bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Improved BM25 for Clinical Decision Support in Precision Medicine Based on Co-word Analysis and Cuckoo Search
Authors: Zhang Zicheng 
Published: November 2020

Abstract
Background: Retrieving gene and disease information from a very large collection of biomedical abstracts to provide doctors with clinical decision support is one of the important research directions of Precision Medicine.Method: We propose a new method for the retrieval of biomedical articles utilizing expanded word and co-word implementations and conducting Cuckoo Search to optimize parameters of the retrieval function in the final stage of the proposed method. The specific goal is to retrieve biomedical abstracts of articles addressing treatments. The method employed in this manuscript first implements the BM25 algorithm to compute the score of the abstract, then we propose a method utilizing the BM25, an improved version of BM25, to compute the scores of expanded words and co-word that lead to a composite retrieval function. Afterward, the retrieval function is optimized using Cuckoo Search. The proposed method is utilized to find both disease and gene in the abstract of the same biomedical article. By doing so, the relevance of articles would tend to increase so would the score of the biomedical article. Besides, the manuscript discusses the influence of different parameters on the retrieval algorithm and summarizes the parameters to meet various retrieval needs.Results: All data are taken from medical articles provided in the Text Retrieval Conference (TREC) utilizing Clinical Decision Support (CDS) Tracks of 2017, 2018, and 2019 in Precision Medicine. 120 standard topics are tested. Three test indicators are employed to make comparisons among the methods utilized. To conduct comparable experiments, only the BM25 algorithm and its improved version of it are utilized. The experimental results show that the proposed algorithm achieves both better results and ranking outcomes.Conclusion: The proposed algorithm, an improved version of the BM25 algorithm, utilizes both co-word implementation and Cuckoo Search and verifies that the proposed algorithm produces better results on a large number of experimental sets. On the other hand, a relatively simple query expansion method is implemented in this manuscript. As a future direction of this research, both the ontology and semantic network to expand the query vocabulary is planned to be conducted.
Impact of superselective intra-arterial and systemic chemoradiotherapy for gingival carcinoma; analysis of treatment outcomes and prognostic factors
Authors: Mukai Yuki , Hayashi Yuichiro , Koike Izumi , Koizumi Toshiyuki , Sugiura Madoka , Oguri Senri , Takano Shoko , Kioi Mitomu , Sato Mizuki , Mitsudo Kenji , Hata Masaharu 
Published: November 2020

Abstract
Background: We compared outcomes and toxicities between concurrent retrograde super-selective intra-arterial chemoradiotherapy (IACRT) and concurrent systemic chemoradiotherapy (SCRT) for gingival carcinoma (GC).　Methods: We included 84 consecutive patients who were treated for non-metastatic GC ≥ stage III, from 2006 to 2018, in this retrospective analysis (IACRT group: n=66; SCRT group: n=18).Results: The median follow-up time was 24 (range: 1–124) months. The median prescribed dose was 60 (6–70.2) Gy (IACRT: 60 Gy; SCRT: 69 Gy). There were significant differences between the two groups in terms of 3-year overall survival (OS; IACRT: 78.8%, 95% confidence interval [CI]: 66.0–87.6; SCRT: 50.4%, 95% CI: 27.6–73.0; P = 0.039), progression-free survival (PFS; IACRT: 75.6%, 95% CI: 62.7–85.2; SCRT: 42.0%, 95% CI: 17.7–70.9; P = 0.028) and local control rates (LC; IACRT: 77.2%, 95% CI: 64.2–86.4; SCRT: 42.0%, 95% CI: 17.7–70.9; P = 0.015). In univariate analysis, age ≥ 65 years, decreased performance status (PS) and SCRT were significantly associated with worse outcomes (P < 0.05). In multivariate analysis, age ≥ 65 years, clinical stage IV, and SCRT were significantly correlated with a poor OS rate (P < 0.05). Patients with poorer PS had a significantly worse PFS rate. Regarding acute toxicity, 22 IACRT patients had grade 4 lymphopenia, and osteoradionecrosis was the most common late toxicity in both groups.Conclusions: This is the first report to compare outcomes from IACRT and SCRT among patients with GC. ALL therapy related toxicities were manageable. IACRT is an effective and safe treatment for GC.
IL-17A polymorphism (rs2275913) and levels are associated with preeclampsia pathogenesis in Chinese patients
Authors: Lang Xiao , Liu Wei , Hou Yanyan , Zhao Wenxia , Yang Xingyu , Chen Lan , Yan Qi , Cheng Weiwei 
Published: November 2020

