bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Improved Method for the Segmentation of Roots from X-ray Computed Tomography 3D Images: Rootine v.2
Authors: Phalempin Maxime , Lippold Eva , Vetterlein Doris , Schlüter Steffen 
Published: October 2020

Abstract
BackgroundX-ray computed tomography is acknowledged as a powerful tool for the study of root system architecture of plants growing in soil. In this paper, we improved the original root segmentation algorithm “Rootine” and present its succeeding version “Rootine v.2”. In addition to grey value information, Rootine algorithms are based on shape detection of cylindrical roots. Both algorithms are macros for the ImageJ software and are made freely available to the public. New features in Rootine v.2 are (1) a pot wall detection and removal step to avoid segmentation artefacts for roots growing along the pot wall, (2) a calculation of the root average grey value based on a histogram analysis, (3) an automatic calculation of thresholds for hysteresis thresholding of the tubeness image to reduce the number of parameters and (4) a false negatives recovery based on shape criteria to increase root recovery. We compare the segmentation results of Rootine v.1 and Rootine v.2 with the results of root washing and subsequent analysis with WinRhizo. We use a benchmark dataset of maize roots (Zea mays L. cv. B73) grown in repacked soil for two scenarios with differing soil heterogeneity and image quality. ResultsWe demonstrate that Rootine v.2 outperforms its preceding version in terms of root recovery and enables to match better the root diameter distribution data obtained with root washing. Despite a longer processing time, Rootine v.2 comprises less user-defined parameters and shows an overall greater usability. ConclusionThe proposed method facilitates higher root detection accuracy than its predecessor and has the potential for improving high-throughput root phenotyping procedures based on X-ray CT data analysis.
Metabolic Profiling Revealed Dysregulated Arachidonic Acid Metabolism and Tryptophan Metabolism in the Lungs from Canines with Pacing-induced Heart Failure
Authors: Zhao Junhan , Wang Jing , Yang Shengwen , Jing Ran , Liu Xi , Gu Min , Cai Chi , Niu Hongxia , Zhang Shu , Hua Wei 
Published: October 2020

Abstract
Background: Lung has critical pathophysiological connections to heart and lung congestion presents one of the hallmark features of heart failure (HF). This study aimed to explore the metabolic signatures and disturbances in lungs under HF condition and provide insights on the pathophysiology of the lungs under HF condition from the perspective of metabolism.Methods: In this study, we established a rapid pacing induced HF canine model and applied a comprehensive untargeted metabolomics method to comparatively assessed the metabolomics profiles in the lung tissues from HF group and sham group. Results: Distinct metabolic signatures were identified in the lungs between beagles in HF group and sham group. 81 dysregulated metabolites were identified as differential metabolites (adjusted P <0.05, FC≥2 or≤0.5) in positive ion mode and 80 dysregulated metabolites in negative ion mode, indicating a profound metabolic alteration in the lungs under HF condition. In pathway analysis, arachidonic acid metabolism and tryptophan metabolism were identified as the most significant dysregulated metabolic pathways in the lungs from HF beagles.Conclusions: In this study, we identified profound metabolic variation and dysregulated metabolic pathways, which may deepen our understanding on the pathophysiology of the lungs under HF condition from the perspective of metabolism and open new avenues in lung congestion management in HF.
Application of Ethnobotanical Indices to Assess the Diversity of Medico-magic Knowledge on Four Herbaceous Species in Benin.
Authors: Dossou-Yovo Hubert Olivier , Kindomihou Valentin , Sinsin Brice 
Published: October 2020

Abstract
Background

Ethnobotanical knowledge on four herbaceous species, Phyllanthus amarus, Spilanthes uliginosa, Momordica charantia and Acalypha ciliata in Benin was investigated.
Methods

Thirty-six herbal medicine traders in six different markets were interviewed using a semi-structured questionnaire. The Relative Frequency Citation, Fidelity Level, Use Value and Rahman Similarity Index were calculated to assess the diversity of medico-magic knowledge.
Results

