bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prognostic factors in sepsis patients after operation of gastrointestinal tumors in ICU
Authors: Chen Ren-Xiong , Wu Zhou-Qiao , Li Zi-Yu , Wang Hong-Zhi , Ji Jia-Fu 
Published: April 2020

Abstract
Background: We studied the clinical profiles and the prognostic factors in patients with sepsis after the gastrointestinal tumor surgery in ICU.Methods: We retrospectively screened patients who underwent the gastrointestinal tumor surgery at the Peking University Cancer Hospital from January, 2015 to December, 2019. Among them, 181 patients who were diagnosed with sepsis in ICU were enrolled in our study. Cox regression was performed for multivariate adjusted factor analyses.Results: The 90-day all-cause mortality rate was 11.1% in our study. The univariate analysis showed that BMI, shock within 48 h after entering ICU, number of blood leukocytes, ratio of lymphocytes to neutrophils, INR, creatinine, procalcitonin, lactic acid, oxygenation index, SOFA score within 24 h after entering ICU, APACHE II score within 24 h after entering ICU were statistically significant. In multiple analysis, we found that BMI༞20 kg/m2 was a protective factor, while lactic acid༞3 mmol/L after entering ICU and APACHE II score༞20 within 24 h after entering ICU were independent risk factors for the prognosis of sepsis after the gastrointestinal tumor surgery in ICU.Conclusions: BMI༞20 kg/m2 was a protective factor, while lactic acid༞3 mmol/L after entering ICU and APACHE II score༞20 within 24 h after entering ICU were independent risk factors for the prognosis of sepsis after the gastrointestinal tumor surgery in ICU.
Comparative Transcriptome Analysis Uncovers Roles of Hydrogen Sulfide for Alleviating Cadmium Toxicity in Tetrahymena Thermophila
Authors: Lv Hongrui , Xu Jing , Bo Tao , Wang Wei 
Published: April 2020

Abstract
BackgroundCadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfide (H2S) effectively alleviates heavy metal toxicity in plants. However, the function of H2S for alleviating heavy metal toxicity in aquatic organisms remains less clear. Tetrahymena thermophila is an important model organism to evaluate toxic contaminants in an aquatic environment. In this study, the molecular roles of exogenously H2S application were explored by RNA sequencing under Cd stress in T. thermophila.ResultsThe exposure of 30 µM Cd resulted in T. thermophila growth inhibition, cell nigrescence, and malondialdehyde (MDA) content considerably increase. However, exogenous H2S (70 µM) significantly alleviated the Cd-induced toxicity and improved antioxidant system. Comparative transcriptome analysis showed that the expression levels of 9152 genes changed under Cd stress (4658 upregulated and 4494 downregulated). However, only 1359 genes were differentially expressed with H2S treatment under Cd stress (1087 upregulated and 272 downregulated). The functional categories of the differentially expressed genes (DEGs) by gene ontology (GO) revealed that the transcripts involved in the oxidation–reduction process, oxidoreductase activity, glutathione peroxidase activity, and cell redox homeostasis were the considerable enrichments between Cd stress and H2S treatment under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the carbon metabolism, glutathione metabolism, metabolism of xenobiotics by cytochrome P450, and ABC transporters were significantly differentially expressed components between Cd stress and H2S treatment under Cd stress in T. thermophila. The relative expression levels of six DEGs were further confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).ConclusionH2S alleviated Cd stress mainly through increasing oxidation resistance, enhancing detoxification, and regulation of transport in free-living unicellular T. thermophila. These findings will expand our understanding for H2S functions in the freshwater protozoa.
Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage
Authors: Nayyeripasand Leila , Garoosi Ghasem Ali , Ahmadikhah Asadollah 
Published: April 2020

Abstract
Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including SL, RL, RDW, RFW, SFW, SDW, RWC and TW in a diverse panel of rice consisted of 202 varieties were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+ Q + K) model.Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified.Conclusion The results for RDW and RFW were found more important than other traits, and known or novel candidate genes in this research can be used for improvement of salinity tolerance in molecular breeding programmes. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level.
The utility of simultaneous CT-guided localization for multiple pulmonary nodules using microcoil before Video-Assisted Thoracic Surgery
Authors: Xu Yanyan , Ma Lingchuan , Sun Hongliang , Huang Zhenguo , Zhang Zhenrong , Xiao Fei , Ma Qianli , Lin Jie , Xie Sheng 
Published: April 2020

