bluuebunny/crossref_metadata_2025_split huggingface dataset:
EDock: blind protein–ligand docking by replica-exchange monte carlo simulation
Authors: Zhang Wenyi , Bell Eric W. , Yin Minghao , Zhang Yang 
Published: May 2020

AbstractProtein–ligand docking is an important approach for virtual screening and protein function annotation. Although many docking methods have been developed, most require a high-resolution crystal structure of the receptor and a user-specified binding site to start. This information is, however, not available for the majority of unknown proteins, including many pharmaceutically important targets. Developing blind docking methods without predefined binding sites and working with low-resolution receptor models from protein structure prediction is thus essential. In this manuscript, we propose a novel Monte Carlo based method, EDock, for blind protein–ligand docking. For a given protein, binding sites are first predicted by sequence-profile and substructure-based comparison searches with initial ligand poses generated by graph matching. Next, replica-exchange Monte Carlo (REMC) simulations are performed for ligand conformation refinement under the guidance of a physical force field coupled with binding-site distance constraints. The method was tested on two large-scale datasets containing 535 protein–ligand pairs. Without specifying binding pockets on the experimental receptor structures, EDock achieves on average a ligand RMSD of 2.03 Å, which compares favorably with state-of-the-art docking methods including DOCK6 (2.68 Å) and AutoDock Vina (3.92 Å). When starting with predicted models from I-TASSER, EDock still generates reasonable docking models, with a success rate 159% and 67% higher than DOCK6 and AutoDock Vina, respectively. Detailed data analyses show that the major advantage of EDock lies in reliable ligand binding site predictions and extensive REMC sampling, which allows for the implementation of multiple van der Waals weightings to accommodate different levels of steric clashes and cavity distortions and therefore enhances the robustness of low-resolution docking with predicted protein structures.
Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens
Authors: Su Hailong , Zhao Yu , Zheng Lirong , Wang Shifeng , Shi Huoying , Liu Xiufan 
Published: May 2020

AbstractH9N2 avian influenza virus has spread worldwide, and vaccination with an inactivated virus is currently the major prevention method in China. To further understand the effect of the selection pressure from antibodies on the evolution of H9N2 avian influenza virus, F/98 (A/Chicken/Shanghai/F/98), which is the vaccine representative of H9N2 avian influenza virus in East China, was used for serial passaging for 20 generations in chickens with and without vaccination. After plaque purification from trachea and lung tissues, 390 quasispecies were obtained. The second-generation quasispecies under the selection pressure of vaccine antibodies had undergone 100% antigen variation, while after passaging to the fifth generation, only 30–40% of the quasispecies displayed antigen variation when there was no selection pressure of vaccine antibodies, implying that the selection pressure of vaccine antibodies promotes the antigen variation of F/98. We found for the first time that there were three mutation hotspots in the HA genes of the quasispecies under the selection pressure of vaccine antibodies, which were K131R, A168T, and N201D. Moreover, under the selection pressure of vaccine antibodies, 10 amino acids (67–76) of the NA protein of all quasispecies were deleted, and PB2 of the quasispecies had undergone a high-frequency R355K mutation. However, without selection pressure of vaccine antibodies, NP had undergone two high-frequency mutations, namely, V186I and L466I, and a high-frequency mutation of L77I appeared in the NS gene. This result shows that the vaccine antibody selection pressure could control and regulate gene variation of the F/98 virus. Compared to that of the parental virus F/98, the EID50 of the twentieth passaged virus under the selection pressure of vaccine antibodies did not change, while the EID50 of the twentieth passaged virus without selection pressure of vaccine antibodies was significantly enhanced by 794 times. Furthermore, the twentieth passaged virus with selection pressure from vaccine antibodies lost its lethal ability in embryonated chicken eggs, whereas the EID50 of the twentieth passaged virus without selection pressure of vaccine antibodies increased to 6.3 times that of the F/98 strain. All the above results show that the selection pressure of vaccine antibodies promotes the antigen variation of H9N2 avian influenza virus and plays a role in regulating and controlling gene mutation of H9N2 avian influenza virus.
A coupled system of generalized Sturm–Liouville problems and Langevin fractional differential equations in the framework of nonlocal and nonsingular derivatives
Authors: Baleanu D. , Alzabut J. , Jonnalagadda J. M. , Adjabi Y. , Matar M. M. 
Published: May 2020

