bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Genotypic Characterization of HBV in HIV-Infected Patients from Kwazulu-Natal, South Africa
Authors: Modise Lorato Mosetsanagape , Sithebe Nomathamsanqa Patricia 
Published: April 2020

Abstract
Introduction: The co-infection of HIV with HBV is very common due to shared mode of transmission. HBV/HIV co-infection impact on low HBeAg expression, high HBV replication, causes progressive liver disease, cirrhosis, liver cancer and high mortality. Coinfection may lead to cross-resistance of HBV and HIV drugs due to drug-related immune therapeutic pressure or hepatotoxicity. These challenges necessitate continuous surveillance for HBV among HIV infected individuals to aid patient treatment management. Hence we conducted this study to characterise HBV among HIV infected patients in Durban, KwaZuluNatal of South Africa.Methods: Serum was screened for HBsAg using ELISA, followed by DNA extraction from all samples. Genotyping of HBV was done through PCR amplification, Sanger sequencing and phylogenetic analysis. Results: Of the 50 samples in this study 100% (n=50/50) were HBsAg positive. HBV/HIV coinfection was 78% (n=41/50) based on PCR amplification of the HBV partial surface gene and 92% (n=38/41) of the amplicons were successfully sequenced. Phylogenetic and sequence analyses identified patients nucleotide sequence as Genotype A. Mutations prevalence in the HBsAg region was 47% (n=18/38); including mutations associated with diagnostic failure (K122R and T143S) and 7 vaccines escape mutations (P127T, G145R, S207N, Y200T, E164D, Y206H and L209V). Prevalence of mutations associated with drug resistance was 57% (n=8/14) within the reverse transcriptase region. Drug resistance mutations included lamivudine resistance at 71% (n=5/7), telbivudine resistance at 57% (n=4/7), 14% (n=1/7) for entecavir resistance and 43% (n=3/7) for adefovir resistance. Mutations causing resistance to lamivudine and telbivudine were M204V, L180M, V163I, and S202K; with S202K also causing resistance to entecavir and adefovir resistance mutation were I253Y, I223V and M250I. The drug susceptibility prevalence was 68% (n=26/38). Multiple drug resistance mutations within a single sample contained L180M, M204V, S202K and M250I mutations. Conclusion: This study shows the predominance of HBV genotype A in HIV-infected patients and the HBV mutations present in HBV/HIV co-infected individuals. HBV mutations associated with drug resistance suggest the need for continuous HBV screening and use of tenofovir ART regimen among HBV/HIV co-infected individuals.
Transcriptional and Free Radical Responses to LVAD Therapy
Authors: Dhar Kajari , Asmini KC , Qiu Fang , Basma Hesham , Savalia Krupak , Jones Jocelyn , Moulton Alexandra M. , Zimmerman Matthew C. , Um John , Anderson Daniel , Hyden Marshall , Lowes Brian D. 
Published: April 2020

Abstract
Background: Myocardial recovery with Left ventricular assistant device (LVAD) therapy is dichotomous with some patients obtaining remission from end-stage heart failure whereas most require transplantation or remain as destination therapy. Our goal was to determine transcriptional and free radical responses to LVAD treatment. Methods: Tissues were collected from patients before and after LVAD placement in non-ischemic dilated cardiomyopathy patients (n=14) along with non-failing controls (n=3). RNA sequencing (RNASeq) analysis quantified transcriptional profiles by using a custom targeted panel of heart failure related genes on the PGM sequencer. The differential expression analysis between groups was conducted using edgeR (Empirical analysis of digital gene expression data in R) package in Bioconductor. Ingenuity Pathway Analysis (IPA) was carried out on differentially expressed genes to understand the biological pathways involved. Electron Paramagnetic Resonance (EPR) Spectroscopy was utilized to measure levels of free radicals in whole blood collected pre- and post-LVAD implantation (n=16). Results: 35 genes were differentially expressed in pre-LVAD failing hearts compared to non-failing controls. In response to LVAD therapy, only Pyruvate dehydrogenase kinase 4 (PDK4) and period circadian protein homolog 1 (PER1) were altered with 34 heart failure related genes still differentially expressed post-LVAD compared to non-failing hearts. IPA showed that DNA methylation-related genes were upregulated in both pre- and post-LVAD and was persistent with a Z-score of 2.00 and 2.36 for DNA Methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B), respectively. Inhibition of micro RNA21 (mir21) was also significant on pathway analysis in the post-LVAD population with a Z-score of -2.00. Levels of free radicals in blood of pre- and post-LVAD patients did not change significantly. Conclusion: LVAD therapy does not reverse many of the transcriptional changes associated with heart failure. Persistent changes in gene expression may be related to ongoing oxidative stress, continued DNA methylation, or changes in metabolism. PDK4 is a key regulator of glucose metabolism and its increased expression by LVAD therapy inhibited pyruvate metabolism.
Corona virus disease 2019: hysteresis effect of chest CT and the correlation of its severity with lymphocyte count in peripheral blood
Authors: Li Kui , Wang Wei , Zhao Chang-Wu , Wu Lei , Zhu Ya-Nan , Ran Ren-Yu , Li Tao , Jiang Zi-Cheng 
Published: April 2020