All informants traded P. amarus, M. charantia and A. ciliata and the majority traded S. uliginosa. Purchase in traders’ own markets was the predominant source of P. amarus, M. charantia and A. ciliata while S. uliginosa was mostly purchased in other more distant markets. A noticeable proportion of traders also collect P. amarus and M. charantia from wild populations. Phyllanthus amarus was the species most demanded by customers followed by M. charantia. Traders confirmed the scarcity of all species in recent years and climate change as well as destruction of natural habitats for logging were the most cited causes. The entire plant of P. amarus was used mainly to treat malaria, diabetes and constipation and decoction with oral administration the most frequent preparation for malaria treatment. To treat diabetes, informants mixed P. amarus with M. charantia used as a decoction with oral administration. Momordica charantia was also used to treat measles and chicken pox. Spilanthes uliginosa and A. ciliata were mostly used for their spiritual use for luck, predominantly by chewing fresh leaves or flowers, and by bathing with the ground plant mixed with soap, respectively. Overall, M. charantia had the greatest use value followed by P. amarus. The majority of traders do not plant the species.
Conclusions

The harvesting and trade of the species threaten their natural populations and urgent tools, including in-situ and ex-situ conservation, are needed to ensure their long-term sustainable exploitation.
CircRNA circFADS2 is Downregulated in Osteoporosis and Suppresses LPS-induced Apoptosis of Osteoblast by Downregulating miR-16-5p
Authors: Zhou Hailong , Jiang Jianmin , Chen Xiaohua , Zhang Zhiwei 
Published: October 2020

Abstract
Background: CircRNA circFADS2 plays protective roles in LPS-induced cell injury, which promotes osteoporosis (OS), suggesting the involvement of circFADS2 in OS. This study aimed to explore the role of circFADS2 in OS.Methods: RT-qPCRs were performed to analyze the expression of circFADS2 and miR-16-5p in plasma samples from OS patients (n=64) and healthy controls (n=64). Correlations between circFADS2 and miR-16-5p were explored by Pearson’s correlation coefficient. In primary osteoblasts, circFADS2 and miR-16-5p were overexpressed to study the interactions between them. Cell apoptosis assay was performed to study the functions of circFADS2 and miR-16-5p in the apoptosis of osteoblasts induced by LPS.Results: CircFADS2 was downregulated in OA and inversely correlated with miR-16-5p. After treatment, circFADS2 was upregulated and miR-16-5p was downregulated. In osteoblasts, LPS treatment decreased the expression of circFADS2 but increased the expression of miR-16-5p. Overexpression of circFADS2 decreased the expression of miR-16-5p. Cell apoptosis analysis showed that circFADS2 overexpression reduced the apoptosis of osteoblasts under LPS-treatment, while miR-16-5p overexpression increased cell apoptosis. Moreover, overexpression of miR-16-5p reduced the effects of circFADS2 overexpression on the apoptosis of osteoblasts. Conclusion: Therefore, CircFADS2 is downregulated in OS and promotes LPS-induced apoptosis of osteoblast by downregulating miR-16-5p.
Heart Disease Detection Using Machine Learning
Authors: T Chithambaram , N Logesh Kannan , M Gowsalya 
Published: October 2020

Abstract
This paper analyzes the detection of heart disease using machine learning algorithms and python programming. Over the post decades, heart disease is common and dangerous disease caused by fat containment. This disease occurs due to over pressure in the human body. Using different types of parameters in the dataset we can predict the cardiac-disease. We have observed a dataset consists of 12 parameters and 70000 individual data values[5] to analyze the performance of patients. The main objective of the paper is to get a better accuracy to detect the heart-disease using algorithms in which the target output counts that a person having heart disease or not.
A Case Report of Prolonged COVID-19 Positive RT-PCR for five months
Authors: Siami Zeinab , Soleimani Alireza , Khavandegar Armin 
Published: October 2020

Abstract
Background: The COViD-19 gold standard assessment tool remained the RT-PCR of upper respiratory tract specimen extracted by the nasopharyngeal swab. A positive result would dwindle through a three-week course and, eventually, would be undetectable. The most prolonged period of detectable viral RNA was 37 days. Besides, COViD-19 RT-PCR remained positive for 74 days in a patient suffering from lymphoma Case presentation: In this study, we have presented a 56-year-old Persian male patient, a known case of lymphoma since 2015, who experiences many episodes of chemotherapy with a five-month positive RT-PCR COViD-19 laboratory test and finally was intubated and then died of opportunistic pulmonary infections. Conclusion: COViD-19 patients who have concurrent lymphoma failed to remove the virus thoroughly, despite providing appropriate treatment regimens.
A Study of 1-Phenyl-3-Methyl-4-Trichloroacetyl Pyrazolone-5 as an Extractant for Uranium (VI) From Buffered Solutions
Authors: Bennett Victoria , Amos-Tautua Bamidele , Kemeakegha Ayasen 
Published: October 2020

