Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombinant Hepatitis E Viruses Harboring Tags in the ORF1 Protein

Hepatitis E virus (HEV) infection is an important cause of acute hepatitis and may lead to chronic infection in immunocompromised patients. Knowledge of the viral life cycle is incomplete due to the limited availability of functional tools. In particular, low levels of expression of the ORF1 protein or limited sensitivity of currently available antibodies or both limit our understanding of the viral replicase. Here, we report the successful establishment of subgenomic HEV replicons and full-length genomes harboring an epitope tag or a functional reporter in the ORF1 protein. These novel tools should allow further characterization of the HEV replication complex and to improve our understanding of the viral life cycle. ABSTRACT Hepatitis E virus (HEV) is one of the most common causes of acute hepatitis and jaundice in the world. Current understanding of the molecular virology and pathogenesis of hepatitis E is incomplete, due particularly to the limited availability of functional tools. Here, we report the development of tagged HEV genomes as a novel tool to investigate the viral life cycle. A selectable subgenomic HEV replicon was subjected to random 15-nucleotide sequence insertion using transposon-based technology. Viable insertions in the open reading frame 1 (ORF1) protein were selected in a hepatoblastoma cell line. Functional insertion sites were identified downstream of the methyltransferase domain, in the hypervariable region (HVR), and between the helicase and RNA-dependent RNA polymerase domains. HEV genomes harboring a hemagglutinin (HA) epitope tag or a small luciferase (NanoLuc) in the HVR were found to be fully functional and to allow the production of infectious virus. NanoLuc allowed quantitative monitoring of HEV infection and replication by luciferase assay. The use of HA-tagged replicons and full-length genomes allowed localization of putative sites of HEV RNA replication by the simultaneous detection of viral RNA by fluorescence in situ hybridization and of ORF1 protein by immunofluorescence. Candidate HEV replication complexes were found in cytoplasmic dot-like structures which partially overlapped ORF2 and ORF3 proteins as well as exosomal markers. Hence, tagged HEV genomes yield new insights into the viral life cycle and should allow further investigation of the structure and composition of the viral replication complex. IMPORTANCE Hepatitis E virus (HEV) infection is an important cause of acute hepatitis and may lead to chronic infection in immunocompromised patients. Knowledge of the viral life cycle is incomplete due to the limited availability of functional tools. In particular, low levels of expression of the ORF1 protein or limited sensitivity of currently available antibodies or both limit our understanding of the viral replicase. Here, we report the successful establishment of subgenomic HEV replicons and full-length genomes harboring an epitope tag or a functional reporter in the ORF1 protein. These novel tools should allow further characterization of the HEV replication complex and to improve our understanding of the viral life cycle.
The orbital period of the V Sge star candidate QU Carinae

Close Binary Supersoft X-ray Sources (CBSS) are considered strong candidates to SN Ia progenitors, but very few CBSS are known in our Galaxy. The galactic counterparts of the CBSS may be the V Sge stars, not detected in X-rays due to the strong absorption by the interstellar gas. Nevertheless, the number of members in the V Sge class is still small. In order to find new members we selected QU Car for photometric and spectroscopic observations. The orbital period of this system was published in the literature as 10.9 h, determined from radial velocity data taken in 1979-1980, but posterior analysis of data taken in 2006-2007 did not confirm this period. We analysed the high variability of its emission line profiles with the Temporal Variance Spectrum (TVS) technique. Besides, we recovered the 10.9 h orbital period from the radial velocities of the He II 4686 A emission line and, for the first time, detected what may be the orbital modulation in the photometric data. This photometric modulation is present only in the lower brightness state data, when the flickering is attenuated. The inclusion of QU Car in the V Sge class is supported by many features like high/low states, strong winds, nebular lines and He II 4686 A/Hbeta line ratios. However, the non-detection of the characteristic O VI 3811-34 A lines in its spectrum claims against this classification. These lines, though, may be highly variable so additional spectra analysed with the TVS technique can, possibly, solve this question.
Nerve growth factor‐induced muscle hyperalgesia facilitates ischaemic contraction‐evoked pain

Intramuscular injection of Nerve Growth Factor (NGF) may influence the responsiveness of active chemo‐sensitive channels affecting muscle pain sensitivity. This double‐blinded crossover study in healthy humans assessed contraction‐evoked pain responses and pain sensitivity during acute ischaemia in the tibialis anterior (TA) muscle before and 24 hr after five distributed NGF injections (1 µg, 4 cm interval) compared with control injections (isotonic‐saline).
Impact of preoperative atrial fibrillation on thromboembolic events and pump thrombosis in long-term left ventricular assist device therapy.