Abstract
Background: To evaluate the feasibility and safety of microcoil in simultaneous localization for multiple pulmonary nodules before video-assisted thoracic surgery (VATS).Methods: Twenty-eight consecutive patients (26 two-nodule, 2 three-nodule; totally 58 nodules; Group A) underwent simultaneous CT-guided localization for multiple pulmonary nodules before VATS using microcoil. Successful targeting, localization, and VATS were defined as implantation of microcoil at the target site on CT image obtained immediately after the marking procedure, visualization of nodule location, and complete resection of the target nodule with adequate margin, respectively. Meanwhile, the clinical characteristics, localization procedure-related variables of the nodules and procedure-related complication in group A were also assessed and compared with those in a control group (221 single-localization procedures in 221 patients; Group B). Results: The similar rates of success targeting, localization and VATS were observed in group A and B (96.6% vs 98.2%; 91.4% vs 91.0%; 100% vs 99.1%). Although the rate of overall complications (including localized pneumothorax and intrapulmonary hemorrhage) was a bit higher in group A than that in group B (32.8% vs 30.8%, p=0.771), only minor complications were observed in the subjects of the two groups with no need for further treatment. In addition, the duration of simultaneous localization procedures was significantly longer than that of single localization ones (24±7.5 vs 13±6 min, p<0.001).Conclusions: CT-guided simultaneous microcoil localization for multiple pulmonary nodules before VATS was clinical feasible and safe with acceptable increasing the procedure time. Compared with localization for a single pulmonary nodule, simultaneous microcoil localizations for multiple nodules were prone to the occurrence of pneumothorax and hemorrhage. However, no statistically significant differences were observed between the two groups.
Breastfeeding and acute lymphoblastic leukaemia: potential leukemogenesis in children in developing countries
Authors: Kakaje Ameer , Alhalabi Mohammad Marwan , Ghareeb Ayham , Karam Bahjat , Hamid Aya , Mansour Bassam , Zahra Bayan , Hamdan Othman 
Published: April 2020

Abstract
Background: Breastfeeding (BF) is known to decrease acute lymphoblastic leukaemia (ALL) incidence. However, most of these studies were conducted in developed countries and mothers in developing countries may be exposed to different substances which could be transferred via breastmilk which emphasise on the importance of conducting studies in developing countries to assess the effect of these different factors.Methods: Our case-control study was conducted in the major paediatric cancer centre in Syria. Information was obtained from the hospital’s records of patients who did not have a hereditary or chromosomal syndrome and aged 4 years and less. The cases were ALL patients and controls were hospital inpatients. The patients were divided into 3 groups depending on their feeding habits before the age of 6 months.Results: Our sample had 70 cases of ALL with 42 males (60%) and 60 controls with 36 males (60%) aging four years and younger. Sixty cases and 41 controls were exclusively breastfed, 8 cases and 6 controls used extra infant formula with BF and two cases and 13 controls relied on only infant formula. We found statistical significant difference when comparing cases and controls and BF (P<0.05) with cases being exclusively breastfed more. In case group, being born with no complication, and having low educational parents educational level were correlated with BF (P<0.05). However, gender, consanguinity, CD10, FAB classification, ALL-subtypes, risk and family history were not significant.Conclusion: There are certain practices among the Syrian people, especially among low educational level parents that makes their children more vulnerable to ALL when BF. We speculate certain substances and behaviours being responsible. Even in the higher educational level parents, the protection factor that BF had was insignificant as they also practice these harmful behaviours but less often. BF had minor effects on the prognosis and subtype of ALL.
Inhibition of COVID-19 RNA-Dependent RNA Polymerase by Natural Bioactive Compounds: Molecular Docking Analysis
Authors: El-Aziz Nourhan M. Abd , Shehata Mohamed G. , Awad Olfat M. Eldin , El-Sohaimy Sobhy A. 
Published: April 2020