Abstract
Chloroform solutions of 1-Phenyl-3-Methyl-4-Trichloroacetylpyrazolone-5 (HTCP) for the extraction of Uranium (VI) (UO22+) from various buffered solutions containing different SO42- ion concentrations was investigated. After extraction processes, colorimetric method was used to determine Uranium(VI) concentrations in aqueous media. Solutions of HTCP in chloroform did not extract U(VI) in buffered solutions containing SO42- ions between pH 0 – 2, which was attributed to the formation of unextractable Sulphate Uranyl (UO2)SO4 complex. However, there was extraction of U(VI) of 88,70 %, 76.84 % and 55.49 % between pH 2.96 – 3.21 for solutions containing 0.01 M, 0.1 M and 1 M SO42- ion respectively. An increase in SO42- ion concentration decreased the optimum extraction of U(VI). The presence of SO42- ion in buffered solutions had a masking effect on the extraction of U(VI). The metal ligand ratio was 1:1 and the adduct complex of the metal characterized as UO2(TCP) was extracted.
Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences
Authors: Gomes Juliana , Masood Aras , Silva Leandro , Ferreira Janderson Romário , Júnior Agostinho Antônio Freire , Rocha Allana Laís , de Oliveira Latícia , Silva Nathália Regina da , Fernandes Bruno José , Santos Wellington dos 
Published: October 2020

Abstract
The proliferation of the SARS-CoV-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the public health resources are critical factors. The RT-PCR with virus DNA identification is still the benchmark Covid-19 diagnosis method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach, and represented by co-occurrence matrices. This technique analyzes the DNA sequences obtained by the RT-PCR method, eliminating sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. Experiments with all 24 virus families and SARS-CoV-2 (multi-class scenario) resulted 0.822222 ± 0.05613 for sensitivity and 0.99974 ± 0.00001 for specificity using Random Forests with 100 trees and 30% overlap. When we compared SARS-CoV-2 with similar-symptoms virus families, we got 0.97059 ± 0.03387 for sensitivity, and 0.99187 ± 0.00046 for specificity with MLP classifier and 30% overlap. In the real test scenario, in which SARS-CoV-2 is compared to Coronaviridae and healthy human DNA sequences, we got 0.98824 ± 0.01198 for sensitivity and 0.99860 ± 0.00020 for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify SARS-CoV-2 DNA sequences faster with higher specificity and sensitivity.
Cognitive Performance and Neuro-Metabolites in HIV Using 3T Magnetic Resonance Spectroscopy: A Cross-Sectional Study from India
Authors: Gupta K. , Shivabalan  , Kumar V. , Vyas S. , Pandey R. M. , Jagannathan N. R. , Sinha S. 
Published: October 2020

Background:
Cognitive impairment in patients with human immunodeficiency virus
(HIV) is associated with higher morbidity. The prevalence of the metabolite changes in the brain associated
with cognitive impairment in anti-retroviral therapy naïve patients with HIV is unknown.

Objective:
To estimate the prevalence of the neurometabolites associated with cognitive impairment
in antiretroviral therapy (ART) naïve patients with HIV.

Methods:
We conducted a cross-sectional study among ART naïve patients with HIV aged 18-50
years in a tertiary care center in India. Cognition was tested using the Post Graduate Institute battery
of brain dysfunction across five domains; memory, attention-information processing, abstraction
executive, complex perceptual, and simple motor skills. We assessed the total N-acetyl aspartyl
(tNAA), creatine (tCr) and glutamate + glutamine (Glx) using 3T magnetic resonance spectroscopy.
Cognitive impairment was defined as an impairment in ≥2 domains.