AbstractIn this paper, we study a coupled system of generalized Sturm–Liouville problems and Langevin fractional differential equations described by Atangana–Baleanu–Caputo (ABC for short) derivatives whose formulations are based on the notable Mittag-Leffler kernel. Prior to the main results, the equivalence of the coupled system to a nonlinear system of integral equations is proved. Once that has been done, we show in detail the existence–uniqueness and Ulam stability by the aid of fixed point theorems. Further, the continuous dependence of the solutions is extensively discussed. Some examples are given to illustrate the obtained results.
Parameter interval of positive solutions for a system of fractional difference equation
Authors: Ghanbari Kazem , Haghi Tahereh 
Published: May 2020

AbstractThis paper deals with a typical system of Caputo fractional difference equations. Using the Guo–Krasnosel’skii fixed point theorem, we find a parameter interval for which at least one positive solution of the system exists. We give two examples to illustrate the results.
Impact of reduction in contact time activity of infected individuals on the dynamics and control of directly transmitted respiratory infections in SIR models
Authors: Safan Muntaser 
Published: May 2020

AbstractThis paper aims to study the impact of using an educational strategy on reducing the efforts needed to control respiratory transmitted infections represented by SIR models, taking into account heterogeneity in contacts between infected and non-infected individuals. Therefore, a new incidence function, in which the difference in contact time activity between infected and non-infected individuals is taken into account, is formulated. Equilibrium and stability analyses of the model have been carried out. The model has been extended to include the effect of herd immunity and the analysis showed that the higher the percent reduction$\widehat{P}_{r}$Pˆrin the contact-activity time of infected individuals is, the lower the critical vaccination coverage level$p_{c}$pcrequired to eliminate the infection is, and therefore, the lower the infection’s minimum elimination effort is. Another extension of the basic model to include a control strategy based on treating infected individuals at rateαwith a maximum capacity treatment$\mathcal{I}$Ihas been considered. The equilibrium analysis showed the existence of multiple subcritical and supercritical endemic equilibria, while the stability analysis showed that the model exhibits a Hopf bifurcation. Simulations showed that the higher the maximum treatment capacity$\mathcal{I}$Iis, the lower the value of the critical reduction in infected individuals’ time activity$P_{r}^{\star}$Pr⋆, at which a Hopf bifurcation is generated, is. Simulations with parameter values corresponding to the case of influenza A have been carried out.
Early discontinuation of empirical antibiotic treatment in neutropenic patients with acute myeloid leukaemia and high-risk myelodysplastic syndrome
Authors: Niessen F. A. , van Mourik M. S. M. , Bruns A. H. W. , Raijmakers R. A. P. , de Groot M. C. H. , van der Bruggen T. 
Published: May 2020

Abstract
Introduction
Current guidelines advocate empirical antibiotic treatment (EAT) in haematological patients with febrile neutropenia. However, the optimal duration of EAT is unknown. In 2011, we have introduced a protocol, promoting discontinuation of carbapenems as EAT after 3 days in most patients and discouraging the standard use of vancomycin. This study assesses the effect of introducing this protocol on carbapenem and vancomycin use in high-risk haematological patients and its safety.