Abstract
Background Chest computed tomography (CT) has been accepted to provide reference for the diagnose and assessment the severity of Corona Virus Disease 2019 (COVID-19). Decrease in the counts of lymphocyte and leukocyte is used as the diagnostic indicator of suspected COVID-19 cases. However, there is few study on exploring the hysteresis of chest CT changes and the predictive role of lymphocyte count in peripheral blood before treatment in the severity of the disease. Methods A retrospective analysis was carried out focusing on the data of patients tested to be positive for RNA nucleic acid test of SARS-CoV-2 with nasopharyngeal swabs in 4 hospitals. An independent assessment was performed by one clinician using the DEXIN FACT Workstation Analysis System, and the assessment results were reviewed by another clinician. Furthermore, the mean hysteresis time was calculated according to the median time from progression to the most serious situation to improvement of chest CT in patients after fever relief. The optimal scaling regression analysis was performed by including variables with statistical significance in univariate analysis. In addition, a multivariate regression model was established to investigate the relationship of the percentage of lesion/total lung volume with lymphocyte and other variables. Results In the included 166 patients with COVID-19, the average value of the most serious percentage of lesion/total lung volume was 6.62, of which 90 patients with fever had an average hysteresis time of 4.5 days after symptom relief, with a similar trend observed in those without fever. Multivariate analysis revealed that lymphocyte count in peripheral blood and transcutaneous oxygen saturation decreased with the increase of the percentage of lesion/total lung volume. Meanwhile, age, fever and C-reactive protein exhibited no such effect in the established model. Conclusions There is a hysteresis effect in the improvement of chest CT image in relative to fever relief in patients with COVID-19. Besides, the percentage of lesion/total lung volume of chest CT correlates negatively with lymphocyte count in peripheral blood and transcutaneous oxygen saturation. Findings in our study may contribute to understanding the disease status of patients with COVID-19 and grasping the opportunity of treatment by clinicians.
A simple transmission dynamics model for predicting the evolution of COVID-19 under control measures in China
Authors: Shang Chenjing , Yang Yang , Chen Gui-Ying , Shang Xiao-Dong 
Published: April 2020

Abstract
Epidemic forecasting provides an opportunity to predict geographic disease spread and counts when an outbreak occurs and plays a key role in preventing or controlling their adverse impact. However, conventional prediction models based on complex mathematical modeling rely on the estimation of model parameters, which yields unreliable and unsustainable results. Herein, we proposed a simple model for predicting the epidemic transmission dynamics based on nonlinear regression of the epidemic growth rate and iterative methods, which is applicable to the progression of the COVID-19 outbreak under the strict control measures of the Chinese government. Our model yields reliable and accurate results as confirmed by the available data: we predicted that the total number of infections in mainland China would be 91,253, and the maximum number of beds required for hospitalized patients would be 62,794. We inferred that the inflection point (when the growth rate turns from positive to negative) of the epidemic across China would be mid-February, and the end of the epidemic would be in late March. This model is expected to contribute to resourceallocation and planning in the health sector while providing a theoretical basis forgovernments to respond to future global health crises or epidemics.
Sofosbuvir as a potential alternative to treat the SARS-CoV-2 epidemic
Authors: Jácome Rodrigo , Campillo-Balderas José Alberto , de León Samuel Ponce , Becerra Arturo , Lazcano Antonio 
Published: April 2020

