bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency?
Authors: Hassanzadeh Reza , Shabani-Mashcool Soheila 
Published: May 2022

Abstract
Predicting drug-target interactions has become an important bioinformatics issue because it is one of the critical and preliminary stages of drug repositioning. Therefore, scientists are trying to develop more accurate computational methods for predicting drug-target interactions. These methods are usually based on machine learning or recommender systems and use biological and chemical information to improve the accuracy of predictions. In the background of these methods, there is a hypothesis that similar drugs have similar targets. So, the similarity between drugs as chemical information is added to the computational methods to improve the prediction results. The question that arises here is whether this claim is actually true? If so, what method should we use to calculate drug-drug similarities? Will we obtain the same improvement from any method we use?Here, we want to investigate this claimed positive effect. For this purpose, we consider different types of real similarities, random similarities, four important datasets and four state-of-the-art methods. Our results show that the type of data, the method which is used to predict the interactions, and the algorithm used to calculate the similarities are all important, and it cannot be easily stated that adding drug-drug similarities can significantly improve the results. Therefore, our results could suggest a checklist for scientists who want to improve their machine learning methods.
Transcriptome research on differentially expressed genes in a thermotolerant yeast strain from Daqu of Luzhou-flavor liquors
Authors: Liu Yanbo , Gu Wenning , Li Haideng , Zhao Zhijun , Han Suna , Wang Xian , Sun Xiyu , Pan Chunmei 
Published: May 2022

Abstract
Background: As for thermotolerance of yeasts, early research focuses on comparative biology. However, there is rare research on genes related to thermotolerance of yeasts.Morphological observation, trehalose concentration, and cellular structure of a thermotolerant yeast strain were basically studied. Together with RNA-Seq, the differentially expressed genes (DGEs) related to the thermotolerance of the liquor-making yeast strain at 28, 37 and 43 ºC were screened out at the transcriptome level. It was found trehalose concentration increment can improve thermotolerance,and the destruction of strain cellular structure led to a decline in thermotolerance.Results: After treatment of the thermotolerant yeast strain at 28 ºC compared with 37 ºC, 517 DGEs were screened out, including 435 upregulated genes and 82 downregulated genes. After treatment at 37 ºC relative to 43 ºC, 632 DGEs were recognized, including 393 upregulated genes and 239 downregulated genes.Conclusions: By combining physicochemical property analysis and transcriptome analysis, this preliminary study uncovers the DEGs responsible for the thermotolerance of a thermotolerant yeast strain, and theoretically underlies further research on the high temperature tolerance of liquor-making yeasts.
Characterization of tungsten distribution in tungsten-rich slag and sediment by leaching experiment
Authors: Song Hongyu , Cao Yaowu , Miao Zheyan , Luo Hao , Guo Qinghai 
Published: May 2022

Abstract
The adverse environmental effects of tungsten have been underestimated for a long time. Recent studies have demonstrated that dissolved tungstate is mobile in aqueous environments and exhibits severe toxicological impacts. If substantial tungsten slags were directly exposed, they would potentially pollute the surrounding waters and soils. The objective of this study was to investigate the pollution and ecological risks of tungsten-rich slags and sediments as a result of leaching. In this study, samples of tungsten-rich slags and sediments were collected from Chenzhou and Tengchong (China), with the highest tungsten concentration up to 378.1 mg/kg. To investigate the pollution and ecological risks of tungsten-rich slags and sediments as a result of leaching, sequential extraction procedures (SEP) and batch leaching experiments were conducted. According to the Tessier SEP results, the residual fraction accounted for more than 90% of the total tungsten in most samples, while the Wenzel SEP results showed over 52% of the hydrous oxides bound fraction except for the samples SP02 and ZN02. Thus, the Tessier SEP underestimated the proportions of the Fe and Al oxides bound fraction and the environmental risks of tungsten. In contrast, the Wenzel SEP was superior to the Tessier SEP in terms of extracting the amorphous hydrous oxides bound fraction and crystalline hydrous oxides bound fraction of tungsten due to the use of more suitable extraction reagents. The leaching experiments demonstrated the tungsten concentrations in the leachate samples were up to 105.6 µg/L. Notably, leaching of tungsten from the tungsten-rich slags and sediments under acid conditions was less effective than under alkaline conditions, which was attributed to the strong adsorption of tungsten onto Fe/Al (hydro)oxides under acid conditions.
Peridynamic simulations of damage in indentation and scratching of 3C-SiC
Authors: Xu Yimeng , Zhu Pengzhe 
Published: May 2022