OBJECTIVES Pump thrombosis (PT) and thromboembolic events (TEs) remain major adverse events in left ventricular assist device (LVAD) therapy at an annual rate of 6-8% supported with the HeartWare HVAD and HeartMate II. PT and TEs are multifactorial events. Understanding the predisposing risk factors for PT and TE is paramount to define preventive strategies. Preoperative atrial fibrillation (AF) is considered a significant and potentially modifiable risk factor. This study investigates whether LVAD patients with AF exhibit a higher rate of PT and TE than those in sinus rhythm (SR). METHODS We evaluated medical records of consecutive patients who underwent implantation of the HeartMate II (n = 195; 25.4%) and HeartWare HVAD (n = 574; 74.6%) at our institution between 2006 and 2015. Only visually confirmed PT was included in the study. TE was defined as any peripheral embolism or cerebral embolism according to the INTERMACS definitions. RESULTS SR was documented preoperatively in 211 patients (SR group) and AF in 558 patients (AF group). The median duration of support was 0.78 years in the AF group and 1.03 years in the SR group. The mean age was 60.27 years in the AF group and 52.04 years in the SR group. In the AF group, 83.0% of the patients were male, compared to 77.3% in the SR group. The cumulative incidence of PT in the SR group was 2.5% [95% confidence interval (CI) 0.3-4.7%] after 1 year and 5.7% (95% CI 2.2-9.2%) after 2 years, and in the AF group 4.9% (95% CI 3.0-6.7%) and 7.8% (95% CI 5.4-10.2%), respectively (P = 0.129). TEs were recorded in the SR group in 4.4% (95% CI 1.6-7.2%) after 1 year and in 6.3% (95% CI 2.8-9.8%) after 2 years, and occurred after a median support time of 214 days (range 120-768). In the AF group, the cumulative incidence was 8.4% (95% CI 6.0-10.7%) and 10.7% (95% CI 8.0-13.4%), respectively, after a median support time of 116 days (range 37-375), P-value = 0.163. In the multivariate analysis, event-free survival was not influenced by the preoperative SR [hazard ratio (HR) 0.86, 95% CI 0.68-1.1; P = 0.19]. CONCLUSIONS Our study showed that the preoperative rhythm has no impact on survival, PT and TEs despite different preoperative risk factor profiles in the AF and SR group. Thus, the effect of a maze procedure, catheter ablation or left atrial appendage closure on PT and TE's for AF patients during LVAD implantation is questionable. However, to obtain a definitive answer, a prospective study would be of value.
CP-Violation from Spin-1 Resonances in a Left-Right Dynamical Higgs Context

New physics field content in the nature, more specifically, from spin-1 resonances sourced by the extension of the SM local gauge symmetry to the larger local group SU(2)L ⊗ SU(2)R ⊗ U(1)B-L, may induce CP-violation signalling NP effects from higher energy regimes. In this work we completely list and study all the CP-violating operators up to the p4-order in the Lagrangian expansion, for a non-linear left-right electroweak chiral context and coupled to a light dynamical Higgs. Heavy right handed fields can be integrated out from the physical spectrum, inducing thus a physical impact in the effective gauge couplings, fermionic electric dipole moment, and CP-violation in the decay h → ZZ* → 4l that are briefly analysed. The final relevant set of effective operators have also been identified at low energies.
Change management for radiation therapists – transitioning to the new Royal Adelaide Hospital