Abstract
As of today, there is no antiviral for the treatment of the SARS-CoV-2 infection, and the development of a vaccine might take several months or even years. The structural superposition of the hepatitis C virus polymerase bound to sofosbuvir, a nucleoside analog antiviral approved for hepatitis C virus infections, with the SARS-CoV polymerase shows that the residues that bind to the drug are present in the latter. Moreover, a multiple alignment of several SARS-CoV-2, SARS and MERS-related coronaviruses polymerases shows that these residues are conserved in all these viruses, opening the possibility to use sofosbuvir against these highly infectious pathogens.
Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames
Authors: Wang Yong , Mao Jun-Ming , Wang Guang-Dong , Qiu Ze , Yao Qin , Chen Ke-Ping 
Published: April 2020

Abstract
The causative agent of COVID-19 is a severe acute respiratory syndrome-related coronavirus which has been officially named SARS-CoV-2. Here we report the discovery of extremely low CG abundance in its open reading frames. We found that CG reduction in SARS-CoV-2 is achieved mainly through mutating C/G into A/T, and CG is the best target for mutation. In view of energy usage, a coronavirus with low CG abundance has higher efficiency in translating its RNA, because the secondary structure formed by viral genome is less stable. 5’-untranslated region of SARS-CoV-2 has much more CGs and is capable of recruiting host ribosomes to initiate translation. Notably, genomes of cellular organisms also have very low CG abundance, suggesting that mutating C/G into A/T occurs universally in all life forms. Moreover, CG is related to mutational hotspots and CpG islands in cellular organisms. The relationship between them is worthy of further investigations.
How American Mineralogist and the Mineralogical Society of America influenced a career in mineralogy, petrology, and plate pushing, and thoughts on mineralogy's future role
Authors: Ernst W.G. 
Published: April 2020

Abstract
My geologic research began at Carleton College. I studied heavy minerals in some midcontinent orthoquartzites, publishing my very first paper in American Mineralogist in 1954. As a master's candidate at the University of Minnesota, I investigated igneous differentiation in a diabase-granophyre sill of the Duluth Gabbro Complex. Later, in a Ph.D. program at Johns Hopkins University, I became Joe Boyd's apprentice at the Geophysical Laboratory (GL), and for a time was phase-equilibrium god of the Na-amphiboles. Doctoral research earned me an offer of a UCLA assistant professorship as a mineralogist in 1960. There, I continued pursuing amphibole P-T stability relations in lab and field. My glaucophane phase equilibrium research would later be found to have instead crystallized Na-magnesiorichterite. However, amphibole research led me to map field occurrences of HP-LT (high P-low T) blueschists of the Franciscan Complex. Thus, when plate tectonics emerged in the late 1960s, I was deep in the subduction zone. My recent studies focused on the petrology and geochemistry of oceanic crustal rocks, Californian calc-alkaline arcs, and coesite ± microdiamond-bearing crustal margin rocks in various parts of Eurasia. Other works treated global mineral resources and population, mineralogy and human health, and early Earth petrotectonic evolution. I tried to work on important problems, but mainly studied topics that fired my interest.
For the future, I see the existential challenge facing humanity and the biosphere as the imperative to stop our overdrafting of mineral resources. This will require reaching a dynamic equilibrium between the use and replenishment of near-surface resources (i.e., nutrients) essential for life. Earth scientists are planetary stewards, so we must lead the way forward in life-supporting mineral usage, recycling, substitution, and dematerialization. In any event, sustainable development will soon return to the Earth's Critical Zone of life because Mother Nature—the ruling terrestrial economist—abhors long-term overdrafting of resources1.
Impacto ambiental y social del vertimiento de residuos sólidos y escombros sobre la calidad del río Medellín y algunos de sus afluentes
Authors: Carvajal Flórez Elizabeth 
Published: April 2020