Abstract
The cubic silicon carbide (3C-SiC) has broad application prospects in many fields due to its excellent material properties. The modeling of damage in 3C-SiC due to contact loads is important yet challenging. In this paper, simulations based on ordinary state-based peridynamics (PD) theory are proposed to model the damage of 3C-SiC in indentation and scratching. The constitutive parameters of 3C-SiC for PD simulation are obtained by performing MD simulations of nanoindentation. It is found that in the indentation simulations the initiation and propagation of cracks are observed, which shows that the PD can model the crack formation and propagation in the indentation process of brittle solid materials. During the scratching process, the variation of friction force is consistent with that of material wear. It is also found that the specific cutting energy increases nonlinearly with the decrease of scratching depth due to size effect. In addition, for the scratching with double indenters, the volume of material removal is more than twice that of scratching with an indenter due to the coupling effect of the two indenters under certain conditions. This paper demonstrates that PD is a powerful tool to investigate the indentation and scratching process of brittle solid materials.
The Comparison of Clinical, Laboratory, and Radiological Findings in Immunocompromised and Immunocompetent Patients with COVID-19: A Case-Control Study
Authors: Abasian Ladan , Jafari Fatemeh , SeyedAlinaghi SeyedAhmad , Yazdi Niloofar Ayoobi , Daraei Morteza , Ahmadinejad Nasrin , Ghiasvand Fereshteh , Khalili Hosein , Seifi Arash , Maydani Mohsen , Behnezhad Farzane , Ahmadinejad Zahra 
Published: May 2022

Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) with significant morbidity and mortality. We reported and compared the clinical and para-clinical findings of immunocompromised and immunocompetent COVID-19 patients in a case-control study at the Imam Khomeini hospital in Tehran, Iran.Methods: A total of 107 immunocompromised COIVD patients as the case group and 107 immunocompetent COVID patients as the control group was recruited in the study. The participants were matched based on age, and sex. The patients’ information was retrieved from the hospital records in an information sheet. Associations between clinical and para-clinical findings with the immune status were assessed using bivariate and multivariate analyses. The clinical trial registration number is not applicable.Results: The initial pulse rate and recovery time were significantly higher in immunocompromised patients (P <0.05). Myalgia, nausea/vomiting, loss of appetite, headache, and vertigo were more frequently reported by the control group (P <0.05). In terms of the duration of prescribed medications, Sofosbovir time was longer in the case group; while Ribavirin time was longer in the control groups (P <0.05). The most common complication in the case group was ARDS although no major complications were observed in the control group. In the multivariate analysis, recovery time and Kaletra prescription were significantly higher in immunocompromised compared to the immunocompetent group. Conclusions: Recovery time was significantly higher in the immunocompromised compared to the immunocompetent group. This informs the current practice of dominant COVID-19 clinical course in immunocompromised patients and communicates the related implications.
An Inactivation Gate of the BsYetJ Calcium Channel That Becomes Functional in the Endoplasmic Reticulum Environment
Authors: Lan Yu-Jing , Cheng Chu-Chun , Chu Shu-Chi , Chen Hung-Ying , Li Chieh-Chin , Kao Te-Yu , Chiang Yun-Wei 
Published: May 2022

Abstract
The transmembrane BAX inhibitor-1-containing motif 6 (TMBIM6) is an anti-apoptotic endoplasmic reticulum (ER) membrane protein. The suppression of apoptosis by TMBIM6 is linked to its role in regulating calcium homeostasis. However, the molecular mechanisms underlying the calcium regulation in the ER remain poorly understood. Using mutagenesis and fluorescence-based functional assays, this study investigates all the highly conserved negatively charged residues in the BsYetJ (a bacterial homolog of TMBIM6) and reveals that the charged residues E49 and R205 cooperatively act as a calcium-selectivity filter determining the channel conductance. This study identifies the conformations of BsYetJ in the ER environment using electron spin resonance and molecular dynamics. Together with the functional data, these previously undescribed structures provide new insights of how BsYetJ regulates calcium-dependent inactivation by interconversion between two coexisting conformations. Overall, this study provides a framework for understanding the non-canonical calcium gated membrane protein, which will facilitate structure-based development of more effective medications for TMBIM6.
RPP-gene Pyramiding Confers Higher Resistance Level to Asian Soybean Rust
Authors: Panho Maiara Cecilia , Fernandes Rogê Afonso Tolentino , Menegazzi Caroline Patrícia , Campagnolli Otavio Ramos , de Quadra Felipe Chade , Madella Laura Alexandra , Meira Daniela , Malone Gaspar , Junior Salvador Lima Brito , Benin Giovani 
Published: May 2022