One of the largest change operations to take place in South Australia was the moving of the Royal Adelaide Hospital (RAH) to its new site in 2017. Change can influence workplace effectiveness and staff satisfaction and morale. Understanding the stages of change, staff experience and carefully managing the process is important. This paper aims to describe the successful move of the radiation therapy department at the RAH to its new site, focusing on the staff experience and management strategies to ensure the success of the move. A four‐stage model of change was used to guide understand, manage and reflect upon the transition of the RAH radiation therapy department to a new site. Key change events and management strategies are described and aligned with the four stages of change. The move to the new site was a great success with a transition period working across two sites enabling a slower ramp up of activity at the new site supporting staff and patients in adjusting to the new environment. The four‐stage model of change assisted in the smooth implementation of a transition plan for radiation oncology. At the RAH, innovation and development are encouraged, along with management having a comprehensive understanding of organisational change enabling the radiation oncology department to successfully navigate rapid change.
A follow-up study of the effect of training using the Hybrid Assistive Limb on Gait ability in chronic stroke patients

ABSTRACT Objectives: Recently, use of the Hybrid Assistive Limb (HAL) that is effective for improvement of gait ability in chronic stroke patients has been reported. However, how long the effects are maintained remains unknown. The purpose of the present study was to investigate whether the effect of gait training using the HAL on gait ability was maintained for 3 months after the intervention. Methods: A longitudinal, observational study with an intervention for a single group that adhered to the STROBE guidelines was performed. Nine chronic stroke patients were enrolled in this study. The patients performed gait training sessions using the HAL, 2–5 sessions/week for 3 weeks. Gait speed, stride length, cadence, and 2-minute walk distance (2MWD) were measured before and after intervention and at 3-month follow-up. The clinical trial registration number of this study is UMIN000012764 R000014756. Results: Compared to the initial status, gait speed (p = .02), stride length (p = .03), cadence (p = .01), and 2MWD (p < .05) were significantly increased immediately after the intervention. Moreover, gait speed (p < .01), cadence (p = .03), and 2MWD (p = .02) remained significantly higher 3 months after the intervention. There were no significant changes in all outcome measures between after intervention and at 3-month follow-up. Conclusions: This study showed that gait training using the HAL resulted in significant improvement of gait ability after the intervention and the effect was maintained for 3 months after the training.
Improving teacher comfort and self-efficacy in asthma management

Abstract Background: Asthma is common among urban school-age children. Though teachers should be prepared to assist children during an asthma attack, studies show they lack self-efficacy in managing asthma. Objective: To assess feasibility of implementing an asthma workshop for elementary school teachers, describe themes of questions raised, and determine workshop’s impact on teachers’ comfort and self-efficacy in asthma management. Methods: We developed and implemented an asthma workshop for teachers from four Bronx elementary schools (2012–2014). Teachers completed a questionnaire evaluating their comfort and self-efficacy in asthma management before and after the workshop. Questions asked during the sessions were recorded and analyzed for themes. Paired t-test and McNemar tests compared before/after scores. Results: 65 out of 70 teachers (92.9%) participated in the educational sessions. Teachers asked questions about school policy for inhalers, medication administration guidelines, and physical activity and asthma. 64/65 (98.5%) teachers completed pre/post surveys (mean age 39.7 years; mean years at the school 8.0). Post-intervention, more teachers reported knowing how to manage an asthma attack (93.8% vs. 64.1%, p < .0001); and felt comfortable assessing (50.8% vs. 30.8%, p = 0.019) and handling an asthma attack (52.3% vs. 33.8%, p = .023). The overall mean self-efficacy score increased post-intervention (43.0 vs. 38.1, p < .0001), as did 8/12 individual self-efficacy items. Post-workshop, 95.3% of teachers agreed that teacher in-service asthma education should be done annually. Conclusions: An asthma workshop was successfully implemented in the school setting and improved teacher comfort and self-efficacy in managing asthma. Annual training may improve teachers’ confidence in assisting students with asthma.
Metabolic Syndrome and Salt-Sensitive Hypertension in Polygenic Obese TALLYHO/JngJ Mice: Role of Na/K-ATPase Signaling