La investigación que se desarrolla a continuación, tiene como objetivo principal evaluar la influencia del vertimiento de residuos sólidos domiciliarios y escombros sobre la calidad del río Medellín y algunos de sus afluentes principales como la quebrada La Hueso, La Iguaná y La García, bajo criterios sanitarios, ambientales y sociales. Se utilizó el método teórico práctico, que aborda el problema de la disposición inadecuada de residuos domiciliarios y escombros sobre las laderas y lechos de las quebradas objeto de estudio, estableciendo en la realidad social una explicación veraz y oportuna de la ocurrencia de dichas prácticas de disposición.El trabajo de campo permitió realizar monitoreos de la calidad de agua a través de los parámetros DBO 5 , DQO, sólidos suspendidos, disueltos y sedimentables, pH, oxígeno disuelto, conductividad y turbiedad, así como la cuantificación y determinación de la composición física de algunos de los materiales encontrados sobre las márgenes y laderas más próximas al cauce. De la misma forma, se determinaron composiciones granulométricas de escombros y materiales de arrastre, se analizaron las causas generadoras de la situación problema y se formuló un esquema de gestión que incluyó cada uno de los componentes del manejo integral de los residuos sólidos. Los recorridos de campo y las metodologías de selección cualitativas y cuantitativas, permitieron clasificar las quebradas bajo tres problemáticas preponderantes: La García con vertimientos recurrentes de escombros, La Hueso con presencia de materiales de arrastre como consecuencia de la explotación en canteras y La Iguaná con el vertimiento de residuos sólidos domiciliarios.En términos generales puede deducirse que la transformación del paisaje de cada una de las quebradas es alta, debido a la gran intervención antrópica relacionada con la explotación de materiales, vertimientos de aguas residuales, escombros, residuos domiciliarios, ganadería, entre otros. Estas a su vez generan problemas como erosión, pérdida de las coberturas vegetales, malos olores, proliferación de vectores, entre otros, además de los graves problemas hidráulicos que desencadenan socavación de márgenes, desbordamientos e inundaciones, que afectan las comunidades cercanas a la microcuenca. Finalmente, el análisis de causalidad determinó que el origen de la problemática estudiada no solo recae en el generador, sino por el contrario se constituye en una responsabilidad compartida de autoridades ambientales, empresas de aseo, autoridades de control, entre otros. El esquema de gestión propuesto tiene como pilar fundamental “La educación y prevención”, entrelazado con un marco normativo y elementos sociales y técnicos, componentes indispensables para garantizar que toda la gestión de los residuos funcione satisfactoriamente en la región.
Hydrogeochemistry and groundwater flow mechanisms in shallow aquifer in Yaoundé, Cameroon
Authors: Fouépé Takounjou Alain , Takem Eyong Gloria , Kuitcha Dorice , Kringel Robert , Fantong Yetoh Wilson , Ndjama Josephine , Tejiobou Alex 
Published: April 2020

Abstract
Hydrogeochemical processes and flow mechanisms of groundwater in the urban area of Yaoundé were investigated using major chemical constituents, stable isotopes (18O and 2H), and multivariate statistical analysis. Thirty five groundwater samples were collected and analysed for various parameters. Hydrogeochemical evolution visualized with the Gibbs diagram showed that the groundwater is mainly controlled by water–rock interactions. Factor analysis on the other hand identified three major groups of geochemical constituents and showed that weathering and anthropogenic inputs are the dominant factors controlling groundwater chemistry in the study area. Isotopic analyses revealed that oxygen-18 of groundwater (18O = −2.96 ‰ VSMOW) is close to that of rainfall (18O = −2.47), indicating that the groundwater is recharged by rainwater without evaporation. The geogenic composition of urban groundwater in Yaoundé is modified by secondary processes and anthropogenic input.
No-regret selection of effective control handles for integrated urban wastewater systems management under parameter and input uncertainty
Authors: Ledergerber J. M. , Maruéjouls T. , Vanrolleghem P. A. 
Published: April 2020

Abstract
Regulatory water quality limits are extended from the wastewater resource recovery facility (WRRF) to the sewer system. It is thus necessary to properly integrate those systems for the evaluation of the overall emissions to the receiving water. The integration of the sewer system and the WRRF, however, leaves us with multiple potential options to reduce these emissions. The proposed approach builds on previous research using global sensitivity analysis (GSA) as a screening method for available control handles. It considers parameter and input uncertainty to select control handles that generate large benefits even if the model differs from reality. Results from a real-life case study indicate that the three top-rated handles are comparably effective for all considered uncertainty and variability scenarios. But the results also showed that this does not apply to lower-rated handles.
An efficient method for removal of pentachlorophenol using adsorption and microwave regeneration with different magnetic carbon nanotubes
Authors: Zhang Xue , Cui Chunyue , Wang Ying , Chang Jing , Ma Dong , Wang Jing 
Published: April 2020