Methods
A retrospective before-after study was performed comparing a cohort from 2007 to 2011 (period I, before restrictive EAT use) with a cohort from 2011 to 2014 (period II, restrictive EAT use). Neutropenic episodes related to chemotherapy or stem cell transplantation (SCT) in patients with acute myeloid leukaemia (AML) or high-risk myelodysplastic syndrome (MDS) were analysed. The primary outcome was the use of carbapenems and vancomycin as EAT during neutropenia, expressed as days of therapy (DOT)/100 neutropenic days and analysed with interrupted time series (ITS). Also the use of other antibiotics was analysed. Safety measurements included 30-day mortality, ICU admittance within 30 days after start of EAT and positive blood cultures with carbapenem-susceptible microorganisms.

Results
Three hundred sixty-two neutropenic episodes with a median duration of 18 days were analysed, involving 201 patients. ITS analysis showed decreased carbapenem use with a step change of − 16.1 DOT/100 neutropenic days (95% CI − 26.77 to − 1.39) and an overall reduction of 21.6% (8.7 DOT/100 neutropenic days). Vancomycin use decreased with a step change of − 13.7 DOT/100 neutropenic days (95% CI − 23.75 to − 3.0) and an overall reduction of 54.7% (14.6 DOT/100 neutropenic days). The use of all antibiotics combined decreased from 155.6 to 138 DOT/100 neutropenic days, a reduction of 11.3%. No deaths directly related to early discontinuation of EAT were identified, also no notable difference in ICU-admission (9/116 in period I, 9/152 in period II) and positive blood cultures (4/116 in period I, 2/152 in period II) was detected.

Conclusion
The introduction of a protocol promoting restrictive use of EAT resulted in reduction of carbapenem and vancomycin use and appears to be safe in AML or high-risk MDS patients with febrile neutropenia during chemotherapy or SCT.
Multidrug-resistant tuberculosis transmission among middle school students in Zhejiang Province, China
Authors: Zhang Yu , Zhou Lin , Liu Zheng-Wei , Chai Cheng-Liang , Wang Xiao-Meng , Jiang Jian-Min , Chen Song-Hua 
Published: May 2020

Abstract
Background
Despite significant advancements in the treatment and diagnosis of tuberculosis (TB) over the past decade, drug-resistant TB remains an increasing threat to public health. TB outbreaks are most commonly reported in schools considering the delay in TB diagnosis, sustained contact, and overcrowding observed in schools. This report describes multidrug-resistant TB (MDR-TB) transmission in a school in Zhejiang Province. We aimed to raise awareness regarding MDR-TB transmission among students.

Case presentation
The index patient was a 16-year-old girl in the second year of junior middle school in Zhejiang Province, China, who had been experiencing persistent cough and expectoration for 37 days since 1 March 2014. She tested positive for smear pulmonary and extrapulmonary TB on 8 April 2014 and was subsequently diagnosed with MDR-TB on 1 May 2014. However, the patient was resistant to isoniazid, rifampicin, ethambutol, and streptomycin. Thus, she was suspended from school for anti-TB treatment. All 54 students who were in close contact with the index patient in the same class were screened, and 5 tested positive on the tuberculin skin test. Their exposure time to the index patient was approximately 37 days. Three classmates were subsequently diagnosed with MDR-TB, with similar resistance profiles nearly two years later. Their average discovery delay was 55 days. These three classmates were also suspended from school for anti-TB treatment. During the treatment period, four students visited the local TB-designated hospital for further consultation every month and were followed up once a month by the local community health service center until they were completely cured.