Abstract
Asian soybean rust (ASR) causes large reductions in soybean yield, affecting the entire grain market. With low fungicide efficiency, the use of resistant cultivars can be an economical, safe, efficient, and sustainable control alternative. However, the great variability and aggressiveness of ASR and the use of Rpp genes are limited. Thus, gene pyramiding is a promising strategy for the development of cultivars with high resistance to a greater number of isolates. Thus, the aim of this study was to evaluate sister lines with different pyramided Rpp gene for resistance to Phakopsora pachyrhizi and identify which combination of Rpp genes had higher levels of resistance under field conditions. All Rpp-pyramided lines showed higher levels of resistance, with significant reductions in sporulation levels (SL), number of uredinia per lesion (NoU), and frequency of lesions with uredinia (%LU), compared to the resistance sources PI200487 (Rpp5), PI200492 (Rpp1), PI230970 (Rpp2), PI459025A (Rpp4), PI506764 (Rpp3, 5), PI587880A (Rpp1-b), PI594538A (Rpp1-b), and PI594723 (Rpp1-b). Rpp-pyramided lines carrying Rpp1-b + Rpp1-b, Rpp2 + Rpp1-b, Rpp4 + Rpp1-b, and single gene Rpp1-b were classified as “highly resistant”. Furthermore, one sister line, 52117-57 (Rpp2 + Rpp1-b), showed immunity under field conditions. The Rpp-pyramided genes are an alternative for achieving high resistance levels against ASR.
The role of superficial and deep layers in the generation of high frequency oscillations in the human epileptic cortex
Authors: Fabo Daniel , Bokodi Virag , Tóth Emilia , Szabó Johanna-Petra , Salami Pariya , Keller Corey J. , Hajnal Boglárka , Thesen Thomas , Devinsky Orrin , Doyle Werner , Mehta Ashesh , Madsen Joseph , Eskandar Emad , Erőss Lorand , Ulbert István , Halgren Eric , Cash Sydney S. 
Published: May 2022

Abstract
Objective:Describing intracortical laminar organization of high frequency oscillations (HFOs).Methods:We recorded potential gradients with laminar microelectrode arrays (LME) for current source density (CSD) and multi-unit activity (MUA) analysis of interictal discharges (IID) and HFOs in the neocortex and mesial temporal lobe of focal epilepsy patients. Results:Ripples were only observed in 9/29 patients, all within the seizure onset zone (SOZ). Ripples variably (≈50%) coincided with IIDs. CSD analysis revealed slow ripples (<150Hz) to exhibit an alternating sink-source pair in the upper cortical layers. In contrast, fast ripples (>150Hz) were biased to the lower layers, tending to precede the superficial activity (10-30ms).Conclusion: Our findings suggest that cortical slow ripples are generated primarily in upper layers while fast ripples and associated MUA in deeper layers. The dissociation of macro- and microdomains suggests that microelectrode recordings may be more selective for SOZ-linked ripples.Significance:We found a complex interplay between neural activity in the neocortical laminae during ripple formation. We observed a potential leading role of cortical neurons in deeper layers, suggesting a refined utilization of LMEs in SOZ localization.
Comparative study: performance of pesticides hybrid configuration electrical sensors of different types of Si nanocrystallites structures incorporated with gold nanoparticles
Authors: Rashid Rasha B. , Alwan Alwan M. , Mohammed Mohammed S. 
Published: May 2022

