of the transformation of cultural field institutions, adaptation to smart cultural management, and the emerging challenges. Further research is planned to analyze the scientific studies prepared by smart cities, to look for specific actions highlighted in them, challenges for the cultural sector in adapting to the gradual transformation of cities into smart cities.
In Silico Investigation of Signal Peptide Sequences to Enhance Secretion of CD44 Nanobodies Expressed in Escherichia coli
Authors: Kavousipour Soudabeh , Mohammadi Shiva , Eftekhar Ebrahim , Barazesh Mahdi , Morowvat Mohammad H. 
Published: October 2020

Background:
The selection of a suitable signal peptide that can direct recombinant proteins from the cytoplasm
to the extracellular space is an important criterion affecting the production of recombinant proteins in Escherichia coli, a
widely used host. Nanobodies are currently attracting the attention of scientists as antibody alternatives due to their specific
properties and feasibility of production in E. coli.

Objective:
CD44 nanobodies constitute a potent therapeutic agent that can block CD44/HA interaction in cancer and inflammatory diseases. This molecule may also function as a drug against cancer cells and has been produced previously in E.
coli without a signal peptide sequence. The goal of this project was to find a suitable signal peptide to direct CD44 nanobody extracellular secretion in E. coli that will potentially lead to optimization of experimental methods and facilitate downstream steps such as purification.

Methods:
We analyzed 40 E. coli derived signal peptides retrieved from the Signal Peptide database and selected the best
candidate signal peptides according to relevant criteria including signal peptide probability, stability, and physicochemical
features, which were evaluated using signalP software version 4.1 and the ProtParam tool, respectively.

Results:
In this in silico study, suitable candidate signal peptide(s) for CD44 nanobody secretory expression were identified.
CSGA, TRBC, YTFQ, NIKA, and DGAL were selected as appropriate signal peptides with acceptable D-scores, and appropriate physicochemical and structural properties. Following further analysis, TRBC was selected as the best signal peptide to
direct CD44 nanobody expression to the extracellular space of E. coli.

Conclusion:
The selected signal peptide, TRBC is the most suitable to promote high level secretory production of CD44
nanobodies in E. coli and potentially will be useful for scaling up CD44 nanobody production in experimental research as
well as in other CD44 nanobody applications. However, experimental work is needed to confirm the data.
A Five-gene Signature for Predicting the Prognosis of Colorectal Cancer
Authors: Hong Junfeng , Lin Xiangwu , Hu Xinyu , Wu Xiaolong , Fang Wenzheng 
Published: October 2020

Background:
Colorectal cancer (CRC) is a kind of tumor with high incidence and its
treatment situation is still very difficult despite the constant renewal and development of treatment
methods.

Objective:
To assist the prognosis, monitoring and survival of CRC patients with a model.

Methods:
In this study, we established a new prognostic model for CRC. Four groups of CRC data
were accessed from the GEO database, and then differential analysis (logFoldChange>1, adjust-
P<0.05) was carried out by using the limma package along with the RobustRankAggreg package
used to identify the overlapping differentially expressed genes (DEGs). Univariate and multivariate
Cox regression analyses were performed on the DEGs to screen the genes related to the patient’s
prognosis, and a five-gene prognostic prediction model (including RPX, CXCL13, MMP10,
FABP4 and CLDN23) was constructed. Then, we further plotted ROC curves to evaluate the predictive
performance of the five-gene prognostic signature in the TCGA data sets (the AUC values
of 1, 3, 5-year survival were 0.68, 0.632, 0.675, respectively) and an external independent data set
GSE2962 (the AUC values of 1, 3, 5-year survival were 0.689, 0.702, 0.631, respectively).

Results:
The results showed that the model could effectively predict the prognosis of CRC patients,
which provides a robust predictive model for the prognosis of CRC patients.

Conclusion:
The model could effectively predict the prognosis of CRC patients, which provides a
robust predictive model for the prognosis of CRC patients.
In vitro Anti-HIV-1 Activity of the Recombinant HIV-1 TAT Protein Along With Tenofovir Drug
Authors: Yadavar-Nikravesh Maryam-Sadat , Milani Alireza , Vahabpour Rouhollah , Khoobi Mehdi , Bakhshandeh Haleh , Bolhassani Azam 
Published: October 2020

Background:
HIV-1 TAT protein is essential for the regulation of viral genome transcription.
The first exon of TAT protein has a fundamental role in the stimulation of the extrinsic
and intrinsic apoptosis pathways, but its anti-HIV activity is not clear yet.

Methods:
In the current study, we firstly cloned the first exon of the TAT coding sequence in the
pET-24a expression vector and then protein expression was done in the Rosetta expression host.
Next, the expressed TAT protein was purified by Ni-NTA column under native conditions. After
that, the protein yield was determined by Bradford kit and NanoDrop spectrophotometry. Finally,
the cytotoxicity effect and anti-Scr-HIV-1 activity of the recombinant TAT protein alone and along
with Tenofovir drug were assessed by MTT and ELISA, respectively.