Abstract
Various magnetic carbon nanotubes (CNTs) Co0.5M0.5Fe2O4-CNTs (M = Cu, Mn, Ni, Zn) were successfully prepared and applied for treatment of pentachlorophenol (PCP) with adsorption and microwave irradiation process. The Co0.5M0.5Fe2O4-CNTs were characterized by transmission electron microscopy, X-ray diffraction, vibrating sample magnetometry, and microwave absorption spectroscopy. The adsorption experiment results showed the adsorption capacity for PCP was in the following order: Co0.5Cu0.5Fe2O4-CNTs &gt; Co0.5Mn0.5Fe2O4-CNTs &gt; Co0.5Ni0.5Fe2O4-CNTs &gt; Co0.5Zn0.5Fe2O4-CNTs. After adsorption, the Co0.5M0.5Fe2O4-CNTs was separated by magnetic field and regenerated by microwave irradiation at 850 W for 180 s. It was confirmed that after six adsorption and microwave regeneration cycles, the regeneration efficiency maintained over 90%. In particular, Co0.5Cu0.5Fe2O4-CNTs exhibited excellent adsorption capacity and reusability. These results can open a new avenue for treatment of chlorinated organic compounds with efficiently and non-secondary pollution.
Application of two-component pressure approach and Harten–Lax–van Leer (HLL) solver to model transient flow with regard to air entrapment
Authors: Ahadzadeh Negin , Tabesh Massoud 
Published: April 2020

AbstractWater distribution systems are basically designed to convey pressurized flow; however, in some situations such as the intermittent operation of the system, the network may experience a transition between free-surface and pressurized flow. On the other hand, combined sewer systems, designed basically for free-surface flow, may undergo pressurization due to extreme rainfalls. During transient flow, free-surface flow changes into a pressurized flow (and vice versa) which could be accompanied by intensive transient pressures causing structural damages to the system. In a pipe filling process, the existing air can be entrapped due to improper ventilation, intensifying the transient pressures in some cases. In this paper, the two-component pressure approach (TPA) and a Harten–Lax–van Leer Riemann solution are applied to model transient flow. The model is validated by comparing its results with the analytical solution of three simple examples, and then the model with an air chamber as the downstream boundary is used to simulate a literature experimental setup that includes air pocket entrapment. As the volume of the air pocket decreases, the errors of the model increase due to the inherent deficiency of the one-dimensional model. Furthermore, it is recommended to limit the Courant number to 0.5 for high acoustic wave speeds.
Assessment of the hydrological response of an urban watershed to rainfall-runoff events in different land use scenarios – Belo Horizonte, MG, Brazil
Authors: Rosa Deyvid W. B. , Nascimento Nilo O. , Moura Priscilla M. , Macedo Gustavo D. 
Published: April 2020

AbstractIntense urbanization results in greater soil sealing and a consequent increase in surface runoff. When high soil sealing rates and high slopes are encountered in small catchments, high volume and short duration precipitation events increase the probability of flash floods. This study evaluates the hydrological response of an urban catchment with regard to rainfall-runoff events in the following scenarios: current land use, without a detention basin which has been part of the system since the 1970s, with the maximum soil sealing allowed by legislation, and with green infrastructure implantation in 100%, 50% and 10% of the suitable area. Hydrological modelling was performed using the Storm Water Management Model (SWMM). Six level gauges installed along the length of the stream provided the data used in model calibration and validation. The model calibration process provided adequate results: the average Nash-Sutcliffe coefficient was 0.72, the mean error of peak flow was 11% and the mean error of the runoff volume was 12%. Rainfall based on 2-, 10-, 50- and 100-year events were simulated for each scenario, as well as two observed events. In the scenario without the detention basin, an average elevation of 10% in the peak flow was observed in the catchment outlet. In the scenario with maximum soil sealing, the catchment outlet peak flow increased by 30% on average. On the other hand, in the scenario with green infrastructure implementation in 100%, 50% and 10% of the available areas, the outlet peak flow was reduced by 60%, 30% and 5%, respectively. Results indicated the efficiency of the detention basin to reduce flooding, the importance of green area preservation to reduce peak flows, as well as the catchment potential of green infrastructure implementation and the hydrological benefits that they can provide, increasing infiltration and reducing runoff volume and peak flow.