bluuebunny/crossref_metadata_2025 huggingface dataset:
Relation Selective Graph Convolutional Network for Skeleton-Based Action Recognition
Authors: Yang Wenjie , Zhang Jianlin , Cai Jingju , Xu Zhiyong
Published: December 2021

Graph convolutional networks (GCNs) have made significant progress in the skeletal action recognition task. However, the graphs constructed by these methods are too densely connected, and the same graphs are used repeatedly among channels. Redundant connections will blur the useful interdependencies of joints, and the overly repetitive graphs among channels cannot handle changes in joint relations between different actions. In this work, we propose a novel relation selective graph convolutional network (RS-GCN). We also design a trainable relation selection mechanism. It encourages the model to choose solid edges to work and build a stable and sparse topology of joints. The channel-wise graph convolution and multiscale temporal convolution are proposed to strengthening the model’s representative power. Furthermore, we introduce an asymmetrical module named the spatial-temporal attention module for more stable context modeling. Combining those changes, our model achieves state-of-the-art performance on three public benchmarks, namely NTU-RGB+D, NTU-RGB+D 120, and Northwestern-UCLA.
Dynamics of Neutralizing Antibody Responses Following Natural SARS-CoV-2 Infection and Correlation with Commercial Serologic Tests. A Reappraisal and Indirect Comparison with Vaccinated Subjects
Authors: Gillot Constant , Favresse Julien , Maloteau Vincent , Dogné Jean-Michel , Douxfils Jonathan
Published: December 2021

Neutralising antibodies (NAbs) represent the real source of protection against SARS-CoV-2 infections by preventing the virus from entering target cells. The gold standard in the detection of these antibodies is the plaque reduction neutralization test (PRNT). As these experiments must be done in a very secure environment, other techniques based on pseudoviruses: pseudovirus neutralization test (pVNT) or surrogate virus neutralization test (sVNT) have been developed. Binding assays, on the other hand, measure total antibodies or IgG, IgM, and IgA directed against one epitope of the SARS-CoV-2, independently of their neutralizing capacity. The aim of this study is to compare the performance of six commercial binding assays to the pVNT and sVNT. In this study, we used blood samples from a cohort of 62 RT-PCR confirmed COVID-19 patients. Based on the results of the neutralizing assays, adapted cut-offs for the binding assays were calculated. The use of these adapted cut-offs does not permit to improve the accuracy of the serological assays and we did not find an adapted cut-off able to improve the capacity of these tests to detect NAbs. For a part of the population, a longitudinal follow-up with at least two samples for the same patient was performed. From day 14 to day 291, more than 75% of the samples were positive for NAbs (n = 87/110, 79.1%). Interestingly, 6 months post symptoms onset, the majority of the samples (N = 44/52, 84.6%) were still positive for NAbs. This is in sharp contrast with the results we obtained 6 months post-vaccination in our cohort of healthcare workers who have received the two-dose regimens of BNT162b2. In this cohort of vaccinated subjects, 43% (n = 25/58) of the participants no longer exhibit NAbs activity 180 days after the administration of the first dose of BNT162b2.
A Combination of M50I and V151I Polymorphic Mutations in HIV-1 Subtype B Integrase Results in Defects in Autoprocessing
Authors: Yang Jun , Hao Ming , Khan Muhammad A. , Rehman Muhammad T. , Highbarger Helene C. , Chen Qian , Goswami Suranjana , Sherman Brad T. , Rehm Catherine A. , Dewar Robin L. , Chang Weizhong , Imamichi Tomozumi
Published: December 2021

We have recently reported that a recombinant HIV-1NL4.3 containing Met-to-Ile change at codon 50 of integrase (IN) (IN:M50I) exhibits suppression of the virus release below 0.5% of WT HIV, and the released viral particles are replication-incompetent due to defects in Gag/GagPol processing by inhibition of the initiation of autoprocessing of GagPol polyproteins in the virions and leads to replication-incompetent viruses. The coexisting Ser-to-Asn change at codon 17 of IN or Asn-to-Ser mutation at codon 79 of RNaseH (RH) compensated the defective IN:M50I phenotype, suggesting that both IN and RH regulate an HIV infectability. In the current study, to elucidate a distribution of the three mutations during anti-retroviral therapy among patients, we performed a population analysis using 529 plasma virus RNA sequences obtained through the MiSeq. The result demonstrated that 14 plasma HIVs contained IN:M50I without the compensatory mutations. Comparing the sequences of the 14 viruses with that of the defective virus illustrated that only Val-to-Ile change at codon 151 of IN (IN:V151I) existed in the recombinant virus. This IN:V151I is known as a polymorphic mutation and was derived from HIVNL4.3 backbone. A back-mutation at 151 from Ile-to-Val in the defective virus recovered HIV replication capability, and Western Blotting assay displayed that the back-mutation restored Gag/GagPol processing in viral particles. These results demonstrate that a combination of IN:M50I and IN:V151I mutations, but not IN:M50I alone, produces a defective virus.
Comparative Susceptibility of Madin–Darby Canine Kidney (MDCK) Derived Cell Lines for Isolation of Swine Origin Influenza A Viruses from Different Clinical Specimens
Authors: Suderman Matthew , Moniwa Mariko , Alkie Tamiru N. , Ojkic Davor , Broes Andre , Pople Neil , Berhane Yohannes
Published: December 2021

Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.
Sampling for SARS-CoV-2 Aerosols in Hospital Patient Rooms
Authors: Lane Morgan A. , Walawender Maria , Webster Andrew S. , Brownsword Erik A. , Ingersoll Jessica M. , Miller Candace , Waggoner Jesse , Uyeki Timothy M. , Lindsley William G. , Kraft Colleen S.
Published: December 2021

Evidence varies as to how far aerosols spread from individuals infected with SARS-CoV-2 in hospital rooms. We investigated the presence of aerosols containing SARS-CoV-2 inside of dedicated COVID-19 patient rooms. Three National Institute for Occupational Safety and Health BC 251 two-stage cyclone samplers were set up in each patient room for a six-hour sampling period. Samplers were place on tripods, which each held two samplers at various heights above the floor. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid. Patient medical data were compared between participants in rooms where virus-containing aerosols were detected and those where they were not. Of 576 aerosols samples collected from 19 different rooms across 32 participants, 3% (19) were positive for SARS-CoV-2, the majority from near the head and foot of the bed. Seven of the positive samples were collected inside a single patient room. No significant differences in participant clinical characteristics were found between patients in rooms with positive and negative aerosol samples. SARS-CoV-2 viral aerosols were detected from the patient rooms of nine participants (28%). These findings provide reassurance that personal protective equipment that was recommended for this virus is appropriate given its spread in hospital rooms.
West Nile Virus Vaccination Protects against Usutu Virus Disease in Mice
Authors: Salgado Rebecca , Hawks Seth , Frere Francesca , Vázquez Ana , Huang Claire , Duggal Nisha
Published: December 2021

West Nile virus (WNV) and Usutu virus (USUV) are mosquito-borne flaviviruses that can cause neuroinvasive disease in humans. WNV and USUV circulate in both Africa and Europe and are closely related. Due to antigenic similarity, WNV-specific antibodies and USUV-specific antibodies have the potential to bind heterologous viruses; however, it is unclear whether this interaction may offer protection against infection. To investigate how prior WNV exposure would influence USUV infection, we used an attenuated WNV vaccine that contains the surface proteins of WNV in the backbone of a dengue virus 2 vaccine strain and protects against WNV disease. We hypothesized that vaccination with this attenuated WNV vaccine would protect against USUV infection. Neutralizing responses against WNV and USUV were measured in vitro using sera following vaccination. Sera from vaccinated CD-1 and Ifnar1−/− mice cross-neutralized with WNV and USUV. All mice were then subsequently challenged with an African or European USUV strain. In CD-1 mice, there was no difference in USUV titers between vaccinated and mock-vaccinated mice. However, in the Ifnar1−/− model, vaccinated mice had significantly higher survival rates and significantly lower USUV viremia compared to mock-vaccinated mice. Our results indicate that exposure to an attenuated form of WNV protects against severe USUV disease in mice and elicits a neutralizing response to both WNV and USUV. Future studies will investigate the immune mechanisms responsible for the protection against USUV infection induced by WNV vaccination, providing critical insight that will be essential for USUV and WNV vaccine development.
Emerging Trends in the Epidemiology of COVID-19: The Croatian ‘One Health’ Perspective
Authors: Vilibic-Cavlek Tatjana , Stevanovic Vladimir , Brlek-Gorski Diana , Ferencak Ivana , Ferenc Thomas , Ujevic-Bosnjak Magdalena , Tabain Irena , Janev-Holcer Natasa , Perkovic Ivana , Anticevic Mario , Bekavac Barbara , Kaic Bernard , Mrzljak Anna , Ganjto Marin , Zmak Ljiljana , Mauric Maljkovic Maja , Jelicic Pavle , Bucic Lovro , Barbic Ljubo
Published: December 2021

During the four pandemic waves, a total of 560,504 cases and 10,178 deaths due to COVID-19 were reported in Croatia. The Alpha variant, dominant from March 2021 (>50% of positive samples), was rapidly replaced by Delta variants (>90%) by August 2021. Several seroprevalence studies were conducted in different populations (general population, children/adolescents, professional athletes, healthcare workers, veterinarians) and in immunocompromised patients (hemodialysis patients, liver/kidney transplant recipients). After the first pandemic wave, seroprevalence rates of neutralizing (NT) antibodies were reported to be 0.2–5.5%. Significantly higher seropositivity was detected during/after the second wave, 2.6–18.7%. Two studies conducted in pet animals (February-June 2020/July–December 2020) reported SARS-CoV-2 NT antibodies in 0.76% of cats and 0.31–14.69% of dogs, respectively. SARS-CoV-2 NT antibodies were not detected in wildlife. Environmental samples taken in the households of COVID-19 patients showed high-touch personal objects as most frequently contaminated (17.3%), followed by surfaces in patients’ rooms (14.6%), kitchens (13.3%) and bathrooms (8.3%). SARS-CoV-2 RNA was also detected in 96.8% affluent water samples, while all effluent water samples tested negative. Detection of SARS-CoV-2 in humans, animals and the environment suggests that the ‘One Health’ approach is critical to controlling COVID-19 and future pandemics.
Detection of a Novel Reassortant H9N9 Avian Influenza Virus in Free-Range Ducks in Bangladesh
Authors: El-Shesheny Rabeh , Turner Jasmine C. M. , Walker David , Franks John , Seiler Patrick , Barman Subrata , Feeroz Mohammed M. , Hasan Md Kamrul , Akhtar Sharmin , Mukherjee Nabanita , Kercher Lisa , McKenzie Pamela , Webster Robert G. , Webby Richard J.
Published: December 2021