We have demonstrated that Na/K-ATPase acts as a receptor for reactive oxygen species (ROS), regulating renal Na+ handling and blood pressure. TALLYHO/JngJ (TH) mice are believed to mimic the state of obesity in humans with a polygenic background of type 2 diabetes. This present work is to investigate the role of Na/K-ATPase signaling in TH mice, focusing on susceptibility to hypertension due to chronic excess salt ingestion. Age-matched male TH and the control C57BL/6J (B6) mice were fed either normal diet or high salt diet (HS: 2, 4, and 8% NaCl) to construct the renal function curve. Na/K-ATPase signaling including c-Src and ERK1/2 phosphorylation, as well as protein carbonylation (a commonly used marker for enhanced ROS production), were assessed in the kidney cortex tissues by Western blot. Urinary and plasma Na+ levels were measured by flame photometry. When compared to B6 mice, TH mice developed salt-sensitive hypertension and responded to a high salt diet with a significant rise in systolic blood pressure indicative of a blunted pressure-natriuresis relationship. These findings were evidenced by a decrease in total and fractional Na+ excretion and a right-shifted renal function curve with a reduced slope. This salt-sensitive hypertension correlated with changes in the Na/K-ATPase signaling. Specifically, Na/K-ATPase signaling was not able to be stimulated by HS due to the activated baseline protein carbonylation, phosphorylation of c-Src and ERK1/2. These findings support the emerging view that Na/K-ATPase signaling contributes to metabolic disease and suggest that malfunction of the Na/K-ATPase signaling may promote the development of salt-sensitive hypertension in obesity. The increased basal level of renal Na/K-ATPase-dependent redox signaling may be responsible for the development of salt-sensitive hypertension in polygenic obese TH mice.
Spectral variability in Cygnus X-3

We model the broad-band X-ray spectrum of Cyg X-3 in all states displayed by this source as observed by the Rossi X-ray Timing Explorer. From our models, we derive for the first time unabsorbed spectral shapes and luminosities for the full range of spectral states. We interpret the unabsorbed spectra in terms of Comptonization by a hybrid electron distribution and strong Compton reflection. We study the spectral evolution and compare with other black hole as well as neutron star sources. We show that a neutron star accretor is not consistent with the spectral evolution as a function of L E and especially not with the transition to a hard state. Our results point to the compact object in Cyg X-3 being a massive, ∼30 M ⊙ black hole.
IRAM: virus capsid database and analysis resource

Abstract IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications.
A PAMP-triggered MAPK-cascade inhibits phosphatidylinositol 4,5-bisphosphate production by PIP5K6 in Arabidopsis thaliana.

•The phosphoinositide kinase PIP5K6 has recently been identified as a target for the MAP-kinase MPK6. Phosphorylation of PIP5K6 inhibited the production of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), impacting membrane trafficking and cell expansion in pollen tubes. Here, we analyzed whether MPK6 regulated PIP5K6 in vegetative Arabidopsis cells in response to the PAMP flg22. •Promoter-GUS analyses and qPCR-data show PIP5K6 expressed throughout Arabidopsis tissues. Upon flg22-treatment of transgenic protoplasts, PIP5K6 protein was phosphorylated, and this modification was reduced for a PIP5K6 variant lacking MPK6-targeted residues, or in protoplasts from mpk6-mutants. •Upon flg22-treatment of Arabidopsis plants, phosphoinositide levels mildly decreased and a fluorescent reporter for PtdIns(4,5)P2 displayed reduced plasma membrane association, contrasting with phosphoinositide increases reported for abiotic stress responses. Flg22-treatment and chemical induction of the upstream MAPKK, MKK5, decreased PI4P 5-kinase-activity in mesophyll protoplasts, indicating that the flg22-activated MAPK-cascade limited PtdIns(4,5)P2-production. PIP5K6 expression or PIP5K6 protein abundance changed only marginally upon flg22-treatment, consistent with posttranslational control of PIP5K6 activity. PtdIns(4,5)P2-dependent endocytosis of FM 4-64, PIN2 and the NADPH-oxidase RbohD were reduced upon flg22-treatment or MKK5-induction. Reduced RbohD-endocytosis correlated with enhanced ROS-production. •We conclude that MPK6-mediated phosphorylation of PIP5K6 limits the production of a functional PtdIns(4,5)P2 pool upon PAMP-perception. This article is protected by copyright. All rights reserved.
Genetic transformation of the dinoflagellate chloroplast

