bluuebunny/crossref_metadata_2025_split huggingface dataset:
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction
Authors: Cortés-Ciriano Isidro , Škuta Ctibor , Bender Andreas , Svozil Daniel 
Published: July 2020

AbstractAffinity fingerprints report the activity of small molecules across a set of assays, and thus permit to gather information about the bioactivities of structurally dissimilar compounds, where models based on chemical structure alone are often limited, and model complex biological endpoints, such as human toxicity and in vitro cancer cell line sensitivity. Here, we propose to model in vitro compound activity using computationally predicted bioactivity profiles as compound descriptors. To this aim, we apply and validate a framework for the calculation of QSAR-derived affinity fingerprints (QAFFP) using a set of 1360 QSAR models generated using Ki, Kd, IC50 and EC50 data from ChEMBL database. QAFFP thus represent a method to encode and relate compounds on the basis of their similarity in bioactivity space. To benchmark the predictive power of QAFFP we assembled IC50 data from ChEMBL database for 18 diverse cancer cell lines widely used in preclinical drug discovery, and 25 diverse protein target data sets. This study complements part 1 where the performance of QAFFP in similarity searching, scaffold hopping, and bioactivity classification is evaluated. Despite being inherently noisy, we show that using QAFFP as descriptors leads to errors in prediction on the test set in the ~ 0.65–0.95 pIC50 units range, which are comparable to the estimated uncertainty of bioactivity data in ChEMBL (0.76–1.00 pIC50 units). We find that the predictive power of QAFFP is slightly worse than that of Morgan2 fingerprints and 1D and 2D physicochemical descriptors, with an effect size in the 0.02–0.08 pIC50 units range. Including QSAR models with low predictive power in the generation of QAFFP does not lead to improved predictive power. Given that the QSAR models we used to compute the QAFFP were selected on the basis of data availability alone, we anticipate better modeling results for QAFFP generated using more diverse and biologically meaningful targets. Data sets and Python code are publicly available at https://github.com/isidroc/QAFFP_regression.
Combined PET/CT with thoracic contrast-enhanced CT in assessment of primary cardiac tumors in adult patients
Authors: Liu En-Tao , Sun Tao-Tao , Dong Hao-Jian , Wang Si-Yun , Chen Ze-Rui , Liu Chao , Shao Dan , Lian Zhou-Yang , Xie Qiu , Wang Shu-Xia 
Published: July 2020

Abstract
Background
18F-FDG PET/CT is a key molecular imaging modality to noninvasively assess and differentiate benign and malignant cardiac tumors. However, few benign cardiac tumors can be characterized by increased 18F-FDG uptake, which makes differential diagnosis difficult. This study sought to retrospectively evaluate whether combined 18F-FDG PET/CT with thoracic contrast-enhanced CT (CECT) helps in assessing primary cardiac tumors in adult patients, compared with CECT or PET/CT alone.

Methods
Forty-six consecutive patients who were diagnosed as primary cardiac tumors were enrolled. All patients underwent 18F-FDG PET/CT followed by thoracic CECT before biopsy or surgery. Visual qualitative interpretation and quantitative analysis were performed, and diagnostic performance was evaluated.

Results
More than half (16/29) of benign tumors exhibited with mild 18F-FDG uptake. There were significant differences in 18F-FDG uptake and the degree of absolute enhancement between benign and malignant tumors (P < 0.001). The combination of two modalities improved the specificity from 79 to 93%, the positive predictive value from 73 to 89%, and the accuracy of diagnosis from 85 to 93%. There were significant differences between PET/CT alone or thoracic CECT alone and combined modalities (P = 0.034 and P = 0.026, respectively). The combination with the optimal SUVmax cutoff value generated 94% sensitivity, 100% specificity, 97% negative predictive values, 100% positive predictive values, and 98% accuracy rates.

