bluuebunny/crossref_metadata_2025_split huggingface dataset:
No detrimental effects of desalination waste on temperate fish assemblages
Authors: Whitmarsh Sasha K , Barbara Greg M , Brook James , Colella Dimitri , Fairweather Peter G , Kildea Tim , Huveneers Charlie 
Published: September 2020

Abstract
Water resources are becoming increasingly scarce due to population growth and global changes in weather patterns. Desalination plants that extract freshwater from brackish or seawater are already being used worldwide, with many new plants being developed and built. The waste product from the extraction processes has an elevated salt concentration and can potentially cause substantial impacts to local marine flora and fauna. The present study assesses the impact of saline waste from a 100 GL/year desalination plant on southern Australian temperate fish assemblages, using baited remote underwater video. The study compared four reference sites to the impact site (desalination outfall) and found no evidence that the saline waste was having a detrimental effect on fish assemblages in proximity to the outfall, with species diversity and abundance comparable to those observed at reference sites. However, species diversity and abundance varied across geographical location, protection from fishing pressure, and reef type. Our study is one of the few assessing the ecological impacts of saline waste discharged from a large desalination plant and shows no decrease in fish diversity or abundance, which is the response typically associated with the negative impacts of anthropogenic activities on fish assemblages.
Nonpharmaceutical Interventions Used to Control COVID-19 Reduced Seasonal Influenza Transmission in China
Authors: Lei Hao , Xu Modi , Wang Xiao , Xie Yu , Du Xiangjun , Chen Tao , Yang Lei , Wang Dayan , Shu Yuelong 
Published: September 2020

Abstract
To suppress the ongoing COVID-19 pandemic, the Chinese government has implemented nonpharmaceutical interventions (NPIs). Because COVID-19 and influenza have similar means of transmission, NPIs targeting COVID-19 may also affect influenza transmission. In this study, the extent to which NPIs targeting COVID-19 have affected seasonal influenza transmission was explored. Indicators of seasonal influenza activity in the epidemiological year 2019–2020 were compared with those in 2017–2018 and 2018–2019. The incidence rate of seasonal influenza reduced by 64% in 2019–2020 (P &lt; .001). These findings suggest that NPIs aimed at controlling COVID-19 significantly reduced seasonal influenza transmission in China.
Bim establishes the B-cell repertoire from early to late in the immune response
Authors: Sugimoto-Ishige Akiko , Harada Michishige , Tanaka Miho , Terooatea Tommy , Adachi Yu , Takahashi Yoshimasa , Tanaka Takashi , Burrows Peter D , Hikida Masaki , Takemori Toshitada 
Published: September 2020

AbstractIn T cell-dependent antibody responses, some of the activated B cells differentiate along extrafollicular pathways into low-affinity memory and plasma cells, whereas others are involved in subsequent germinal center (GC) formation in follicular pathways, in which somatic hypermutation and affinity maturation occur. The present study demonstrated that Bim, a proapoptotic BH3-only member of the Bcl-2 family, contributes to the establishment of the B-cell repertoire from early to late stages of immune responses to T cell-dependent antigens. Extrafollicular plasma cells grew in the spleen during the early immune response, but their numbers rapidly declined with the appearance of GC-derived progeny in wild-type mice. By contrast, conditional Bim deficiency in B cells resulted in expansion of extrafollicular IgG1+ antibody-forming cells (AFCs) and this expansion was sustained during the late response, which hampered the formation of GC-derived high-affinity plasma cells in the spleen. Approximately 10% of AFCs in mutant mice contained mutated VH genes; thus, Bim deficiency appears not to impede the selection of high-affinity AFC precursor cells. These results suggest that Bim contributes to the replacement of low-affinity antibody by high-affinity antibody as the immune response progresses.
Framing middle power foreign policy: trade, security, and human rights frames in Canadian and Australian foreign policy attitudes
Authors: Gravelle Timothy B 
Published: September 2020

AbstractMiddle power states in the Indo-Pacific region face a challenging foreign policy environment in light of geopolitical and economic rivalry between the United States and China. In this context, what factors shape the foreign policy attitudes of middle power publics? This article presents results from a set of survey-based experiments conducted in Canada and Australia, two archetypal middle power states located on the Pacific Rim. Demographically representative samples of both publics were presented with randomized vignettes highlighting facets of bilateral relations with the United States, regional partners (Mexico in the Canadian case, and Indonesia in the Australian case), and China. Results indicate that making different aspects of a particular relationship salient as part of the vignette shapes perceptions of and preferences toward relations with the state in question. Foreign policy attitudes are thus amenable to framing effects. Still, results point to different frames having greater relevance to different bilateral relationships.
Molecular mechanisms driving thein vivodevelopment of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDRPseudomonas aeruginosainfections
Authors: Arca-Suárez Jorge , Lasarte-Monterrubio Cristina , Rodiño-Janeiro Bruno-Kotska , Cabot Gabriel , Vázquez-Ucha Juan Carlos , Rodríguez-Iglesias Manuel , Galán-Sánchez Fátima , Beceiro Alejandro , González-Bello Concepción , Oliver Antonio , Bou Germán 
Published: September 2020