Abstract
Background: Preeclampsia (PE) is a pregnancy-related condition that affects both the infant and the mother. Although the role of various inflammatory molecules in PE has been demonstrated, the importance of pro-inflammatory molecules such as IL-17A, IL-23 is not well understood. In the present investigation, a potential association of common genetic variants in the IL-17A and IL-23A genes with PE was investigated. Methods: 115 PE clinically diagnosed patients who registered to the International Peace Maternity and Child Health Hospital were enrolled in this research. 102 pregnant women and 147 healthy Chinese women were also included. ELISA was used to measure IL-17A and IL-23 serum levels in all enrolled subjects. Common genetic polymorphisms in IL-17A (rs 2275913, rs1974226, and rs1974226), IL-23A (rs11171806), and IL-12B (rs3212227) were genotyped using the PCR-RFLP or TaqMan probe-based method. Results: Elevated serum IL-17A levels were found in PE patients compared to pregnant (P<0.0001) and healthy women (P<0.0001). However, IL-23 levels were comparable across various clinical groups. In addition, heterozygous (GA) and minor allele (A) for IL-17A (rs2275913) and IL-23A (rs11171806) were more prevalent in PE patients compared to pregnant women indicating an important role in the predisposition to PE growth. Interestingly, IL-17A (r 2275913) mutants were associated with elevated IL-17A levels relative to wild type (GG). Conclusions: IL-17A (rs2275913) variants are associated with higher serum levels of cytokine, and predisposed PE development.
Modified silicone stent for the treatment of post-surgical bronchopleural fistula: A clinical observation of 17 cases
Authors: Zeng Junli , Wu Xuemei , Chen Zhide , Zhang Meihua , Ke Mingyao 
Published: November 2020

Abstract
Background: Bronchopleural fistula is a rare but life-threatening event with limited therapeutic options. We aimed to investigate the efficacy and safety of the modified silicone stent in patients with post-surgical bronchopleural fistula.Methods: Between March 2016 and April 2020, we retrospectively reviewed the records of 17 patients with bronchopleural fistula and who underwent bronchoscopic placement of the Y-shaped silicone stent. The rate of initial success, clinical success and clinical cure, and complications were analyzed. Results: Stent placement was successful in 16 patients in the first attempt (initial success rate: 94.1%). The median follow-up time was 107 (range, 5-431) days. All patients achieved amelioration of respiratory symptoms. The clinical success rate was 76.5%. Of the 14 patients with empyema, the daily drainage was progressively decreased in 11 patients, and empyema completely disappeared in six patients. Seven stents were removed during follow-up: four (26.7%) for the cure of fistula, two for severe proliferation of granulomatous tissue and one for stent dislocation. No severe adverse events (i.e. massive hemoptysis, suture dehiscence) took place. Seven patients died (due to progression of malignancy, uncontrolled infection, myocardial infarction and left heart failure).Conclusions: The modified silicone stent may be an effective and safe option for patients with post-surgical bronchopleural fistula patients in whom conventional therapy is contraindicated.
Polymorphisms of TGF-β1 and TGF-β3 in Chinese women with Gestational Diabetes Mellitus
Authors: Xu Yinglei , Wei Chunlian , Wu Cuijiao , Han Mengmeng , Wang Jingli , Hou Huabin , Zhang Lu , Liu Shiguo , Chen Ying 
Published: November 2020