Abstract
Till now there is no approved treatment for COVID-19. Phenolic compounds are known to have antiviral activity against many viruses such as HCV and HIV, through their phenol rings interaction with viral proteins and/or RNA, or via its regulating MAP kinase signaling in host cell defense. The present study aimed to assess polyphenolic compounds (gallic acid, quercetin, caffeine, resveratrol, naringenin, benzoic acid, oleuropein and ellagic acid) as COVID-19 RNA-dependent RNA polymerase (PDB ID 6M71) inhibitors, using a molecular docking. Molecular docking of these polyphenols were performed using Autodock 4.0 and Chimera 1.8.1 programs. Drug likeness and polyphenols pharmacokinetic properties were calculated using SWISSADME prediction website (http://www.swissadme.ch/). Remdesivir and ribavirin were used as standard antiviral drugs for comparison. Docking analysis results, ranked by binding energy value (ΔG) of several tested ligands toward COVID-19 polymerase were; remdesivir > gallic acid > quercetin > caffeine > ribavirin > resveratrol > naringenin > benzoic acid > oleuropein > ellagic acid. The binding energies were -8.51, - 7.55, - 7.17, -6.10, - 6.01, - 5.79, - 5.69, - 5.54, - 4.94 and -4.59 kcal/mol, respectively. All tested polyphenols performed hydrogen bonds with one or two of the nucleotide triphosphate entry channel (NTP) amino acids in COVID-19 polymerase (ARG 555, ARG 555, LYS 545), except caffeine and oleuropein. Binding of polyphenols to NTP of COVID-19 polymerase may influence in the entry of the substrate and divalent cations into the central active site cavity, inhibiting the enzyme activity. It appears promising that, gallic acid and quercetin exhibited high binding affinity than ribavirin toward COVID-19 polymerase and expressed good drug likeness and pharmacokinetic properties. Therefore, gallic acid and quercetin may represent a potential treatment option for COVID-19. Further researches are urgently required to investigate the potential uses of these polyphenols in COVID-19 treatment. Additionally, resveratrol, naringenin, benzoic and ellagic acid seem to have the best potential to act as COVID-19 polymerase inhibitors.
Targeting furin activity through in silico and in vitro drug repurposing strategy for SARS-CoV-2 spike glycoprotein cleavage repression
Authors: Villoutreix Bruno O. , Creemers John , Léger Yannick , Siegfried Geraldine , Decroly Etienne , Evrard Serge , Khatib Abdel-Majid 
Published: April 2020

Abstract
In December 2019, a new coronavirus was identified in the Hubei province of central china and named SRAS-CoV-2. This new virus induces COVID-19, a severe respiratory disease with high death rate. The spike protein (S) of SARS-CoV-2 contains furin-like cleavage sites absent the other SARS-like viruses. The viral infection requires the priming or cleavage of the S protein and such processing seems essential for virus entry into the host cells. Furin is highly expressed in the lung tissue and the expression is further increased in lung cancer, suggesting the exploitation of this mechanism by the virus to mediate enhanced virulence as shown by the higher risk of COVID-19 in these patients. In this study, we used structure- based virtual screening and a collection of about 8,000 unique approved and investigational drugs suitable for docking to search for molecules that could inhibits furin activity. Sulconazole, a broad-spectrum anti-fungal agent, was found to be of potential interest. Using Western blot analysis, Sulconazole was found to inhibit the cleavage of the cell surface furin substrate MT1-MMP that contains two furin cleavage sites similar to those of the SARS- CoV-2 spike protein. Sulconazole and analogs could be interesting for repurposing studies and to probe the yet not fully understood molecular mechanisms involved in cell entry.
Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Lanza Daniel C. F. , Lima João P. M. S. , Jerônimo Selma M. B. 
Published: April 2020

Abstract
Accurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false negative results and decreasing the need for standardization across different PCR protocols. In this work, we designed and described a set of primers and probes targeting conserved regions identified from a multiple sequence alignment of 2341 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes from the Global Initiative on Sharing All Influenza Data (GISAID). Those primers and probes were subsequently validated in 3067 SARS-CoV-2 whole-genome sequences. From these analyses, we obtained nine systems (forward primer + reverse primer + probe) that potentially anneal to highly conserved regions of the virus genome. In silico predictions also demonstrated that those primers do not bind to nonspecific targets for human, bacterial, fungal, or apicomplexan sequences. The availability of these primer and probe sequences will make it possible to accelerate the beginning of in vitro tests in order to validate more efficient protocols for the identification of SARS-CoV-2.
Estimating the malaria transmission over the Indian subcontinent in a warming environment using a dynamical malaria model
Authors: Chaturvedi Shweta , Dwivedi Suneet 
Published: April 2020