AbstractBackgroundThe development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning.ObjectivesCharacterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections.MethodsFour paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes.ResultsThe same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold.ConclusionsModification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.
Efficacy of chloroquine or hydroxychloroquine in COVID-19 patients: a systematic review and meta-analysis
Authors: Kashour Zakariya , Riaz Muhammad , Garbati Musa A , AlDosary Oweida , Tlayjeh Haytham , Gerberi Dana , Murad M Hassan , Sohail M Rizwan , Kashour Tarek , Tleyjeh Imad M 
Published: September 2020

Abstract

Objectives
Clinical studies of chloroquine (CQ) and hydroxychloroquine (HCQ) in COVID-19 disease reported conflicting results. We sought to systematically evaluate the effect of CQ and HCQ with or without azithromycin on outcomes of COVID-19 patients.

Methods
We searched multiple databases, preprints and grey literature up to 17 July 2020. We pooled only adjusted-effect estimates of mortality using a random-effect model. We summarized the effect of CQ or HCQ on viral clearance, ICU admission/mechanical ventilation and hospitalization.

Results
Seven randomized clinical trials (RCTs) and 14 cohort studies were included (20 979 patients). Thirteen studies (1 RCT and 12 cohort studies) with 15 938 hospitalized patients examined the effect of HCQ on short-term mortality. The pooled adjusted OR was 1.05 (95% CI 0.96–1.15, I2 = 0%). Six cohort studies examined the effect of the HCQ+azithromycin combination with a pooled adjusted OR of 1.32 (95% CI 1.00–1.75, I2 = 68.1%). Two cohort studies and four RCTs found no effect of HCQ on viral clearance. One small RCT demonstrated improved viral clearance with CQ and HCQ. Three cohort studies found that HCQ had no significant effect on mechanical ventilation/ICU admission. Two RCTs found no effect for HCQ on hospitalization risk in outpatients with COVID-19.

Conclusions
Moderate certainty evidence suggests that HCQ, with or without azithromycin, lacks efficacy in reducing short-term mortality in patients hospitalized with COVID-19 or risk of hospitalization in outpatients with COVID-19.
Verification of Low-Density Lipoprotein Cholesterol Levels Measured by Anion-Exchange High-Performance Liquid Chromatography in Comparison with Beta Quantification Reference Measurement Procedure
Authors: Manita Daisuke , Yoshida Hiroshi , Koyama Isao , Nakamura Masakazu , Hirowatari Yuji 
Published: September 2020

Abstract

Background
A new lipoprotein testing method based on anion-exchange HPLC (AEX-HPLC) was recently established. We verified the accuracy of LDL-C levels, a primary therapeutic target for the prevention of cardiovascular disease (CVD), measured by AEX-HPLC comparing with LDL-C levels measured by beta quantification-reference measurement procedure (BQ-RMP), homogenous assays, and calculation methods.

Methods
We compared LDL-C levels measured by AEX-HPLC (adLDL-Ch: LDL-Ch and IDL-Ch) and BQ-RMP using blood samples from 52 volunteers. AdLDL-Ch levels were also compared with those measurements by homogeneous assays and calculation methods (Friedewald equation, Martin equation, and Sampson equation) using blood samples from 411 participants with dyslipidemia and/or type 2 diabetes.

Results
The precision and accuracy of adLDL-Ch were verified by BQ-RMP. The mean percentage bias [bias (%)] for LDL-C was 1.2%, and the correlation was y = 0.990x + 3.361 (r = 0.990). These results met the acceptable range of accuracy prescribed by the National Cholesterol Education Program. Additionally, adLDL-Ch levels were correlated with LDL-C levels measured by the 2 homogeneous assays (r &gt; 0.967) and the calculation methods (r &gt; 0.939), in serum samples from patients with hypertriglyceridemia.