Conclusions
Combining 18F-FDG PET/C with thoracic CECT significantly improved specificity and accuracy compared to CECT or PET/CT alone in detecting tumors. This combination of diagnostic imaging is effective in differentiating malignant from benign masses.
Connecting Disjoint Nodes Through a UAV-Based Wireless Network for Bridging Communication Using IEEE 802.11 Protocols
Authors: Ullah Hanif , Abu-Tair Mamun , McClean Sally , Nixon Paddy , Parr Gerard , Luo Chunbo 
Published: July 2020

AbstractCooperative aerial wireless networks composed of small unmanned aerial vehicles(UAVs) are easy and fast to deploy and provide on the fly communication facilities in situations where part of the communication infrastructure is destroyed and the survivors need to be rescued on emergency basis. In this article, we worked on such a cooperative aerial UAV-based wireless network to connect the two participating stations. The proposed method provides on the fly communication facilities to connect the two ground stations through a wireless access point (AP) mounted on a UAV using the IEEE 802.11a/b/g/n. We conducted our experiments both indoor and outdoor to investigate the performance of IEEE 802.11 protocol stack including a/b/g/n. We envisioned two different cases: line of sight (LoS) and non-line of sight (NLoS). In LoS, we consider three different scenarios with respect to UAV altitude and performed the experiments at different altitudes to measure the performance and applicability of the proposed system in catastrophic situations and healthcare applications. Similarly, for NLoS, we performed a single set of experiments in an indoor environment. Based on our observations from the experiments, 802.11n at 2.4 GHz outperforms the other IEEE protocols in terms of data rate followed by 802.11n at 5 GHz band. We also concluded that 802.11n is the more suitable protocol that can be practiced in disastrous situations such as rescue operations and healthcare applications.
A new bound for the Jensen gap pertaining twice differentiable functions with applications
Authors: Khan Shahid , Adil Khan Muhammad , Butt Saad Ihsan , Chu Yu-Ming 
Published: July 2020

AbstractIn this paper, we present a new bound for the Jensen gap with the help of a Green function. Using the bound, we deduce a converse of the Hölder inequality as well. Finally, we present some applications of the main result in information theory.
Synchronization of bidirection multiple neural networks with impulsive coupling control
Authors: Wang Yong , Wu Ailong , Li Biwen 
Published: July 2020

AbstractThis paper is devoted to the study of the global synchronization of multiple neural networks (MNNs) via impulsive coupling control. Compared to one-layer neural networks, MNNs have more complex dynamics behavior and greater practical significance. In this paper, two interconnected bidirection MNNs are constructed; for this type of neural network system, each node in their network will be affected by the corresponding node in another network, then the synchronization problem of unidirection MNNs is extended to bidirection MNNs. In order to achieve synchronization of the bidirection MNNs, we adopt the method of impulsive coupling control, and together with the appropriate Lyapunov function, we deduce the relationship of the synchronization error system at the adjacent two impulsive moments, through iteration, and we finally obtain sufficient conditions to realize the global synchronization of the two interconnected bidirection MNNs. We illustrate the effectiveness of the results by simulation.
The first nationwide multicenter study of Acinetobacter baumannii recovered in Serbia: emergence of OXA-72, OXA-23 and NDM-1-producing isolates
Authors: Lukovic Bojana , Gajic Ina , Dimkic Ivica , Kekic Dusan , Zornic Sanja , Pozder Tatjana , Radisavljevic Svetlana , Opavski Nataša , Kojic Milan , Ranin Lazar 
Published: July 2020

Abstract
Background
The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. The aim of this nationwide study was to investigate the prevalence of CRAB isolates in Serbia and to characterize underlying resistance mechanisms and their genetic relatedness.

Methods
Non-redundant clinical samples obtained from hospitalized patients throughout Serbia were included in the prospective, observational, multicenter study conducted from January to June 2018. Samples were initially screened for the presence of Acinetobacter baumannii-calcoaceticus (Acb) complex using conventional bacteriological techniques. Acb complexes recovered from clinical samples obtained from inpatients with confirmed bacterial infections were further evaluated for the presence of A. baumannii. Identification to the species level was done by the detection of the blaOXA-51 gene and rpoB gene sequence analysis. Susceptibility testing was done by disk diffusion and broth microdilution method. CRAB isolates were tested for the presence of acquired carbapenemases (blaOXA-24-like, blaOXA-23-like,blaOXA-58-like, blaOXA-143-like, blaIMP, blaVIM, blaGIM, blaSPM, blaSIM, blaNDM) by PCR. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