Abstract
Malaria is a major public health problem in India. The malaria transmission is sensitive to climatic parameters. The regional population-related factors also influence malaria transmission. To take into account temperature and rainfall variability and associated population-related effects (in a changing climate) on the malaria transmission over India, a regional dynamical malaria model, namely VECTRI (vector-borne disease community model) is used. The daily temperature and rainfall data derived from the historical (years 1961–2005) and representative concentration pathway (years 2006–2050) runs of the Coupled Model Intercomparison Project Phase 5 models have been used for the analysis. The model results of the historical run are compared with the observational data. The spatio-temporal changes (region-specific as well as seasonal changes) in the malaria transmission as a result of climate change are quantified over the India. The parameters related to the breeding cycle of malaria as well as those which estimate the malaria cases are analyzed in the global warming scenario.
A risk-based evaluation of onsite, non-potable reuse systems developed in compliance with conventional water quality measures
Authors: Schoen Mary E. , Jahne Michael A. , Garland Jay 
Published: April 2020

Abstract
Water quality standards (WQSs) based on water quality measures (e.g., fecal indicator bacteria (FIB)) have been used by regulatory agencies to assess onsite, non-potable water reuse systems. A risk-based approach, based on quantitative microbial risk assessment, was developed to define treatment requirements that achieve benchmark levels of risk. This work compared these approaches using the predicted annual infection risks for non-potable reuse systems that comply with WQSs along with the benchmark risk levels achieved by the risk-based systems. The systems include a recirculating synthetic sand filter or an aerobic membrane bioreactor (MBR) combined with disinfection. The greywater MBR system had predicted risks in the range of the selected benchmark levels. However, wastewater reuse with systems that comply with WQSs had uncertain and potentially high predicted risks (i.e., &gt;10−2 infections per person per year) in residential applications, due to exposures to viruses and protozoa. The predicted risks illustrate that WQSs based on FIB treatment performance do not ensure adequate treatment removal of viruses and protozoa. We present risk-based log10 pathogen reduction targets for intermediate-sized non-potable systems, which are 0.5 log10 less than those previously proposed for district-sized systems. Still, pathogen treatment performance data are required to better manage non-potable reuse risk.
Pressure loss reduction of pipe elements
Authors: Gönczi Gábor 
Published: April 2020

Abstract
A theoretical research was conducted from 2016 to 2018 which aimed to reduce the head loss of pipe networks in the pump stations. The results were promising and predicted an average head loss reduction by 30%. Afterwards, physical experiments were carried out to test the effectiveness of the new pipe designs. Two new prototype pipe sections were installed into one of our pump stations. The experiment was successful as two unique pipe sections installed in the discharge pipe reduced the head loss of the pump station by 25–26%. According to these results, we can set a target value of 30% head loss reduction at full pump station pipe reconstruction.
Novel Rapid Isocratic RP-HPLC Method for Simultaneous Estimation of Phenylephrine Hydrochloride, Paracetamol, Caffeine, Diphenhydramine Hydrochloride
Authors: Sonone Revati , Tandel Leena , Jain Vandana 
Published: April 2020

Background:
A tablet dosage form widely used in the treatment of cough and cold, containing
phenylephrine hydrochloride, paracetamol, caffeine, and diphenhydramine hydrochloride as active
pharmaceutical ingredient was selected for the development of a novel, rapid, simultaneous isocratic
reversed phase-high performance liquid chromatography (RP-HPLC) method.

Objective:
The objective of this paper was to develop and validate a novel, rapid, simple, precise, accurate
and reproducible RP-HPLC method for simultaneous estimation of phenylephrine hydrochloride,
paracetamol, caffeine, diphenhydramine hydrochloride in bulk and pharmaceutical dosage form.

Method:
Optimized chromatographic conditions were an isocratic elution with prontosil C18-column
(250×4.6 mm, 5 μ), methanol and 20mM phosphate buffer (55:45 v/v, pH 3 ) as mobile phase, flow rate
1.0 mL/min and UV detector set at λ max 220 nm. The method was validated for specificity, precision,
linearity, accuracy, sensitivity, and robustness as per the International Council for Harmonization guidelines.

Result:
The retention times of phenylephrine hydrochloride, paracetamol, caffeine, diphenhydramine
hydrochloride were found to be 2.8 min, 3.3 min, and 4.0 min and 7.3 min, respectively. This novel
method was found to be rapid, simple, linear (R2> 0.99), preciserelative standard deviation < 2.0 %),
accurate (recovery 98-102%), sensitive and robust.

Conclusion:
The proposed novel isocratic RP-HPLC method is rapid (short run time below 10min),
highly selective, precise, accurate, sensitive and robust. The method was successfully applied for the
simultaneous analysis of phenylephrine hydrochloride, paracetamol, caffeine, diphenhydramine hydrochloride
in a pharmaceutical dosage form.