Coral reefs are some of the most important and ecologically diverse marine environments. At the base of the reef ecosystem are dinoflagellate algae, living in symbiosis with coral. Efforts to understand the relationship between alga and coral have been greatly hampered by the lack of an appropriate dinoflagellate genetic transformation technology. By making use of the plasmid-like fragmented chloroplast genome, we have introduced novel genetic material into the dinoflagellate chloroplast genome. We have shown that the introduced genes are expressed and confer the expected phenotypes. Genetically modified cultures have been grown for five months with subculturing, maintaining the introduced genes and phenotypes. This indicates that cells continue to divide after transformation and that the transformation is stable.
Systematic review with a meta-analysis: clinical effects of statins on the reduction of portal hypertension and variceal haemorrhage in cirrhotic patients

Background Statins may improve outcomes in patients with cirrhosis. We performed a systematic review and meta-analysis to evaluate the effect of statins on patients with cirrhosis and related complications, especially portal hypertension and variceal haemorrhage. Methods Studies were searched in the PubMed, Embase and Cochrane library databases up to February 2019. The outcomes of interest were associations between statin use and improvement in portal hypertension (reduction >20% of baseline or <12 mm Hg) and the risk of variceal haemorrhage. The relative risk (RR) with a 95% CI was pooled and calculated using a random effects model. Subgroup analyses were performed based on the characteristics of the studies. Results Eight studies (seven randomised controlled trials (RCTs) and one observational study) with 3195 patients were included. The pooled RR for reduction in portal hypertension was 1.91 (95% CI, 1.04 to 3.52; I2=63%) in six RCTs. On subgroup analysis of studies that used statin for 1 month, the RR was 2.01 (95% CI, 1.31 to 3.10; I2=0%); the pooled RR for studies that used statins for 3 months was 3.76 (95% CI, 0.36 to 39.77; I2=75%); the pooled RR for studies that used non-selective beta-blockers in the control group was 1.42 (95% CI, 0.82 to 2.45; I2=64%); the pooled RR for studies that used a drug that was not reported in the control group was 4.21 (95% CI, 1.52 to 11.70; I2=0%); the pooled RR for studies that used simvastatin was 2.20 (95% CI, 0.92 to 5.29; I2=69%); RR for study using atorvastatin was 1.82 (95% CI, 1.00 to 3.30). For the risk of a variceal haemorrhage, the RR based on an observational study was 0.47 (95% CI, 0.23 to 0.94); in two RCTs, the pooled RR was 0.88 (95% CI, 0.52 to 1.50; I2=0%). Overall, the summed RR was 0.64 (95% CI, 0.42 to 0.99; I2=6%). Conclusion Statins may improve hypertension and decrease the risk of variceal haemorrhage according to our assessment. However, further and larger RCTs are needed to confirm this conclusion.
Contrasting Asymptomatic and Drug Resistance Gene Prevalence of Plasmodium falciparum in Ghana: Implications on Seasonal Malaria Chemoprevention

Malaria is a significant public health problem in Ghana. Seasonal Malaria Chemoprevention (SMC) using a combination of sulfadoxine-pyrimethamine and amodiaquine has been implemented since 2015 in northern Ghana where malaria transmission is intense and seasonal. In this study, we estimated the prevalence of asymptomatic P. falciparum carriers in three ecological zones of Ghana, and compared the sensitivity and specificity of different molecular methods in identifying asymptomatic infections. Moreover, we examined the frequency of mutations in pfcrt, pfmdr1, pfdhfr, and pfdhps that relate to the ongoing SMC. A total of 535 asymptomatic schoolchildren were screened by microscopy and PCR (18s rRNA and TARE-2) methods. Among all samples, 28.6% were detected as positive by 18S nested PCR, whereas 19.6% were detected by microscopy. A high PCR-based asymptomatic prevalence was observed in the north (51%) compared to in the central (27.8%) and south (16.9%). The prevalence of pfdhfr-N51I/C59R/S108N/pfdhps-A437G quadruple mutant associated with sulfadoxine-pyrimethamine resistance was significantly higher in the north where SMC was implemented. Compared to 18S rRNA, TARE-2 serves as a more sensitive molecular marker for detecting submicroscopic asymptomatic infections in high and low transmission settings. These findings establish a baseline for monitoring P. falciparum prevalence and resistance in response to SMC over time.