Results
Acb complex was isolated in 280 out of 2401 clinical samples (11.6%). Overall, A. baumannii was identified in 237 out of 280 Acb complex (84.6%). CRAB prevalence was found to be 93.7% (237/222). The MIC50/MIC90 for imipenem and meropenem were 8/> 32 μg/mL and 16/> 32 μg/mL, respectively. Although susceptibility was high for colistin (95.7%; n = 227) and tigecycline (75.1%; n = 178), ten isolates (4.3%) were classified as pandrug-resistant. The following carbapenemases-encoding genes were found: 98 (44.2%) blaOXA-24-like, 76 (34.5%) blaOXA-23-like, and 7 (3.2%) blaNDM-1. PFGE analysis revealed six different clusters. MLST analysis identified three STs: ST2 (n = 13), ST492 (n = 14), and ST636 (n = 10). Obtained results evaluated that circulating CRAB clones in Serbia were as follows: blaOXA66/blaOXA23/ST2 (32.4%), blaOXA66/blaOXA23/blaOXA72/ST2 (2.7%), blaOXA66/blaOXA72/ST492 (37.8%), and blaOXA66/blaOXA72/ST636 (27.1%).

Conclusion
This study revealed extremely high proportions of carbapenem resistance among A. baumannii clinical isolates due to the emergence of blaOXA-72, blaOXA-23, and blaNDM-1 genes among CRAB isolates in Serbia and their clonal propagation.
Early morning off in patients with Parkinson’s disease: a Chinese nationwide study and a 7-question screening scale
Authors: Han Chao , Mao Wei , An Jing , Jiao Lifei , Chan Piu ,   on behalf of the China Early Morning Off (EMO) Study Group
Published: July 2020

Abstract
Background
Early morning off (EMO) is a common feature of Parkinson’s disease (PD). This study aimed to characterize its clinical features and develop a convenient and pragmatic self-assessment instrument in a Chinese nationwide population.

Methods
This study was conducted on 942 PD patients admitted to 55 clinic centers for movement disorders between June 2018 and May 2019 in China. Stepwise logistic regression analyses were performed to determine potential risk factors and the most predictive symptoms of EMO, as well as whether EMO was an independent risk factor of functional dependency in daily life. Based on this, a 7-question scale was derived for EMO screening. Diagnostic accuracy of this scale was assessed from the area under the receiver operative characteristic curve (AUROC) and its 95% confidence intervals (CIs). We further calculated sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the optimal cutoff point.

Results
EMO occurred in 49.2% of PD patients across all disease stages. We identified 7 symptoms most predictive of EMO, including bradykinesia or rigidity, excessive sweating or salivation, difficulty in turning on or getting out of bed, muscle cramp, fatigue or sleepiness, frozen state or freezing gait, and tremor. The resulting 7-item scale was confirmed to be of good discrimination with a relatively large AUROC of 0.83, a relatively high sensitivity of 75.7%, specificity of 77.5%, PPV of 76.5%, and NPV of 76.7%. Nonideal nighttime sleep, long PD duration, advanced H&Y stages, posture instability gait difficulty-dominant or mixed subtypes, and high levodopa dose were independently associated with increased risk of EMO. EMO patients were at 87% higher (OR = 1.87, 95%CI: 1.07–3.32) risk of experiencing functional dependency in daily living compared with their counterparts.

Conclusions
We demonstrated that EMO is a common feature for PD patients across all disease stages and put forward an EMO-specific screening card of sufficient accuracy and brevity. Meanwhile we have thrown some light upon potential determinants and negative health effects of EMO. Our findings may exert great impact on improving the awareness, recognition and management of EMO in PD patients.
Heat exposure impairs porcine oocyte quality with suppressed actin expression in cumulus cells and disrupted F-actin formation in transzonal projections
Authors: Yin Chao , Liu Jie , Chang Zhanglin , He Bin , Yang Yang , Zhao Ruqian 
Published: July 2020