Abstract
Background: Gestational diabetes mellitus (GDM) is a pregnancy-specific carbohydrate intolerance Which can cause a large number of perinatal and postpartum complications. The members of Transforming growth factor-β (TGF-β) superfamily play key roles in the homeostasis of pancreatic β-cell and may involve in the development of GDM. This study aimed to explore the association between the polymorphisms of TGF-β1, TGF-β3 and the risk to GDM in Chinese women.Methods: This study included 919 GDM patients (464 with preeclampsia and 455 without preeclampsia) and 1177 healthy pregnant women. TaqMan allelic discrimination real-Time PCR was used to genotype the TGF-β1 (rs4803455) and TGF-β3 (rs2284792 and rs3917201), The Hardy-Weinberg equilibrium (HWE) was evaluated by chi-square test.Results: An increased frequency of TGF-β3 rs2284792 AA and AG genotype carriers was founded in GDM patients (AA vs. AG+GG: χ²=6.314, P=0.012, OR=1.270, 95%CI 1.054-1.530; AG vs. GG+AA: χ²=8.545, P=0.003, OR=0.773, 95%CI 0.650-0.919). But there were no significant differences in the distribution of TGF-β1 rs4803455 and TGF-β3 rs3917201 between GDM and healthy women. In addition, no significant differences were found in allele and genotype frequencies among GDM patients with preeclampsia (PE).Conclusions: The AA and AG genotype of TGF-β3 rs2284792 polymorphism may be significantly associated with increased risk of GDM in Chinese population.
ASD Toddlers Exhibit Impaired Development of Neural Systems That Respond to and Guide Mother-Child Interactions
Authors: Xiao Yaqiong , Wen Teresa , Kupis Lauren , Eyler Lisa , Goel Disha , Lombardo Michael , Pierce Karen , Courchesne Eric 
Published: November 2020

Abstract
Motherese is an experience-expectant, human-specific and innate form of parent speech that enhances social and language learning, and affect and emotion development in infants. An early sign of ASD is the child’s lack of responding to motherese and reduced social mother-child interactions. To learn why, we devised a novel experiment quantifying (a) neural responses to motherese and other emotion speech with sleep fMRI and (b) active behavioral preference for motherese with eye tracking in ASD and TD toddlers. We combined the power of diverse neural and clinical data types using Similarity Network Fusion to reveal four neural-clinical clusters. The ASD cluster with the weakest neural responses to motherese and the poorest social and language abilities had the lowest eye tracking attention to motherese, while the TD cluster with the strongest neural response to motherese showed the opposite effects. We conclude that the ASD child’s impairment in engaging in social mother-child interactions is due to impaired development of innate neural systems that normally respond to and guide behavior that maintains mother-child interactions.
Transcapillary Escape Rate of 125I-albumin in Relation to Timing of Blood Sampling: The Need for Standardization.
Authors: Chahid Youssef , Rorije Nienke , Boujoufi Soufian el , Mathot Ron , Vogt Liffert , Verberne Hein 
Published: November 2020

Abstract
BackgroundIncreased vascular permeability is an early sign of vascular damage and can be measured with the transcapillary escape rate of albumin (TERalb). Although TERalb has a multi-exponential kinetic model, most published TERalb data are based on mono-exponential kinetic models with variation in blood sampling schemes. Aim of this study was to evaluate the influence of variation in blood sampling schemes and the impact of mono- or bi-exponential analyses on the calculation of TERalb. Study subjects were part of a cross-over intervention study protocol, investigating effects of sodium loading on blood pressure, endothelial surface layer and microcirculation. Multiple blood samples were drawn between 3 and 60 minutes after injection of radioactive iodide labeled human serum albumin (rHSA). ResultsIn total 27 male subjects were included. For all subjects the maximum serum radioactivity was reached within 20 minutes, while 86% of the subjects had their maximum serum activity within 10 min. The TERalb calculated with the subsequently chosen T20 – 60 min reference scheme (5.97 ± 0.39%/h) was significantly lower compared to the TERalb of the T3 – 60 min, T5 – 60 min, T10 – 60 min, and Tmax – 60 min schemes. There was no significant difference between the T20 – 60 min reference scheme and the T15 – 60 min scheme. Bi-exponential kinetic modeling did not result in significant different observations compared to the mono-exponential kinetic analysis.ConclusionsAs there is variation in the timing of the maximum serum radioactivity of rHSA, blood sampling schemes starting before 15-20 minutes after administration of rHSA will result in a significant overestimation of TERalb. In addition, variation in kinetic modeling did not result in significant changes in TERalb. Therefore, we emphasize the need to standardize TERalb and for practical and logistical reasons advocate the use of a mono-exponential model with blood sampling starting 20 minutes after rHSA administration.
Impact of Traditional Plants and their Secondary Metabolites in the Discovery of COVID-19 Treatment
Authors: Bibi Shabana , Sarfraz Ayesha , Mustafa Ghazala , Ahmad Zeeshan , Zeb Muhammad A. , Wang Yuan-Bing , Khan Tahir , Khan Muhammad S. , Kamal Mohammad A. , Yu Hong 
Published: November 2020

Background:
Coronavirus Disease-2019 belongs to the family of viruses which cause serious pneumonia
along with fever, breathing issues and infection of lungs, and was first reported in China and later spread
worldwide.