Abstract
Four hybrid configuration pesticide electrical sensors were synthesized by incorporating gold nanoparticles AuNPs on pore-like, mud-like, horizontally aligned nanopillars (HA-Si nanopillars), and Si quantum dots (SiQDs) silicon structures. Laser-induced etching; at different power densities, was employed to synthesize the Si nanostructures. The hybrid configurations were produced via an easy, low cost and fast dipping process in an aqueous solution of HAuCl4. Two configurations of pesticide electrical sensors: Al/Si nano/n c-Si/Al and Al/AuNPs/Si nano/n c-Si/Al were prepared and studied. Electrical properties of the sensors with and without chlorpyrifos pesticide were recorded at room temperature. The results displayed sensors’ performance affected by Au nanoparticles' grain size, deposition manner, specific surface area (SSA) of AuNPs, and morphological features of the Si nanostructure. A significant improvement in sensitivity and stability of the hybrid configuration were achieved. The pore-like hybrid configurations sensors showed better performance than the hybrid configuration sensors; due to the higher integrated SSA and the deposition of AuNPs on pore boundaries, in addition to the high pores density.
Contamination and health risk assessment of heavy metals in surface sediments from the Arabian Gulf, Saudi Arabia
Authors: El-Sorogy Abdelbaset S. , Al-Kahtany Khaled 
Published: May 2022

Abstract
The coastline of the Arabian Gulf attracts people throughout the year for tourism and fishing activities. The present work aimed to document the contamination and human health assessment of heavy metals (HMs) in 34 surface sediment samples collected along the Ras Abu Ali coastline. Enrichment factor (EF), contamination factor (CF), and sediment quality guideline (SQG) were calculated and used to estimate sediment contamination, while the chronic daily intake (CDI), hazard index (HI), cancer risk (CR), and total lifetime cancer risk (LCR) were determined for human health assessment via ingestion, inhalation and dermal contact pathways on both adults and children. The averages of the HMs (μg/g dry weight) were in the following: Fe (4808) > Ni (13.00) > Zn (6.89) > Cr (7.86) > V (6.67) > Pb (3.50) > Cu (4.14) > As (2.47) > Co (1.43). Results of EF indicated minor enrichment with Ni, Pb, and As, and no enrichment with the remaining HMs. Based on CF, the coastal sediments of Ras Abu Ali showed low contamination with HMs. CDI and HI values were higher among children in comparison to adults, suggesting that children were at higher risk of non-carcinogenic exposure than adults. LCR values indicated that that no significant health hazards for people inhabited the study area from the carcinogenic Pb, Cr, and As.
Digital health applications and the fast-track pathway to public health coverage in Germany: Challenges and opportunities based on first results
Authors: Lantzsch Hendrikje , Eckhardt Helene , Campione Alessandro , Busse Reinhard , Henschke Cornelia 
Published: May 2022

Abstract
Objectives
Evidence-based decision-making is the sine qua non for safe and effective patient care and the long-term functioning of health systems. Since Digital Health Applications (DiHA) in Germany have been undergoing a systematic pathway to be reimbursed by statutory health insurance for more than one and a half years, the procedure is also attracting attention in other European countries. We therefore investigate current coverage decisions in Germany and the underlying evidence on care effects for DiHA.
Methods
Based on public available data of the German Institute for Medicines and Medical Devices and further literature, all DiHA that can be reimbursed in Germany were systematically investigated on the basis of predefined criteria (e.g. security, data protection, quality) and presented descriptively. Studies that are used as the evidence base for the decision on reimbursement were examined for their quality. Furthermore, a framework was used to determine potential evidence requirements to be used for DiHA assessments.
Results
By February 2022, 30 DiHA had been included in the DiHA register and can thus be reimbursed by the statutory health insurance. Most DiHA were therapeutic applications for mental illness and were based on cognitive behavioural therapy. One third of all DiHA were permanently included in the benefit basket while two thirds were initially included conditionally. For each of permanently included DiHA, a randomised controlled trial had been conducted to demonstrate positive care effects, with the majority of studies having a high risk of bias.
Conclusions
The so far unique system of evidence-based decision-making on coverage of DiHA in Germany leaves room for improvements both in terms of study reporting and the use of patient-relevant structure and process outcomes to demonstrate the effects of care in addition to the medical benefits. New study designs are needed, which at the same time open up the way for the use of real-world data. With appropriate evidence, DiHA can offers an opportunity in care as an adjunct to existing therapy. However, the risk of bias assessment raises doubts about the evidence and consequently also about the justification of their high costs averaging around € 150 per month.
The safety assessment of irrigation fluid management for shoulder arthroscopy and its effect on postoperative efficacy
Authors: Zhuang Chengyu , Yang Renhao , Xu Yang , Song Yanyan , Zhang Yin , Liu Jingfeng , Yang Fan , Huang Xiaohong , Liu Jia , Wang Xiaoning , Wang Yin , Wang Lei 
Published: May 2022