AbstractBackgroundTranszonal projections (TZPs) constitute a structural basis for the communication between the oocyte and its surrounding cumulus cells (CCs), which play critical roles in promoting the oocyte maturation. Previously we found that heat stress (HS) causes loss of TZPs in porcine cumulus-oocyte complexes (COCs) with decreased density of filamentous actin (F-actin). However, the time-course responses of F-actin and its monomeric actins (β-actin and γ-actin) during thein vitromaturation of oocytes remain unclear.ResultsIn this study, excised porcine ovaries were exposed to HS at 41.5 °C for 1 h before COCs were isolated and maturedin vitrofor 44 h. HS significantly reduced oocyte quality, characterized by impaired cumulus expansion, delayed meiotic resumption and lower survival rate and polar body extrusion rate, as well as decreased expression of mitochondrial DNA-encoded genes and elevated mitochondrial reactive oxygen species concentration. Expression of β-actin and γ-actin in CCs increased gradually with oocytes maturation, which was significantly reduced in HS group, especially at 24 h and/or 44 h ofin vitromaturation. By contrast, the number of TZPs and the fluorescence intensity of F-actin in zona pellucida decreased gradually during oocytes maturation, which were significantly reduced by HS at 24 h ofin vitromaturation. Moreover, colocalization analyses revealed both β-actin and γ-actin contribute to the F-actin formation in porcine TZPs, and the colocalization of F-actin with GJ protein connexin 45 was significantly reduced in heat-exposed COCs.ConclusionsThe results indicate that the suppression of actin expressions in CCs, which may lead to the F-actin unstabilization in TZPs, will subsequently contribute to the compromised quality of oocytes under HS.
Evaluation of the effect of fatigue on the coping behavior of international truck drivers
Authors: Pourabdian Siamak , Lotfi Saeid , Yazdanirad Saeid , Golshiri Parastoo , Hassanzadeh Akbar 
Published: July 2020

Abstract
Background
Fatigue can affect the behavior of drivers. While the driver must be able to respond and cope appropriately to the critical situations, which is known as the ability to cope with a crisis. It is likely that the fatigue can change the people’s coping style and thereby increase the chance of the crashes. Therefore, the present study aimed to investigate the effects of fatigue on the coping behavior of international truck drivers.

Methods
This study was conducted on 239 of international truck drivers employed in Iran. The Endler and Parker coping strategies questionnaire (CISS) and Persian version of the Fatigue Multidimensional Fatigue Inventory (MFI) were used to evaluate the coping styles of the drivers and the drivers’ fatigue, respectively.

Results
The mean values of the total fatigue before and after traveling were 36.77 and 76.13, respectively. The mean values of coping styles of the problem-oriented, emotion-oriented, and avoidance before traveling were 53.66, 40.91, and 38.17, respectively, and those after traveling were 45.59, 51.18, and 36.45, respectively. The chi-square test demonstrated that there was a significant difference in the coping style of drivers before and after the trip (P <  0.001), and the percent of individuals with emotion-oriented increased.

Conclusions
In general, the results showed that fatigue due to traveling could change the coping styles of subjects from problem-oriented to emotion-oriented and avoidance. This can increase the statistics of driving accidents.
Estimating runtime of a job in Hadoop MapReduce
Authors: Peyravi Narges , Moeini Ali 
Published: July 2020

AbstractHadoop MapReduce is a framework to process vast amounts of data in the cluster of machines in a reliable and fault-tolerant manner. Since being aware of the runtime of a job is crucial to subsequent decisions of this platform and being better management, in this paper we propose a new method to estimate the runtime of a job. For this purpose, after analysis the anatomy of processing a job in Hadoop MapReduce precisely, we consider two cases: when a job runs for the first time or a job has run previously. In the first case, by considering essential and efficient parameters that higher impact on runtime we formulate each phase of the Hadoop execution pipeline and state them by mathematical expressions to calculate runtime of a job. In the second case, by referring to the profile or history of a job in the database and use a weighting system the runtime is estimated. The results show the average error rate is less than 12% in the estimation of runtime for the first run and less than 8.5% when the profile or history of the job has existed.
Disrupted classes, undisrupted learning during COVID-19 outbreak in China: application of open educational practices and resources
Authors: Huang Ronghuai , Tlili Ahmed , Chang Ting-Wen , Zhang Xiangling , Nascimbeni Fabio , Burgos Daniel 
Published: July 2020