Wild aquatic birds are the primary natural reservoir for influenza A viruses (IAVs). In this study, an A(H9N9) influenza A virus (A/duck/Bangladesh/44493/2020) was identified via routine surveillance in free-range domestic ducks in Bangladesh. Phylogenetic analysis of hemagglutinin showed that the H9N9 virus belonged to the Y439-like lineage. The HA gene had the highest nucleotide identity to A/Bean Goose (Anser fabalis)/South Korea/KNU 2019-16/2019 (H9N2). The other seven gene segments clustered within the Eurasian lineage.
The Contribution of Human Herpes Viruses to γδ T Cell Mobilisation in Co-Infections
Authors: Martini Fanny , Champagne Eric
Published: December 2021

γδ T cells are activated in viral, bacterial and parasitic infections. Among viruses that promote γδ T cell mobilisation in humans, herpes viruses (HHVs) occupy a particular place since they infect the majority of the human population and persist indefinitely in the organism in a latent state. Thus, other infections should, in most instances, be considered co-infections, and the reactivation of HHV is a serious confounding factor in attributing γδ T cell alterations to a particular pathogen in human diseases. We review here the literature data on γδ T cell mobilisation in HHV infections and co-infections, and discuss the possible contribution of HHVs to γδ alterations observed in various infectious settings. As multiple infections seemingly mobilise overlapping γδ subsets, we also address the concept of possible cross-protection.
Retrospective Characterization of Initial Peste des petits ruminants Outbreaks (2008–2012) in the Democratic Republic of the Congo
Authors: Mulumba-Mfumu Leopold K. , Mahapatra Mana , Diallo Adama , Clarke Brian , Twabela Augustin , Matondo-Lusala Jean Pierre , Njeumi Felix , Parida Satya
Published: December 2021

Peste des petits ruminants (PPR) is an acute, contagious viral disease of small ruminants, goats and sheep. The Democratic Republic of the Congo (DRC) was a PPR-free country until 2007, although in 2006, scare alerts were received from the east and the southwest of the country, reporting repeated mortalities, specifically in goats. In 2008, PPR outbreaks were seen in several villages in the west, leading to structured veterinary field operations. Blood, swabs and pathological specimens consisting of tissues from lungs, spleens, lymph nodes, kidneys, livers and hearts were ethically collected from clinically infected and/or dead animals, as appropriate, in 35 districts. Epidemiological information relating to major risk factors and socio-economic impact was progressively collected, revealing the deaths of 744,527 goats, which converted to a trade value of USD 35,674,600. Samples from infected and dead animals were routinely analyzed by the Central Veterinary Laboratory at Kinshasa for diagnosis, and after official declaration of PPR outbreaks by the FAO in July 2012, selected tissue samples were sent to The Pirbright Institute, United Kingdom, for genotyping. As a result of surveys undertaken between 2008 and 2012, PPR virus (PPRV)-specific antibodies were detected in 25 locations out of 33 tested (75.7%); PPRV nucleic acid was detected in 25 locations out of 35 (71.4%); and a typical clinical picture of PPR was observed in 23 locations out of 35 (65.7%). Analysis of the partial and full genome sequences of PPR viruses (PPRVs) obtained from lymphoid tissues of dead goats collected in Tshela in the DRC in 2012 confirmed the circulation of lineage IV PPRV, showing the highest homology (99.6−100%) with the viruses circulating in the neighboring countries of Gabon, in the Aboumi outbreak in 2011, and Nigeria (99.3% homology) in 2013, although recent outbreaks in 2016 and 2018 in the western part of the DRC that borders with East Africa demonstrated circulation of lineage II and lineage III PPRV.
Transcriptome Sequencing of the Spleen Reveals Antiviral Response Genes in Chickens Infected with CAstV
Authors: Sajewicz-Krukowska Joanna , Jastrzębski Jan Paweł , Grzybek Maciej , Domańska-Blicharz Katarzyna , Tarasiuk Karolina , Marzec-Kotarska Barbara
Published: December 2021