Results:
Among 43 patients eligible for this study, the median age was 32 years (IQR 29, 40) and
30% were women. Median CD4 count and viral load were 317 cells/μL (IQR 157, 456) and 9.3
copies/ μL (IQR 1.4, 38), respectively. Impairment in at least one cognitive domain was present in
32 patients (74.4%). Impairment in simple motor skills and memory was present in 46.5% and
44% of patients, respectively. Cognitive impairment, defined by impairment in ≥2 domains, was
found in 22 (51.2%) patients. There was a trend towards higher concentration of tNAA (7.3 vs. 7.0
mmol/kg), tGlx (9.1 vs. 8.2 mmol/kg), and tCr (5.5 vs. 5.2 mmol/kg) in the frontal lobe of patients
with cognitive impairment vs. without cognitive impairment but it did not reach statistical significance
(p>0.05 for all). There was no difference in the concentration of these metabolites in the two
groups in the basal ganglia.

Conclusions:
There is a high prevalence of cognitive impairment in ART naïve patients with HIV.
There is no difference in metabolites in patients with or without cognitive impairment. Further
studies, with longitudinal follow-up are required to understand the underlying pathophysiological
mechanisms.
Influence of Lung Hyperinflation on Respiratory Muscles Pressures During a Submaximal Test in Patients With COPD: A Clinical Perspective
Authors: Porto Elias F. , Clares Sabrina , Ferracioli Ana M.J. , de Sousa Marcio R.P. , de Oliveira Leite José Renato , Malheiros Rafael T. , De Castro Antonio A.M. 
Published: October 2020

Background and Objective:
Reduction of exercise tolerance is associated with expiratory
flow-limitation (EFL) and lung hyperinflation; those are only partially reversible to bronchodilator.
Lung hyperinflation lowers the diaphragm muscle provoking a mechanical disadvantage that,
eventually, reduces maximal inspiratory (MIP) and expiratory (MEP) pressures. We aimed to assess
the influence of the dynamic lung hyperinflation on respiratory pressures changes at rest and
after a submaximal exercise test in COPD patients with and without a bronchodilator.

Methods::
We prospectively analyzed 16 COPD patients (FEV1 36.4±10% pred.; age 61.0±8 years,
height 165±12 cm and BMI 25.9±6 kg/m2). MIP and MEP were measured before and after performing
the six minutes walking test (6MWT) with and without bronchodilator (400 mcg of albuterol).

Results::
Nine of 16 patients increased IC more than 150 ml after bronchodilator use. Right after
the 6MWT was accomplished without bronchodilator, IC decreased by 7.05% as compared to the
6MWT baseline value (p<0.01). Nine patients decreased IC more than 150ml. After bronchodilator
use, patients performed the 6MWT without any IC significant reduction (p>0.05). Twelve patients
increased the MIP (ranging from 70±11cmH2O to 77±10cmH2O, p = 0.0043) using 400mcg of albuterol.
Thirteen patients reduced MIP after the 6MWT without bronchodilator use (p <0.007).
There was no significant reduction (p> 0.05) in MIP when patients performed the 6MWT after
bronchodilator use. We also found a significant correlation between MIP and inspiratory capacity
(IC) and MEP and the IC before and after the 6MWT (r=0.61, p=0.0054; r=0.60, p=0.0031, respectively).

Conclusions::
Dynamic pulmonary hyperinflation directly interferes with the ability of respiratory
muscles to generate inspiratory and expiratory pressures. The previous use of bronchodilators in patients
with COPD reduced dynamic hyperinflation when accomplishing a sub-maximal exercise.
Identifying the Predictors of Self-Management Behaviors in Patients with Diabetes Based on Ecological Approach: A Systematic Review
Authors: Davari Mahnaz , Moghaddam Hamed Rezakhani , Soola Aghil Habibi 
Published: October 2020

Background:
Recognizing and promoting the factors that affect the self-management behaviors
of diabetes lead to a reduction in the number of patients and an improvement in the quality
of care. The ecological approach focuses on the nature of people's interactions with their physical
and socio-cultural environments.

Objective:
The purpose of this study was to identify the predictors of self-management behaviors
with a comprehensive approach in these patients.

Methods:
The keywords were investigated in the relevant national and international databases, including
PubMed, Google Scholar, Science Direct, Scopus, and Scientific Information Database,
Magiran, and Iran Medex, to obtain the articles published from 2009 to 2019. The search and article
selection strategy was developed based on the Prisma checklist and was carried out in three
steps.