AbstractWith the coronavirus (COVID-19) outbreak in China, the Chinese government decided to ban any type of face-to-face teaching, disrupting classes and resulting in over 270 million students being unable to return to their universities/schools. Therefore, the Ministry of Education (MoE) launched an initiative titled ‘Ensuring learning undisrupted when classes are disrupted’ by reforming the entire educational system and including an online education component. However, this quick reform in this unexpected critical situation of widespread COVID-19 cases harbours several challenges, such as the lack of time and teacher/student isolation. This paper discusses the possibility of using open educational resources (OER) and open educational practices (OEP) as an effective educational solution to overcome these challenges. Particularly, this study presents a generic OEP framework built on existing open-practice definitions. It then presents, based on this framework and based on the challenges reported by several Chinese education specialists during two national online seminars, a set of guidelines for the effective use of OER and OEP for both teaching and learning. Finally, this study presents some recommendations for the better adoption of OER and OEP in the future. The findings of this study can help researchers and educators apply OER and OEP for better learning experiences and outcomes during the COVID-19 outbreak.
Clinical and prognostic value of tumor volumetric parameters in melanoma patients undergoing 18F-FDG-PET/CT: a comparison with serologic markers of tumor burden and inflammation
Authors: Reinert Christian Philipp , Gatidis Sergios , Sekler Julia , Dittmann Helmut , Pfannenberg Christina , la Fougère Christian , Nikolaou Konstantin , Forschner Andrea 
Published: July 2020

Abstract
Background
To investigate the association of tumor volumetric parameters in melanoma patients undergoing 18F-FDG-PET/CT with serologic tumor markers and inflammatory markers and the role as imaging predictors for overall survival.

Methods
A patient cohort with advanced melanoma undergoing 18F-FDG-PET/CT for planning metastasectomy between 04/2013 and 01/2015 was retrospectively included. The volumetric PET parameters whole-body MTV and whole-body TLG as well as the standard uptake value (SUV) peak were quantified using 50%-isocontour volumes of interests (VOIs) and then correlated with the serologic parameters lactate dehydrogenase (LDH), S-100 protein, c-reactive protein (CRP) and alkaline phosphatase (AP). PET parameters were dichotomized by their respective medians and correlated with overall survival (OS) after PET/CT. OS was compared between patients with or without metastases and increased or not-increased serologic parameters.

Results
One hundred seven patients (52 female; 65 ± 13.1yr.) were included. LDH was strongly associated with MTV (rP = 0.73, p <  0.001) and TLG (rP = 0.62, p <  0.001), and moderately associated with SUVpeak (rP = 0.55, p <  0.001). S-100 protein showed a moderate association with MTV (rP = 0.54, p <  0.001) and TLG (rP = 0.48, p <  0.001) and a weak association with SUVpeak (rP = 0.42, p <  0.001). A strong association was observed between CRP and MTV (rP = 0.66, p <  0.001) and a moderate to weak association between CRP and TLG (rP = 0.53, p <  0.001) and CRP and SUVpeak (rP = 0.45, p <  0.001). For differentiation between patients with or without metastases, receiver operating characteristic (ROC) analysis revealed a cut-off value of 198 U/l for serum LDH (AUC 0.81, sensitivity 0.80, specificity 0.72).
Multivariate analysis for OS revealed that both MTV and TLG were strong independent prognostic factors. TLG, MTV and SUVpeak above patient median were accompanied with significantly reduced estimated OS compared to the PET parameters below patient median (e.g. TLG: 37.1 ± 3.2 months vs. 55.9 ± 2.5 months, p <  0.001). Correspondingly, both elevated serum LDH and S-100 protein were accompanied with significantly reduced OS (36.5 ± 4.9 months and 37.9 ± 4.4 months) compared to normal serum LDH (49.2 ± 2.4 months, p = 0.01) and normal S-100 protein (49.0 ± 2.5 months, p = 0.01).

Conclusions
Tumor volumetric parameters in 18F-FDG-PET/CT serve as prognostic imaging biomarkers in patients with advanced melanoma which are associated with established serologic tumor markers and inflammatory markers.