Astrovirus infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as a decreased egg production, breeding disorders, poor weight gain, and even increased mortality. The commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for the “white chicks syndrome” associated with an increased embryo/chick mortality. CAstV-mediated pathogenesis in chickens occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV–chicken interactions remain unclear, and there is no information available regarding possible changes in gene expression in the chicken spleen in response to CAstV infection. We aim to investigate changes in gene expression triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of five birds each. One group was inoculated with CAstV, and the other used as the negative control. At 4 days post infection, spleen samples were collected and immediately frozen at −70 °C for RNA isolation. We analyzed the isolated RNA, using RNA-seq to generate transcriptional profiles of the chickens’ spleens and identify differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative reverse-transcription PCR (qRT-PCR). A total of 31,959 genes was identified in response to CAstV infection. Eventually, 45 DEGs (p-value < 0.05; log2 fold change > 1) were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on four genes (IFIT5, OASL, RASD1, and DDX60) confirmed the RNA-seq results. The most differentially expressed genes encode putative IFN-induced CAstV restriction factors. Most DEGs were associated with the RIG-I-like signaling pathway or more generally with an innate antiviral response (upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, and IFI6; downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, and YWHAB). The study provides a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proves that, in the spleen, CAstV infection in chickens predominantly affects the cell cycle and immune signaling.
Antibody Generation and Immunogenicity Analysis of EBV gp42 N-Terminal Region
Authors: Hong Junping , Wei Dongmei , Wu Qian , Zhong Ling , Chen Kaiyun , Huang Yang , Zhang Wanlin , Chen Junyu , Xia Ningshao , Zhang Xiao , Chen Yixin
Published: December 2021

Epstein–Barr virus (EBV) is the first reported oncogenic virus and infects more than 90% of adults worldwide. EBV can establish a latent infection in B lymphocytes which is essential for persistence and transmission. Glycoprotein gp42 is an indispensable member of the triggering complex for EBV entry into a B cell. The N-terminal region of gp42 plays a key role in binding to gH/gL and triggering subsequent membrane fusion. However, no antibody has been reported to recognize this region and the immunogenicity of gp42 N-domain remains unknown. In the present study, we have generated a panel of nine mAbs against the gp42 N-terminal region (six mAbs to gp42-44-61aa and three mAbs to gp42-67-81aa). These mAbs show excellent binding activity and recognize different key residues locating on the gp42 N-domain. Among the nine mAbs, 4H7, 4H8 and 11G10 cross-react with rhLCV-gp42 while other mAbs specifically recognize EBV-gp42. Our newly obtained mAbs provide a useful tool for investigating the gp42 function and viral infection mechanism of γ-Herpesvirus. Furthermore, we assess the immunogenicity of the gp42 N-terminal region using the HBc149 particle as a carrier protein. The chimeric VLPs can induce high antibody titers and elicit neutralizing humoral responses to block EBV infection. More rational and effective designs are required to promote the gp42-N terminal region to become an epitope-based vaccine.
A Novel Picornavirus Discovered in White Leg Shrimp Penaeus vannamei
Authors: Liu Shuang , Xu Tingting , Wang Chong , Jia Tianchang , Zhang Qingli
Published: December 2021

Global shrimp farming is increasingly threatened by various emerging viruses. In the present study, a novel picornavirus, Penaeus vannamei picornavirus (PvPV), was discovered in moribund White leg shrimp (Penaeus vannamei) collected from farm ponds in China in 2015. Similar to most picornaviruses, PvPV is non-enveloped RNA virus, with a particle diameter of approximately 30 nm. The sequence of the positive single-stranded RNA genome with a length of 10,550 nts was characterized by using genome sequencing and reverse transcription PCR. The existence of PvPV related proteins was further proved by confirmation of viral amino acid sequences, using mass spectrometry analysis. Phylogenetic analysis based on the full-length genomic sequence revealed that PvPV was more closely related to the Wenzhou shrimp virus 8 than to any other dicistroviruses in the order Picornavirales. Genomic sequence conservative domain prediction analysis showed that the PvPV genome encoded a large tegument protein UL36, which was unique among the known dicistroviruses and different from other dicistroviruses. According to these molecular features, we proposed that PvPV is a new species in the family Dicistroviridae. This study reported the first whole-genome sequence of a novel and distinct picornavirus in crustaceans, PvPV, and suggests that further studies of PvPV would be helpful in understanding its evolution and potential pathogenicity, as well as in developing diagnostic techniques.
Halovirus HF2 Intergenic Repeat Sequences Carry Promoters
Authors: Russ Brendan , Pfeiffer Friedhelm , Dyall-Smith Mike
Published: December 2021

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.
HIV-1 Packaging Visualised by In-Gel SHAPE
Authors: D’Souza Aaron R. , Jayaraman Dhivya , Long Ziqi , Zeng Jingwei , Prestwood Liam J. , Chan Charlene , Kappei Dennis , Lever Andrew M. L. , Kenyon Julia C.
Published: December 2021

HIV-1 packages two copies of its gRNA into virions via an interaction with the viral structural protein Gag. Both copies and their native RNA structure are essential for virion infectivity. The precise stepwise nature of the packaging process has not been resolved. This is largely due to a prior lack of structural techniques that follow RNA structural changes within an RNA–protein complex. Here, we apply the in-gel SHAPE (selective 2’OH acylation analysed by primer extension) technique to study the initiation of HIV-1 packaging, examining the interaction between the packaging signal RNA and the Gag polyprotein, and compare it with that of the NC domain of Gag alone. Our results imply interactions between Gag and monomeric packaging signal RNA in switching the RNA conformation into a dimerisation-competent structure, and show that the Gag–dimer complex then continues to stabilise. These data provide a novel insight into how HIV-1 regulates the translation and packaging of its genome.
Characterization of Ictalurid herpesvirus 1 Glycoprotein ORF59 and Its Potential Role on Virus Entry into the Host Cells
Authors: Li Shu-Xin , Yu Fei , Chen Hong-Xun , Zhang Xiao-Dong , Meng Li-Hui , Hao Kai , Zhao Zhe
Published: December 2021