Conclusions
AEX-HPLC is a reliable method for measuring LDL-C levels for CVD risk in daily clinical laboratory analyses.
Evaluation of Systemic Imidacloprid and Herbicide Treatments on Flatheaded Borer (Coleoptera: Buprestidae) Management in Field Nursery Production
Authors: Addesso Karla M , Oliver Jason B , Youssef Nadeer N , Fare Donna C 
Published: September 2020

Abstract
The flatheaded appletree borer, Chrysobothris femorata (Olivier) (Coleoptera: Buprestidae), and related species are deciduous tree pests. Female beetles prefer to oviposit at tree bases, and larvae tunnel beneath the bark, which weakens or kills young or newly transplanted trees. In the first objective of this study, Discus N/G (2.94% imidacloprid + 0.7% cyfluthrin) applied at six lower-than-labeled rates (0.0, 0.98, 1.97, 3.94, 5.91, and 7.87 ml/cm of average trunk dia.) was evaluated for protection of field-grown maples. A second objective evaluated imidacloprid with and without herbicides to assess the impact of weed competition at the tree base on insecticide effectiveness. A third objective determined relative imidacloprid concentrations in leaf tissue samples with ELISA and related to insecticide rates, herbicide treatments, and the level of flatheaded borer protection. In two trials, higher rates of insecticide were more effective at protecting trees, with rates ≥3.94 ml product/cm trunk diameter performing equivalently. Weed-free trees had more borer attacks and grew faster than trees in weedy plots. Imidacloprid content in leaf tissues had a trend for higher concentrations in smaller, weedy trees in the first season, but that pattern disappeared in subsequent years. Based on fewer attacks in weedy versus weed-free trees (60−90% reduction), it was concluded that weed presence can reduce borer attack success in nurseries independent of insecticide treatment, but tree growth was reduced by weed presence. In addition, Discus applied at rates &gt;3.94 ml/cm did not confer added borer damage protection in weedy plots.
Novel −75°C SEM cooling stage: application for martensitic transformation in steel
Authors: Tsuzazki Kaneaki , Koyama Motomichi , Sasaki Ryosuke , Nakafuji Keiichiro , Oie Kazushi , Shibata Akinobu , Gondo Takashi , Miyazaki Hiroya , Akamine Hiroshi , Nishida Minoru 
Published: September 2020

Abstract
Microstructural changes during the martensitic transformation from face-centred cubic (FCC) to body-centred cubic (BCC) in an Fe-31Ni alloy were observed by scanning electron microscopy (SEM) with a newly developed Peltier stage available at temperatures to  −75°C. Electron channelling contrast imaging (ECCI) was utilized for the in situ observation during cooling. Electron backscatter diffraction analysis at ambient temperature (20°C) after the transformation was performed for the crystallographic characterization. A uniform dislocation slip in the FCC matrix associated with the transformation was detected at −57°C. Gradual growth of a BCC martensite was recognized upon cooling from −57°C to −63°C.
Ovarian malignant mixed Müllerian tumor: a rare case report from Tanzania
Authors: Pallangyo Angela , Pyuza Jeremia J , Andongolile Alice A , Mbwambo Daniel , Claver Jackson P , Koosa Ummil-Khairat , Lema Kennedy , Amsi Patrick , Nkya Gilbert , Mremi Alex 
Published: September 2020

Abstract
Malignant mixed Müllerian tumor of the ovary is rare aggressive tumor that is histologically defined by the presence of malignant epithelial and stromal components. We report a 37-year-old woman who consulted our facility complaining of abdominal distention and a painful palpable mass over her lower abdomen. Physical examination including computerized tomography revealed a complex cystic mass lesion on the left ovary with extensive omental involvement. Ovarian cancer was suspected and the patient underwent debulking surgery. The histopathology of the specimen revealed a high-grade tumor composed of both malignant epithelial and sarcomatous elements. Both epithelial and stromal components stained positive for p53 immunostaining. Before the initiation of chemotherapy, on 5th day postoperation, the patient was found unresponsive. The stage of the disease seems to be the most important prognostic factor, thus emphasis should be made to identify it in earlier stages.
An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome
Authors: Valach Matus , Gonzalez Alcazar José Angel , Sarrasin Matt , Lang B Franz , Gray Michael W , Burger Gertraud 
Published: September 2020

Abstract
The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
Evolutionary Genomics of Niche-Specific Adaptation to the Cystic Fibrosis Lung in Pseudomonas aeruginosa
Authors: Dettman Jeremy R , Kassen Rees 
Published: September 2020