Results:
Most studies have shown that personal factors had the highest prediction power for the
self-management of diabetes. The interpersonal factors, society and policy-making factors, and
group and organization factors were then the most frequently reported predictors of self-management
behaviors in diabetic patients.

Conclusion:
Self-management of diabetes is necessary for controlling it because 95% of care is
done by the patient. When designing self-management interventions, factors are based on the individual
level that is to increase self-management behaviors.
Purification of Bacteriocin from Lactobacillus plantarum KY449289 and its Role in the Preservation of Mixed Fruit Juice
Authors: Mounika Ranga , Siddique Jannatul F. , Anbalagan Nivetha , Devi Subathra C. , V Mohanasrinivasan 
Published: October 2020

Background::
The aim of this study is to isolate, extract and purify the antibacterial protein
from Lactobacillus plantarum KY449289 and to assess its bio preservative potential.

Objective::
The present study was conducted to evaluate the laxative activity of Hydroethanolic
Pericarp Extract of sapindus emarginatus (HESE) in animal models.

Methods::
Bacteriocins are antimicrobial peptides synthesized ribosomally which can be used as
bio-preservative reducing the risk of chemical preservative’s effect and also replacing the thermal
treatments. This study aims to isolate, purify the antibacterial protein from Lactobacillus plantarum
KY449289 and to assess its bio preservative potential. In this study, twenty strains were isolated
from a yogurt sample and preliminary characterization was carried out, such as morphological,
biochemical, and molecular levels as a preliminary assay.

Results::
The characterized strains were assessed for the antibacterial activity by well diffusion assay,
whereas all twenty strains were shown to have a antibacterial activity against foodborne pathogens,
among which two strains VITMM04 and VITMM05 shows the highest zone of inhibition of
15 mm and 10 mm respectively against Listeria monocytogenes. The potent isolate VITMM05 solely
showed a broad spectrum antibacterial activity against the pathogens. These strains were further
subjected to optimization, purification, and application studies. A high increase in the inhibition
zone was recorded with an optimum temperature of 35°C and its activity was found to be stable up
to 85°C, optimum pH 6, and 5 mM of EDTA as an enhancer surfactant. On subjected to RP-HPLC,
the purified sample showed a distinct peak at 2.192 min corresponding to the peak at 2.192 min for
standard bacteriocin.

Conclusion::
The six-fold purified bacteriocin was effective in controlling 87% of the microbial
population with 20mm zone of inhibiton against the Listeria monocytogenes and this shows the effective
role of purified bacteriocin in inhibiting bacterial growth in a greater extent.
Novel Reverse-Phase High-Performance Liquid Chromatography (RPHPLC) Method for the Quantification of Apigenin in Ocimum Basilicum Linn Seeds (Tukmaria)
Authors: Parikh Nisha H. , Kothari Charmy 
Published: October 2020

Background::
Ocimum basilicum L. seeds, is commonly also known as Takhmaria in
Gujarat. It is a common constituent present in fruits, plant-derived beverages, vegetables, wheat,
sprouts, and some seasonings.

Objective::
A simple, specific, precise, accurate, and sensitive method for the quantification of
apigenin by reverse-phase high-performance liquid chromatography (RP-HPLC) was developed
and validated.

Methods::
Analysis was carried out on Inertsil ODS-3V-C18 column (250 mm × 4.6 mm i.d, 5
μm) as stationary phase and methanol-acetonitrile (55:45 v/v) as a mobile phase at a flow rate of
1.0 mL/ min. Detection was carried out at 340 nm. The retention time of apigenin was found to be
8.30 min. The proposed method was validated according to ICH Guidelines, Q2 (R1).

Results::
The developed method showed good linearity in the range of 10-50 μg/mL with a correlation
coefficient (R2= 0.9998). The LOD and LOQ were found to be 1.23 μg/mL and 4.05
μg/mL, respectively. The percentage recovery for apigenin was found to be 97.75-100.5%. All
validation parameters were found within acceptable limits and demonstrated good reliability in
the quantification of apigenin.

Conclusion::
Thus, the newly developed and validated method can be successfully applied for the
quantification of apigenin from seeds of O. basilicum L. and can also be applied for the standardization
of polyherbal formulation containing O. basilicum seeds. Assay results showed good recovery
when statistically compared with the high-performance thin-layer chromatography
(HPTLC) method.