The channel catfish virus (CCV, Ictalurid herpesvirus 1) has caused sustained economic losses in the fish industry because of its strong infectivity and pathogenicity. Thus, it is necessary to determine the function of viral proteins in the CCV infection process. The present study aimed to characterize CCV glycoprotein ORF59 and explore its impact on virus infection in host cells. Firstly, its exclusive presence in the membrane fraction of the cell lysate and subcellular localization verified that CCV ORF59 is a viral membrane protein expressed at late-stage infection. A protein blocking assay using purified His6 tagged ORF59, expressed in sf9 insect cells using a baculovirus expression system, indicated a dose-dependent inhibitory effect of recombinant ORF59 protein on virus invasion. Knockdown of the ORF59 using a short hairpin (shRNA) showed that ORF59 silencing decreased the production of infectious virus particles in channel catfish ovary cells. The results of this study suggest that recombinant ORF59 protein might inhibit CCV entry into the host cells. These findings will promote future studies of the key functions of glycoprotein ORF59 during CCV infection.
Combination of Antiretroviral Drugs Zidovudine and Efavirenz Impairs Tumor Growths in a Mouse Model of Cancer
Authors: Schneider Marcel , Buzdin Anton , Weber Achim , Clavien Pierre-Alain , Borger Pieter
Published: December 2021

LINE1 retrotransposons, which are thought to be the remnants of ancient integrations of retrovirus-like elements, are aberrantly (re)activated in many cancer cells. Due to LINE1-induced alterations in target gene expression and/or chromosomal rearrangements, they may be important drivers of tumorigenesis. Moreover, LINE1 encoded proteins, Open Reading Frame (ORF)1 and ORF2, may have pro-oncogenic potential through inductors of oncogenic transcription factors or inhibitors of cell cycle suppressors. The current study therefore aimed to investigate in vitro and in vivo anti-tumorigenic effects of two well-known antiretroviral drugs, zidovudine, a nucleoside analogue inhibitor of RT (NRTI), and efavirenz, a non-nucleoside RT inhibitor (NNRTI). Our data demonstrate that both drugs in clinically relevant doses significantly reduced the proliferation of murine and human cancer cell lines, as well as growth of tumors in a murine subcutaneous model. Intriguingly, we found that the combination of both zidovudine and efavirenz almost entirely blocked tumorigenesis in vivo. Because both drugs are FDA-approved agents and the combination was very well tolerated in mice, the combination therapy as presented in our paper might be an opportunity to treat colorectal tumors and metastasis to the liver in an inexpensive way.
Removal of Various Hazardous Materials Using a Multifunctional Biomass-Derived Hydroxyapatite (HAP) Catalyst and Its Antibacterial Effects
Authors: Jang Sanha , Park Kyeongmun , Song Sehwan , Lee Haksoo , Park Sungkyun , Youn Buhyun , Park Kanghyun
Published: December 2021

In the present study, oyster shells, a cause of environmental pollution, were employed effectively to synthesize hydroxyapatite (HAP) by facile oxidation and phosphorylation. The ability of HAP to adsorb various metal cations and inhibit bacterial growth was validated. The biomass-derived HAP catalyst exhibited high metal cation adsorption in water at room temperature and under various acidic conditions (M = Cr, Mn, Ni, Cu, Cd, Ba, and Pb). HAP was demonstrated to have a maximum removal efficiency of 92.8% for the heavy metal Pb. Even under different pH conditions, HAP was demonstrated to be effective for the removal of three harmful heavy metals, Cr, Cd, and Pb, with a particularly high removal efficiency demonstrated for Pb under all conditions (average removal efficiency of Cr: 63.0%, Cd: 59.9%, and Pb: 91.6%). In addition, HAP had a significant influence on phosphate ion adsorption in aqueous solution, eliminating 98.1% after 3 min. Furthermore, biomass-derived HAP was demonstrated to have significant antibacterial activity against E. coli and S. aureus (5 mM: 74% and 78.1%, 10 mM: 89.6% and 96.0%, respectively).
Assessment of Water Quality for Aquaculture in Hau River, Mekong Delta, Vietnam Using Multivariate Statistical Analysis
Authors: Mutea Fridah Gacheri , Nelson Howard Kasigwa , Au Hoa Van , Huynh Truong Giang , Vu Ut Ngoc
Published: December 2021

The deterioration signs of water quality in the Hau River are apparent. The present study analyzed the surface water quality of the Hau River using multivariate statistical techniques, including principal component analysis (PCA) and Cluster Analysis (CA). Eleven water quality parameters were analyzed at 19 different sites in An Giang and Can Tho Provinces for 12 months from January to December 2019. The findings show high levels of Biological Oxygen Demand (BOD), Total Soluble Solids (TSS), and total coliform, all year round. The PCA revealed that all the water quality parameters influenced the water quality of the Hau River, hence the relevance for water sample scrutiny. The dendrogram of similarity between sampling sites showed a maximum similarity of 95.6%. The Accumulation Factor (AF) trend showed that the concentrations/values of TSS, BOD, and phosphate (PO43−) in the downstream were 1.29, 1.53, and 1.52 times, respectively, greater than the upstream levels. Despite most of the parameters analyzed supporting aquaculture production, caution is needed in the regulation of pollution point sources to undertake sustainable aquaculture production.
Implementing an Operational Framework to Develop a Streamflow Duration Assessment Method: A Case Study from the Arid West United States
Authors: Mazor Raphael D. , Topping Brian J. , Nadeau Tracie-Lynn , Fritz Ken M. , Kelso Julia E. , Harrington Rachel A. , Beck Whitney S. , McCune Kenneth S. , Allen Aaron O. , Leidy Robert , Robb James T. , David Gabrielle C. L.
Published: December 2021