Abstract
The comparative genomics of the transition of the opportunistic pathogen Pseudomonas aeruginosa from a free-living environmental strain to one that causes chronic infection in the airways of cystic fibrosis (CF) patients remain poorly studied. Chronic infections are thought to originate from colonization by a single strain sampled from a diverse, globally distributed population, followed by adaptive evolution to the novel, stressful conditions of the CF lung. However, we do not know whether certain clades are more likely to form chronic infections than others and we lack a comprehensive view of the suite of genes under positive selection in the CF lung. We analyzed whole-genome sequence data from 1,000 P. aeruginosa strains with diverse ecological provenances including the CF lung. CF isolates were distributed across the phylogeny, indicating little genetic predisposition for any one clade to cause chronic infection. Isolates from the CF niche experienced stronger positive selection on core genes than those derived from environmental or acute infection sources, consistent with recent adaptation to the lung environment. Genes with the greatest differential positive selection in the CF niche include those involved in core cellular processes such as metabolism, energy production, and stress response as well as those linked to patho-adaptive processes such as antibiotic resistance, cell wall and membrane modification, quorum sensing, biofilms, mucoidy, motility, and iron homeostasis. Many genes under CF-specific differential positive selection had regulatory functions, consistent with the idea that regulatory mutations play an important role in rapid adaptation to novel environments.
Genome maintenance functions of a putative Trypanosoma brucei translesion DNA polymerase include telomere association and a role in antigenic variation
Authors: Leal Andrea Zurita , Schwebs Marie , Briggs Emma , Weisert Nadine , Reis Helena , Lemgruber Leandro , Luko Katarina , Wilkes Jonathan , Butter Falk , McCulloch Richard , Janzen Christian J 
Published: September 2020

AbstractMaintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to offspring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to host-parasite interactions. Here, we describe a dual function of one putative translesion Pol in African trypanosomes, which we now name TbPolIE. Previously, we demonstrated that TbPolIE is associated with telomeric sequences and here we show that RNAi-mediated depletion of TbPolIE transcripts results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. We also show that TbPolIE displays pronounced localization at the nuclear periphery, and that its depletion leads to chromosome segregation defects and increased levels of endogenous DNA damage. Finally, we demonstrate that TbPolIE depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this putative translesion DNA polymerase to host immune evasion by antigenic variation.
CK2 kinase-mediated PHF8 phosphorylation controls TopBP1 stability to regulate DNA replication
Authors: Feng Haihua , Lu Jingchen , Song Xiaotian , Thongkum Angkana , Zhang Fan , Lou Lihong , Reizes Ofer , Almasan Alexandru , Gong Zihua 
Published: September 2020

Abstract
ATR functions as a master regulator of the DNA-damage response. ATR activation requires the ATR activator, topoisomerase IIβ-binding protein 1 (TopBP1). However, the underlying mechanism of TopBP1 regulation and how its regulation affects DNA replication remain unknown. Here, we report a specific interaction between TopBP1 and the histone demethylase PHF8. The TopBP1/PHF8 interaction is mediated by the BRCT 7+8 domain of TopBP1 and phosphorylation of PHF8 at Ser854. This interaction is cell-cycle regulated and phosphorylation-dependent. PHF8 is phosphorylated by CK2, which regulates binding of PHF8 to TopBP1. Importantly, PHF8 regulates TopBP1 protein level by preventing its ubiquitination and degradation mediated by the E3 ligase UBR5. Interestingly, PHF8pS854 is likely to contribute to regulation of TopBP1 stability and DNA replication checkpoint. Further, both TopBP1 and PHF8 are required for efficient replication fork restart. Together, these data identify PHF8 as a TopBP1-binding protein and provide mechanistic insight into how PHF8 regulates TopBP1 stability to maintain DNA replication.
Post-translational modifications of hnRNP A1 differentially modulate retroviral IRES-mediated translation initiation
Authors: Barrera Aldo , Ramos Hade , Vera-Otarola Jorge , Fernández-García Leandro , Angulo Jenniffer , Olguín Valeria , Pino Karla , Mouland Andrew J , López-Lastra Marcelo 
Published: September 2020

Abstract
The full-length mRNAs of the human immunodeficiency virus type-1 (HIV-1), the human T-cell lymphotropic virus type-1 (HTLV-1), and the mouse mammary tumor virus (MMTV) harbor IRESs. The activity of the retroviral-IRESs requires IRES-transacting factors (ITAFs), being hnRNP A1, a known ITAF for the HIV-1 IRES. In this study, we show that hnRNP A1 is also an ITAF for the HTLV-1 and MMTV IRESs. The MMTV IRES proved to be more responsive to hnRNP A1 than either the HTLV-1 or the HIV-1 IRESs. The impact of post-translational modifications of hnRNP A1 on HIV-1, HTLV-1 and MMTV IRES activity was also assessed. Results show that the HIV-1 and HTLV-1 IRESs were equally responsive to hnRNP A1 and its phosphorylation mutants S4A/S6A, S4D/S6D and S199A/D. However, the S4D/S6D mutant stimulated the activity from the MMTV-IRES to levels significantly higher than the wild type hnRNP A1. PRMT5-induced symmetrical di-methylation of arginine residues of hnRNP A1 enabled the ITAF to stimulate the HIV-1 and HTLV-1 IRESs while reducing the stimulatory ability of the ITAF over the MMTV IRES. We conclude that retroviral IRES activity is not only dependent on the recruited ITAFs but also relies on how these proteins are modified at the post-translational level.