Conclusions
Discovery delay for an index patient played a primary role in MDR-TB transmission inside the school. To immediately detect TB, morning examinations in schools should be performed. TB trackers and case managers should work closely with public health workers and physicians in cases of TB outbreaks or transmissions involving students. Moreover, individuals who are in close contact with MDR-TB patients should undergo careful clinical follow-up for at least two years. Implementing a joint examination strategy to ensure early detection, diagnosis, and treatment of MDR-TB transmission is recommended.
Blue whale (Balaenoptera musculus) sightings off the coast of Virginia
Authors: Engelhaupt Dan T. , Pusser Todd , Aschettino Jessica M. , Engelhaupt Amy G. , Cotter Mark P. , Richlen Michael F. , Bell Joel T. 
Published: May 2020

AbstractWe report on two sightings of individual blue whales (Balaenoptera musculus) off the coast of Virginia during marine mammal surveys. On 11 April 2018, during a vessel survey off the coast of Virginia, a single blue whale was observed approximately 100 km east-northeast of Virginia Beach. On 10 February 2019, another single blue whale was recorded during an aerial survey approximately 135 km east-southeast of Virginia Beach. These observations mark the first time this endangered species has been documented with photographs off the coast of Virginia, and represent the southernmost confirmed sightings in waters of the United States Atlantic Exclusive Economic Zone (EEZ). At the time of the vessel observation, numerous fin whales (Balaenoptera physalus), humpback whales (Megaptera novaeangliae), and North Atlantic right whales (Eubalaena glacialis), were observed within the same approximately 8 km2area as the blue whale. For the aerial sighting, the blue whale was seen feeding among at least 15 fin whales in an area approximately 4 km2. These sightings contribute to the small body of information existing for the late winter/early spring distribution of blue whales in waters of the western North Atlantic.
Pattern of recovery and outcomes of patient reported physical function and pain interference after ankle fusion: a retrospective cohort study
Authors: Kohring Jessica M. , Houck Jeffrey R. , Oh Irvin , Flemister Adolf S. , Ketz John P. , Baumhauer Judith F. 
Published: May 2020

Abstract
Background
Research on outcomes after ankle fusion focuses on basic activities of daily living, fusion rates, and gait parameters. Little has been reported on the patient’s perspective after surgery. The purpose of this study was to determine the change in patient reported physical function and pain interference after ankle fusion surgery to guide patient expectations and improve provider communication.

Methods
This was a retrospective review of prospectively collected patient reported outcome measurement information system (PROMIS) data in 88 ankle arthrodesis procedures performed from May 2015 to March 2018. The PROMIS Physical function (PF) and pain interference (PI) measures were collected as routine care. Linear mixed models were used to assess differences at each follow-up point for PF and PI. Preoperative to last follow-up in the 120–365 day interval was assessed using analysis of variance. Outcomes included T-scores, z-scores, and PROMIS-Preference (PROPr) utility scores for PF and PI and the percentage of patients improving by at least 4 T-score points.

Results
The linear mixed model analysis for PF after the 120–149 days, and for PI, after 90–119 days, indicated recovery plateaued at 39–40 for PF and 57–59 for PI T-scores. The change in the PI T-score was the greatest with a mean T-score improvement of − 5.4 (95% CI − 7.7 to − 3.1). The proportion of patients improving more than 4 points was 66.2% for either PF or PI or both. The change in utility T-scores for both PF (0.06, 95% CI 0.02 to 0.11) and PI (0.15, 95% CI 0.09 to 0.20) was significantly improved, however, only PI approached clinical significance.

Conclusion
Average patients undergoing ankle fusion experience clinically meaningful improvement in pain more so than physical function. Average patient recovery showed progressive improvement in pain and function until the four-month postoperative time point. Traditional dogma states that recovery after an ankle fusion maximizes at a year, however based on the findings in this study, 4 months is a more accurate marker of recovery. A decline in function or an increase in pain after 4 months from surgery may help to predict nonunion and other complications after ankle arthrodesis.

Level of evidence
Level II, prospective single cohort study.
Effect of fluoride on the learning and memory ability of larvae of Zaprionus indianus
Authors: Mishra Diksha , Kumari Rishu , Ranjan Smita , Yasmin Shahla 
Published: May 2020

Abstract
Background
Many pesticides contain fluoride that enters the food chain and affect the non-target organisms. Fluoride is a known neurotoxin and may cause neurobehavioral defects. A study was conducted to see the effect of fluoride on the learning and memory ability of larvae of Zaprionus indianus. The learning and memory ability of 2nd instar larvae of normal (control) and sodium fluoride (NaF)-treated Zaprionus indianus was compared.