Streamflow duration information underpins many management decisions. However, hydrologic data are rarely available where needed. Rapid streamflow duration assessment methods (SDAMs) classify reaches based on indicators that are measured in a single brief visit. We evaluated a proposed framework for developing SDAMs to develop an SDAM for the Arid West United States that can classify reaches as perennial, intermittent, or ephemeral. We identified 41 candidate biological, geomorphological, and hydrological indicators of streamflow duration in a literature review, evaluated them for a number of desirable criteria (e.g., defensibility and consistency), and measured 21 of them at 89 reaches with known flow durations. We selected metrics for the SDAM based on their ability to discriminate among flow duration classes in analyses of variance, as well as their importance in a random forest model to predict streamflow duration. This approach resulted in a “beta” SDAM that uses five biological indicators. It could discriminate between ephemeral and non-ephemeral reaches with 81% accuracy, but only 56% accuracy when distinguishing 3 classes. A final method will be developed following expanded data collection. This Arid West study demonstrates the effectiveness of our approach and paves the way for more efficient development of scientifically informed SDAMs.
Spatiotemporal Landslide Susceptibility Mapping Incorporating the Effects of Heavy Rainfall: A Case Study of the Heavy Rainfall in August 2021 in Kitakyushu, Fukuoka, Japan
Authors: Li Jiaying , Wang Weidong , Li Yange , Han Zheng , Chen Guangqi
Published: December 2021

Landslide represents an increasing menace causing huge casualties and economic losses, and rainfall is a predominant factor inducing landslides. Landslide susceptibility assessment (LSA) is a commonly used and effective method to prevent landslide risk, however, the LSA does not analyze the impact of the rainfall on landslides which is significant and non-negligible. Therefore, the spatiotemporal LSA considering the inducing effect of rainfall is proposed to improve accuracy and applicability. In this study, the influencing factors are selected using the chi-square test, out-of-bag error and multicollinearity test. The spatial LSA are thus obtained using the random forest (RF) model, deep belief networks model and support vector machine, and compared using receiver operating characteristic curve and seed cell area index to determine the optimal assessment result. According to the heavy rainfall characteristics in the study area, the rainfall period is divided into four stages, and the effective rainfall model is employed to generate the rainfall impact (RI) maps of the four stages. The spatiotemporal LSAs are obtained by coupling the optimal spatial LSA and various RI maps and verified using the landslide warning map. The results demonstrate that the optimal spatiotemporal LSA is obtained using the spatial LSA of the RF model and temporal LSA of the rainfall data in the peak stage. It can predict the area where rainfall-induced landslides are likely to occur and prevent landslide risk.
Effects of Escherichia coli Alkaline Phosphatase PhoA on the Mineralization of Dissolved Organic Phosphorus
Authors: Zhou Yanwen , Zhang Tingxi , Jin Shengyan , Chen Siyu , Zhang Yinlong
Published: December 2021

Alkaline phosphatases, which play the key role in the mineralization of organic phosphorus, have been grouped into three distinct families, PhoA, PhoX, and PhoD. PhoA is still an important component of the Pho regulon for many microbes although its distribution is not as wide as that of PhoX and PhoD. However, several questions remain unclear about the effect of PhoA mineralization of dissolved organic phosphorus. In this study, the role of Escherichia coli alkaline phosphatase PhoA (hereinafter referred to as PhoA) in the mineralization of different organic phosphorus including phosphate monoesters, phosphate diesters, and phytic acids was investigated. The influence of the reaction time, organic phosphorus concentration, and L-amino acid on PhoA mineralization was examined. The results show that PhoA specifically hydrolyzes phosphate monoesters except for phytic acid and the optimal reaction time is around 12 h. The PhoA mineralization rate of glucose 6-phosphate disodium (G6P), 5′-adenosine monophosphate (AMP), and sodium glycerophosphate (BGP) significantly decreased by 38.01%, 55.31%, and 57.08%, respectively (p < 0.01), while the concentration of organic phosphorus increased from 0.50 to 5.00 mg/L. Overall, L-amino acids inhibited PhoA mineralization in a concentration-independent manner. The inhibitory effect of neutral amino acids serine (L-Ser) and tyrosine (L-Tyr) was significantly higher than that of basic amino acids arginine (L-Arg), lysine (L-Lys), and histidine (L-His). All the five amino acids can inhibit PhoA mineralization of AMP, with the highest inhibition rate observed for L-Tyr (23.77%), the lowest—for L-Arg (1.54%). Compared with other L-amino acids, L-Tyr has the highest G6P and BGP mineralization inhibition rate, with the average inhibition rates of 12.89% and 11.65%, respectively. This study provides meaningful information to better understand PhoA mineralization.
Rice Straw as a Natural Sorbent in a Filter System as an Approach to Bioremediate Diesel Pollution
Authors: Taufik Siti Hajar , Ahmad Siti Aqlima , Zakaria Nur Nadhirah , Shaharuddin Noor Azmi , Azmi Alyza Azzura , Khalid Farah Eryssa , Merican Faradina , Convey Peter , Zulkharnain Azham , Abdul Khalil Khalilah
Published: December 2021