Objective:
Several studies and clinical trials have been conducted to identify potential drugs and vaccines for
Coronavirus Disease-2019. The present study listed natural secondary metabolites identified from plant sources
with antiviral properties and could be a safer and tolerable treatment for Coronavirus Disease-2019.

Methods:
A comprehensive search on the reported studies was conducted using different search engines such as
Google Scholar, SciFinder, Sciencedirect, Medline PubMed, and Scopus for the collection of research articles
based on plant-derived secondary metabolites, herbal extracts, and traditional medicine for coronavirus infections.

Results:
Status of COVID-19 worldwide and information of important molecular targets involved in COVID-
19 are described, and through literature search, it is highlighted that numerous plant species and their extracts
possess antiviral properties and are studied with respect to coronavirus treatments. Chemical information, plant
source, test system type with a mechanism of action for each secondary metabolite are also mentioned in this
review paper.

Conclusion:
The present review has listed plants that have presented antiviral potential in the previous coronavirus
pandemics and their secondary metabolites, which could be significant for the development of novel and a
safer drug which could prevent and cure coronavirus infection worldwide.
Ideational Fluency in Patients with Rheumatoid Arthritis
Authors: Mednieks Janis , Naumovs Vladimrs , Skilters Jurgis 
Published: November 2020

Background:
Neuropsychiatric symptoms have been well documented in several systemic
inflammatory conditions, for example, systemic lupus erythematosus (SLE). Increased prevalence
of cognitive decline and psychiatric issues has been reported in patients with rheumatoid
arthritis (RA). However, there is limited evidence of which exact cognitive domains are affected
and to what degree.

Aim:
To test the performance of cognition in the domain of ideational fluency (Thing Categories
Test in particular) in patients with RA and compare the results with the general population and to
the results with cognitive and depression screening scores in both groups.

Methods:
Patient Health Questionnaire 9 (PHQ-9), Generalized Anxiety Disorder 7 (GAD-7) assessment,
Montreal Cognitive Assessment (MoCA), and Thing Categories Test (TCT) were used
to evaluate patients with RA, as well as the control group.

Results:
Twenty patients with RA and 20 controls were tested, with 7 and 4 men, and 13 and 16
women in the study and control group, respectively. Average scores in TCT at three minutes were
7.50 (IQR6.0-10.0) and 6.0 (IQR3.0-8.0) for category “blue”; 17.50 (IQR15.0-19.0) and 16.0
(10.0-18.0) for category “round” in the control and study group, respectively. A statistically significant
difference was established between the study and the control group in TCT for the category
“blue” (p<0.025). The average score for GAD7 was 2.0 (IQR 0.0-5.75) and 3.0 (IQR0.50-6.00) in
the control and study group, respectively. The average score for PHQ-9 was 2.0 (IQR0.25-4.75)
and 4.0 (IQR2.00-5.50) in the control and study group, respectively. Finally, the average score for
the MoCA scale was 27.0 (IQR25.25-28.00) and 26.0 (IQR23.50-28.00) in the control and study
group, respectively.

Conclusions:
Preliminary evidence suggests that RA at least partially affects the cognitive domain
of ideational fluency. However, further research with larger experimental groups is needed to provide
more conclusive evidence.
In silico Screening of Pyridoxine Carbamates for Anti-Alzheimer’s Activities
Authors: Baswar Dnyaneshwar , Sharma Abha , Mishra Awanish 
Published: November 2020

Background:
Alzheimer’s disease (AD), an irreversible complex neurodegenerative
disorder, is the most common type of dementia, with progressive loss of cholinergic neurons.
Based on the multi-factorial etiology of Alzheimer’s disease, novel ligands strategy appears as an
up-coming approach for the development of newer molecules against AD. This study is envisaged
to investigate anti-Alzheimer’s potential of 10 synthesized compounds. The screening of compounds
(1-10) was carried out using in silico techniques.

Methods:
For in silico screening of physicochemical properties of compounds, Molinspiration property
engine v.2018.03, Swiss ADME online web-server and pkCSM ADME were used. For pharmacodynamic
prediction, PASS software was used, while the toxicity profile of compounds was analyzed
through ProTox-II online software. Simultaneously, molecular docking analysis was performed
on mouse AChE enzyme (PDB ID:2JGE, obtained from RSCB PDB) using Auto Dock Tools 1.5.6.