Results
Sublethal concentration of NaF for Z. indianus was found to be 0.8 ppm. Olfactory assay results showed that the larvae of normal (control) Z. indianus had better learning and memory ability in comparison to NaF-treated larvae.

Conclusions
This study indicates that the insects exposed to pesticides containing fluoride may have difficulty in locating food sources and carrying out pollination.
A rare chest X-ray sign in the diagnosis of an intracardiac bullet: case report
Authors: Osman Mohamed , Khalil Reham , Abdalla Ahmed Hany , Katta Azza , Nashef Samer , Elameen Sameh 
Published: May 2020

Abstract
Background
Gunshot injuries to the heart are often seen in cardiac surgical practice. Victims are usually investigated with various types of imaging modalities, including simple chest X-ray (CXR) which is a primary imaging modality that can easily locate a bullet and is useful in monitoring before surgical intervention as bullets may migrate.

Case presentation
A 32-year-old man was admitted as an emergency in a primary hospital after being injured by a gunshot to the chest. The bullet entry was over the back of the left shoulder with no exit point seen. The chest X-ray showed left pleural effusion and a retained intrathoracic bullet. A chest drain was inserted and drained 2200 ml of blood. Computed tomography (CT) scan showed an intracardiac bullet associated with left lower lobe contusion and left-sided hemothorax. He was urgently transferred to theater for exploration via left thoracotomy. The bullet could not be found so the inlet point in the left ventricle was sutured. After stabilizing the patient, he was referred to a specialized cardiac center for further management.
The patient arrived at our center 2 days after the injury, fully conscious and hemodynamically stable. On arrival, chest X-rays were obtained to rule out possible migration of the bullet and revealed that the retained bullet was still within the cardiac silhouette. The X-ray appearance of the bullet showed a characteristically double contour, strongly suggesting that the bullet had lodged in the heart muscle and was moving with each heartbeat.
The patient was transferred to the theater for median sternotomy. The aorta, superior vena cava, and inferior vena cava were cannulated, and cardiopulmonary bypass was initiated. The aorta was cross-clamped and the cardioplegia was given. Palpation of the still heart readily identified the bullet within the interventricular septum. The left ventricle was opened 1 cm from the left anterior descending artery just on top of the bullet. The bullet was successfully retrieved. The bullet was transfixing the septum causing a small ventricular septal defect which was closed using a Teflon patch and the ventricle was repaired.

Conclusion
The double contour appearance of the bullet indicates that the bullet is moving and strongly suggests an intramyocardial position.
Response of economic growth to the dynamics of service sector in Nigeria
Authors: Adetokunbo Abiodun Moses , Edioye Ochuwa Priscillia 
Published: May 2020

AbstractThe misconception of services as being non-productive has led to the neglect of the service sector in both economic theory and applied economic researches. The Nigerian economy highly depends on the oil sector to generate revenue for the entire economy. This study examines the response of economic growth to the dynamics of the service sector in Nigeria from the windows of governance indicators. Using annual data series, endogenous growth model, and autoregressive distributed lag technique, transportation and communication service subsector is significant and positively related to economic growth. Health service subsector and transportation and communication subservice sector are significant and positively related to economic growth when governance indicators were accounted for. Interaction of the subservice sectors with governance indicators shows that none of the service subsectors were significant but were positively related to economic growth. The study shows that the activities of the education subsector have not contributed significantly to economic growth. Thus, for education to contribute positively to economic growth there is a need for increase in budgetary allocation to education subsector. Efforts made to control corruption and promote government effectiveness should be reviewed frequently to checkmate the processes of governance, so that bureaucratic processes would not hinder services from contributing significantly to economic growth.