Rice straw, an agricultural waste product generated in huge quantities worldwide, is utilized to remediate diesel pollution as it possesses excellent characteristics as a natural sorbent. This study aimed to optimize factors that significantly influence the sorption capacity and the efficiency of oil absorption from diesel-polluted seawater by rice straw (RS). Spectroscopic analysis by attenuated total reflectance infrared (ATR-IR) spectroscopy and surface morphology characterization by variable pressure scanning electron microscopy (VPSEM) and energy-dispersive X-ray microanalysis (EDX) were carried out in order to understand the sorbent capability. Optimization of the factors of temperature pre-treatment of RS (90, 100, 110, 120, 130 or 140 °C), time of heating (10, 20, 30, 40, 50, 60 or 70 min), packing density (0.08, 0.10, 0.12, 0.14 or 0.16 g cm−3) and oil concentration (5, 10, 15, 20 or 25% (v/v)) was carried out using the conventional one-factor-at-a-time (OFAT) approach. To eliminate any non-significant factors, a Plackett–Burman design (PBD) in the response surface methodology (RSM) was used. A central composite design (CCD) was used to identify the presence of significant interactions between factors. The quadratic model produced provided a very good fit to the data (R2 = 0.9652). The optimized conditions generated from the CCD were 120 °C, 10 min, 0.148 g cm−3 and 25% (v/v), and these conditions enhanced oil sorption capacity from 19.6 (OFAT) to 26 mL of diesel oil, a finding verified experimentally. This study provides an improved understanding of the use of a natural sorbent as an approach to remediate diesel pollution.
Testing the Sensitivity and Limitations of Frequently Used Aquatic Biota Indices in Temperate Mountain Streams and Plain Streams of China
Authors: Zhang Nan , Shang Guangxia , Dai Yang , Zhang Yuan , Ding Sen , Gao Xin
Published: December 2021

Different biological groups show biased responses to similar or different environmental stressors on different scales. The selection of bioindicators based on pressure characteristics is the basis for accurately assessing ecological quality. In this study, we investigated the responses of common bioindicators, namely, macroinvertebrates and fish, to multiple stressors in temperate mountain and plain streams of northeast China. We used 56 indices, including the single biological evaluation index and biological evaluation index system, to analyze and compare characteristic response to different scales under varying environmental stressors. The principal component analysis (PCA) showed that PCA axis 1 in the catchment scale explained 83.6% and 96.1% of the variance in mountain and plain rivers, respectively, which characterized the comprehensive pressure gradient integrated by land-use development and water pollution. PCA axis 1 explained 40.7% and 53.9% of variance in mountain and plain rivers on the reach scale and 63.1% and 61.8% of variance on the site scale. The correlation analysis showed responses of different indices to abiotic variables which did not overlap. Macroinvertebrate and fish indices successfully explained the change in water chemistry on a small scale, whereas fish indices additionally explained the change in land use on a large scale. Macroinvertebrate and fish indices were recommended because of their rich responses to environmental stressors, particularly in plain rivers. For mountain stream biomonitoring programs, especially in the Taizi River of northeastern China, we suggest that macroinvertebrates and fish should be used separately or jointly according to the actual capacity and cost, Moreover, compared with the possible differences in the evaluation results of different single biological evaluation indexes, the biological evaluation index system shows more stable monitoring results, and the single sensitivity index is more significant in biological evaluation, and more sensitive to some special environmental factors.
Kinetics, Isotherms and Adsorption–Desorption Behavior of Phosphorus from Aqueous Solution Using Zirconium–Iron and Iron Modified Biosolid Biochars
Authors: Rahman Md. Aminur , Lamb Dane , Kunhikrishnan Anitha , Rahman Mohammad Mahmudur
Published: December 2021

Excessive discharge of phosphorus (P) to aquatic ecosystems can lead to unpleasant eutrophication phenomenon. Removal and recovery of P is challenging due to low C/N ratios in wastewater, hence the development of efficient removal and recovery of P strategies is essential. In this study, zirconium–iron (Zr–FeBC) and iron modified (Fe–BC) biosolid biochars were examined to investigate their capacity for the removal of P by batch experiments. The influence of solution pH, biochar dose, initial P concentration, ionic strength, interfering ions and temperature were also studied to evaluate the P adsorption performance of biochars. The P experimental data were best described with pseudo-second order kinetics and the Freundlich isotherm model. The maximum P adsorption capacities were reached to 33.33 and 25.71 mg g−1 for 24 h by Zr–FeBC and Fe-BC at pH 5 and 4, respectively. Desorption studies were performed to investigate the reusability, cost-effectiveness and stability of the adsorbents Zr–FeBC and Fe-BC. The adsorption–desorption study suggests that both examined biochars have considerable potentiality as adsorbent candidates in removing as well as recovery of P from wastewaters. Results also reveal that the regenerated Zr–FeBC and Fe–BC could be utilized repetitively in seven adsorption–desorption cycles using NaOH as a desorbing agent, which greatly reduces the P-removal cost from wastewaters. Thus, P enriched biochar could potentially be used as fertilizer in the agriculture sector.
Modeling of Groundwater Potential Using Cloud Computing Platform: A Case Study from Nineveh Plain, Northern Iraq
Authors: Al-Ozeer Ali ZA. , Al-Abadi Alaa M. , Hussain Tariq Abed , Fryar Alan E. , Pradhan Biswajeet , Alamri Abdullah , Abdul Maulud Khairul Nizam
Published: December 2021