Results:
Based on in silico studies, compound 9 and 10 have been found to have better druglikeness,
LD50 value, better anti-Alzheimer’s, and nootropic activities. However, these compounds
had poor blood-brain barrier (BBB) permeability. Compounds 4 and 9 were predicted with
a better docking score for the AChE enzyme.

Conclusion:
The outcome of in silico studies has suggested, out of various substitutions at different
positions of pyridoxine-carbamate, compound 9 has shown promising drug-likeness, with
better safety and efficacy profile for anti-Alzheimer’s activity. However, BBB permeability appears
as one of the major limitations of all these compounds. Further studies are required to confirm
its biological activities.
Proteome Analysis of CD4+ T Cells Reveals Differentially Expressed Proteins in Infertile Polycystic Ovary Syndrome Patients
Authors: Nasri Fatemeh , Zare Maryam , Doroudchi Mehrnoosh , Gharesi-Fard Behrouz 
Published: November 2020

Background:
Polycystic ovary syndrome (PCOS) is the most frequent endocrine disorder affecting 6–7% of
premenopausal women. Recent studies revealed that the immune system especially CD4+ T helper cells are important in the
context PCOS. Proteome analysis of CD4+ T lymphocytes can provide valuable information regarding the biology of these
cells in the context of PCOS.

Objective:
To investigate immune dysregulation in CD4+ T lymphocytes at the protein level in the context of PCOS using
two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS).

Methods:
In the present study, we applied two-dimensional gel electrophoresis / mass spectrometry to identify proteins differentially expressed by peripheral blood CD4+ T cells in ten PCOS women compared with ten healthy women. Western
blot technique was used to confirm the identified proteins.

Results:
Despite the overall proteome similarities, there were significant differences in the expression of seven spots between two groups (P <0.05). Three proteins, namely phosphatidylethanolamine-binding protein 1, proteasome activator
complex subunit 1 and triosephosphate isomerase 1 were successfully identified by Mass technique and confirmed by western blot. All characterized proteins were over-expressed in CD4+ T cells from patients compared to CD4+ T cells from controls (P <0.05). In-silico analysis suggested that the over-expressed proteins interact with other proteins involved in cellular
metabolism especially glycolysis and ferroptosis pathway.

Conclusion:
These findings suggest that metabolic adjustments in CD4+ T lymphocytes, which is in favor of increased glycolysis and Th2 differentiation are important in the context of PCOS.
Evaluation of Safety, Antileishmanial, and Chemistry of Ethanolic Leaves Extracts of Seven Medicinal Plants: An In-vitro Study
Authors: Shaheen Nargis , Qureshi Naveeda Akhter , Iqbal Attiya , Ashraf Asma , Fatima Huma 
Published: November 2020

Background:Cutaneous leishmaniasis is a neglected tropical disease that currently affects people among 98 countries and causes significant morbidity and mortality. Current chemotherapeutic intervention is unsatisfactory and has various limitations that highlight the necessity to develop safe and effective therapeutic approaches from natural products.Objective:The main objective of current study was the evaluation of the antileishmanial activity along with toxicity assessment of selected plant extracts.Methods:The ethanolic leaves extracts of selected plants were evaluated for their qualitative and quantitative phytochemical screening by standard protocols. The antioxidant potential of plant extracts was determined by total antioxidant capacity, ferric reducing power and DPPH radical scavenging assays. The cytotoxicity analysis using brine shrimp lethality assay andin-vitroantileishmanial activity against promastigotes of L. tropica (Accession# MN891719) were also evaluated.Results:The preliminary examination of crude extracts revealed that P. armeniaca showed the highest total phenolic and flavonoid content (279.62±5.40µgGAE/mgDW and 205.70 ±2.41µgQA/mgDW, respectively), among others. P. armeniaca showed strongest antioxidants (120.37±4.90 µgAAE/mgDW) and FRP values (278.71±1.03µgAAE/mgDW). All the plant extracts showed cytotoxicity in safety range >1000µg/ml except F. glomerata having LC50 values of 454.34 µg/ml. In the present study, P. communis and P. pashia showed some level of activity (LC50 56.68 and 60.95µg/ml respectively) while P. armeniaca demonstrated the highest antileishmanial activity (LC50 16.18µg/ml).Conclusion:The findings are highly encouraging so, further and extensive investigations of P. arminica should be carried out; especially bio guided fractionation to identify the active fraction and further chemical characterization of structure.