Abstract
Background context: With the popularity of shoulder arthroscopy, the releted complications have recently studied, among which the excessive fluid extravasation is a potentially dangerous complication. Most relevant studies involve respiratory system, while the reports fouced on the cardiovascular system and postoperative function recovery are rare. The objective is to reveal the effects of the excessive fluid extravasation on cardiovascular system and postoperative functionMethod: A retrospective analysis was made on the clinical data of 92 patients, in whom 84 cases of rotator cuff injury, 3 cases of shoulder instability, 3 cases of fracture of the greater tuberosity of the humerus, and 2 cases of frozen shoulder. The basic information of the patients, ASES and VAS scores in each period before and after surgery, cardiac index (CI) and pulse pressure variation (PPV) before and after anesthesia, and changes in arm circumference and deltoid muscle circumference before and after surgery were recorded and evaluated. Result: The preoperative CI was affected by changes in anesthesia status and body position, while PPV is not affected by anesthesia and body position. Multivariate mixed-effects model analysis of CI found that there was a statistically significant difference between patients older than 55 years old and those with obesity (BMI>24). After the operation, the retention of irrigation fliud had an effect on the circumference of the deltoid, neck and arm, but the effect on the circumference of the deltoid was statistically significant (P<0.001 (95%CI: [0.30, 1.00]). The multivariate analysis of ASES scores at 3 and 6 months after surgery showed that the fluid retention volume was correlated with the ASES score at 3 months after surgery, especially when the retention volume was greater than 2L (P=0.001 (95%). %CI: [-12.49,-3.22]). Conclusion: The retention of irrigation fliud after shoulder arthroscopic surgery causes swelling of local limbs, and also has a certain effect on peripheral blood vessels, which is mainly reflected in its influence on PPV and the postoperation function. Therefore, the surgeon needs to improve the surgical technique, shorten the operation time and reduce the fluid retention.
Chemical composition, antioxidant and antibacterial activities of Drymaria cordata (Linn.) Willd. against chloramphenicol-resistant Bacillus subtilis and β-lactams-resistant Pseudomonas aeruginosa
Authors: Arya Atul , Kumar Suresh , Kain Dolly , Ahanger Ab Majeed , Suryavanshi Amrita , Kumar Vandana 
Published: May 2022

Abstract
The current study was done to evaluate the chemical composition, antioxidant and antibacterial activities of Drymaria cordata extract in three solvents i.e. methanol (DCM), hexane (DCH) and water (DCW) against chloramphenicol-resistant Bacillus subtilis and β-lactams-resistant Pseudomonas aeruginosa. Phytochemical screening and Fourier transform-infrared spectroscopy (FTIR) showed the presence of phenols, amines, hydroxy group, and amino-related components. Gas chromatography-mass spectrometry (GCMS) depicts the presence of antibacterial compounds such as hexanedioic acid, hexadecanoic acid, nonadecadiene, hexadecen-1-ol, octadecadienoic acid and neophytadiene. DPPH free radicals scavenging assay exhibit maximum percentage inhibition in DCM (71.57 %) at the concentration of 1000μg/ml. The total antioxidant through phosphomolybdate assay was observed in DCM with values 834.44 ± 4.01 mg AAE/g of extract. For antibacterial activities, DCM shows best zone of inhibition (ZOI) (8 mm at 100 µg/ml to 15.17 mm at 1000 µg/ml) and minimum inhibitory concentration (MIC) (75 µg/ml) as compared to other extracts against Bacillus subtilis. Also, DCM shows zone of inhibition (ZOI) (6.83 mm to 13.17 mm) and minimum inhibitory concentration (MIC) (70 µg/ml) as compared to other extracts against Pseudomonas aeruginosa. These results indicate that the Drymaria cordata methanol extract possesses good antibacterial and antioxidant properties which justify its use against pathogenic bacteria.