Knowledge of the groundwater potential, especially in an arid region, can play a major role in planning the sustainable management of groundwater resources. In this study, nine machine learning (ML) algorithms—namely, Artificial Neural Network (ANN), Decision Jungle (DJ), Averaged Perceptron (AP), Bayes Point Machine (BPM), Decision Forest (DF), Locally-Deep Support Vector Machine (LD-SVM), Boosted Decision Tree (BDT), Logistic Regression (LG), and Support Vector Machine (SVM)—were run on the Microsoft Azure cloud computing platform to model the groundwater potential. We investigated the relationship between 512 operating boreholes with a specified specific capacity and 14 groundwater-influencing occurrence factors. The unconfined aquifer in the Nineveh plain, Mosul Governorate, northern Iraq, was used as a case study. The groundwater-influencing factors used included elevation, slope, curvature, topographic wetness index, stream power index, soil, land use/land cover (LULC), geology, drainage density, aquifer saturated thickness, aquifer hydraulic conductivity, aquifer specific yield, depth to groundwater, distance to faults, and fault density. Analysis of the contribution of these factors in groundwater potential using information gain ratio indicated that aquifer saturated thickness, rainfall, hydraulic conductivity, depth to groundwater, specific yield, and elevation were the most important factors (average merit > 0.1), followed by geology, fault density, drainage density, soil, LULC, and distance to faults (average merit < 0.1). The average merits for the remaining factors were zero, and thus, these factors were removed from the analysis. When the selected ML classifiers were used to estimate groundwater potential in the Azure cloud computing environment, the DJ and BDT models performed the best in terms of all statistical error measures used (accuracy, precision, recall, F-score, and area under the receiver operating characteristics curve), followed by DF and LD-SVM. The probability of groundwater potential from these algorithms was mapped and visualized into five groundwater potential zones: very low, low, moderate, high, and very high, which correspond to the northern (very low to low), southern (moderate), and middle (high to very high) portions of the study area. Using a cloud computing service provides an improved platform for quickly and cheaply running and testing different algorithms for predicting groundwater potential.
Laboratory and Numerical Study of Saltwater Upconing in Fractured Coastal Aquifers
Authors: Etsias Georgios , Hamill Gerard A. , Thomson Christopher , Kennerley Samuel , Águila Jesús F. , Benner Eric M. , McDonnell Mark C. , Ahmed Ashraf A. , Flynn Raymond
Published: December 2021

This study investigated the saltwater upconing mechanism in fractured coastal aquifers. Head-induced saline intrusion was initiated into three narrow sandbox aquifers containing individual horizontal discontinuities placed on different positions. Subsequently, using a peristaltic pump, freshwater was abstracted from the aquifers’ center, triggering saltwater upconing. Progressively larger pumping rates were applied until critical conditions, resulting in the wells’ salinization, were achieved. Advanced image analysis algorithms were utilized to recreate the saltwater concentration fields and quantify the extent of the saline wedges with a high accuracy. A numerical model was successfully employed to simulate the laboratory results and conduct a comprehensive sensitivity analysis, further expanding the findings of this investigation. The impact of the fractures’ length, permeability and position on the upconing mechanism was identified. It was established that the presence of high permeability discontinuities significantly affected aquifer hydrodynamics. The conclusions of this study could constitute a contribution towards the successful management of real-world fractured coastal aquifers.
Rapid Assessment Method for Evaluation of the Weighted Contribution of Anthropogenic Pollution: A Case Study of Lake Burullus, Egypt
Authors: Moussa M. S. , Mostafa Mohamed K.
Published: December 2021

This paper proposes a pragmatic approach for rapid assessment of the weighted contribution of the main waste streams contributing to pollution of surface water bodies. A case study was conducted on Lake Burullus in Egypt. The lake suffers from pollution due to many human-based activities around the lake, such as domestic, industrial, agriculture, fish farming, and solid wastes. The weighted contribution of these activities was assessed in terms of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP). The results showed that the highest organic load is due to the domestic wastewater pollution component (63.2% of COD load), followed by fish aquaculture (35.4%). The highest TN (43.9%) and TP (58.3%) pollutant loads to Lake Burullus are due to the agricultural pollution component, followed by fish aquaculture with pollutant loads of 28.5% and 25.3%, respectively. The industrial wastewater pollution component has a very small effect on the pollution of Lake Burullus. The assessment of this study will help identify and magnify the key polluters and thus guide the decision-makers to prioritize investment planning for depollution intervention projects. For example, if the target is to reduce COD loads, investments must be directed toward the rehabilitation and expansion of wastewater treatment plants (WWTPs).