Results:
The recombinant TAT protein was successfully generated in E. coli, as confirmed by
13.5% SDS-PAGE and western blotting. The protein yield was ~150-200 μg/ml. In addition, the recombinant
TAT protein at a certain dose with low toxicity could suppress Scr-HIV replication in
the infected HeLa cells (~30%) that was comparable with a low toxic dose of Tenofovir drug
(~40%). It was interesting that the recombinant TAT protein could enhance anti-HIV potency of
Tenofovir drug up to 66%.

Conclusion:
Generally, a combination of TAT protein and Tenofovir drug could significantly inhibit
HIV-1 replication. It will be required to determine their mechanism of action in the next
studies.
Alpha-1-Antichymotrypsin: A Common Player for Type 2 Diabetes and Alzheimer's Disease
Authors: Guzmán-Herrera Nataly , Pérez-Nájera Viridiana C. , Salazar-Olivo Luis A. 
Published: October 2020

Background:
Numerous studies have shown a significant association between Type 2
Diabetes Mellitus (T2D) and Alzheimer's Disease (AD), two pathologies affecting millions of people
worldwide. Chronic inflammation and oxidative stress are two conditions common to these diseases,
also affecting the activity of the serpin Alpha-1-antichymotrypsin (ACT), but a possible common
role for this serpin in T2D and AD remains unclear.

Objective:
To explore the possible regulatory networks linking ACT to T2D and AD.

Materials and Methods:
A bibliographic search was carried out in PubMed, Medline, Open-i, ScienceDirect,
Scopus, and SpringerLink for data indicating or suggesting association among T2D,
AD, and ACT. Searched terms like “alpha-1-antichymotrypsin”, “type 2 diabetes”, “Alzheimer's
disease”, “oxidative stress”, “pro-inflammatory mediators” among others were used. Moreover,
common therapeutic strategies between T2D and AD as well as the use of ACT as a therapeutic target
for both diseases were included.

Results:
ACT has been linked with the development and maintenance of T2D and AD and studies
suggest their participation through the activation of inflammatory pathways and oxidative stress,
mechanisms also associated with both diseases. Likewise, evidences indicate that diverse therapeutic
approaches are common to both diseases.

Conclusion:
Inflammatory and oxidative stresses constitute a crossroad for T2D and AD, where
ACT could play an important role. In-depth research on ACT involvement in these two dysfunctions
could generate new therapeutic strategies for T2D and AD.
Studying the Anti-Tumor Effects of siRNA Gene Silencing of Some Metabolic Genes in Pancreatic Ductal Adenocarcinoma
Authors: Al Hanjori Ahmad S. , Alshaer Walhan , Al-Anati Bayan , Wehaibi Suha , Zihlif Malek 
Published: October 2020

Background:
Earlier diagnosis and advances in treatment strategies have increased the
average survival of cancer patients over the last decades. Despite the increased number of new anti-
neoplastic agents, there has been no adequate therapy for intricate malignancies, such as pancreatic
cancer. Cancer metabolism is the main building block standing behind cancer promotion and progression,
even in the presence of a harsh environment. Targeting metabolic pathways, such as glycolysis
and pentose phosphate pathway, are regarded as a promising new strategy for cancer treatment.

Objective:
The current study aimed to investigate the effects of knocking-down pancreatic cancer
glycolytic and pentose phosphate pathway's regulators (HIF-1α, ARNT, PFKFB4, and RBKS) on
cell’s viability and resistance to Gemcitabine and Doxorubicin, using small interference RNA.

Methodology:
The human pancreatic ductal adenocarcinoma cell line, Panc-1, was used to study
the anti-proliferative activity of targeting HIF-1α, ARNT, PFKFB4, and RBKS mRNAs by transfection
with small interference RNAs, alone and in combination. The transfected cells were also treated
with Doxorubicin and Gemcitabine to study the relationship between the concerned genes and
the resistance of Panc-1 cells to these drugs. The effect on cell proliferation was determined using
a colorimetric assay and Inhibitory Concentration ((IC50) calculation. A cross-talk study was done
to investigate the silencing effect of one of the above genes on the expression of others using Real
Time-Polymerase Chain Reaction.

Results:
In vitro transfection with small interference-RNAs, siHIF-1α, siPFKFB4, and siARNT decreased
tumor cell proliferation with a maximum effect shown by siPFKFB4; but there was no anti-
proliferative effect with RBKS silencing. Suppression of transcription of HIF-1α, ARNT,
PFKFB4, and RBKS sensitize pancreatic cancer cells, Panc-1, to Doxorubicin and Gemcitabine.

Conclusion:
This study demonstrated the major tumor-promoting and progressive effects of
PFKFB4, while HIF-1α and ARNT had modulator effects in pancreatic cancer cells (Panc-1).
RBKS had a chemo-resistant role, justifying its enhanced expression in Panc-1 cells, but not a proliferative
one. Silencing of all genes of interest decreased Doxorubicin and Gemcitabine's resistance
and improved their antitumor effect Din the pancreatic cancer cell line, Panc-1.