Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C

INTRODUCTION

HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C.

METHODS

Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict  the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability.

RESULTS

The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region.

CONCLUSIONS

We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.

Survey of ASCO Sponsored Oncology Interest Groups in the United States Assessing Medical Student Perceptions of Education in Radiation Oncology and Future Employment Prospects

PURPOSE/OBJECTIVE(S)

Over the last five years, applications to radiation oncology residency programs among graduates of medical schools in the United States (US) have declined by nearly 50% with a corresponding increase in unfilled positions in the National Resident Matching Program. This has led to ongoing concern regarding the future of the radiation oncology workforce and speculation regarding contributing factors. There are no published data substantiating medical student viewpoints on these issues. To better understand medical student perceptions of oncology specialties (medical oncology (MO), radiation oncology (RO), and surgical oncology/surgical subspecialties (SO)) and factors contributing to their career choices, we conducted a survey among oncology interest groups sponsored by the American Society of Clinical Oncology (ASCO). Survey content emphasized relative impressions of oncology specialties, exposure to these fields during medical school, and perceptions of future employment prospects.

MATERIALS/METHODS

An IRB-approved thirty-item questionnaire was distributed electronically via SurveyMonkey to US medical student members of ASCO sponsored interest groups. Participation was optional at the institutional and individual level and responses anonymous. Chi square test or Fisher's exact test was used to compare categorical variables.

RESULTS

Two-hundred seventy-nine students completed the survey (37% male, 62% female; 42% White, 40% Asian, 18% underrepresented minorities). Students report receiving less exposure to radiation oncology during medical school: 19% report RO is not included in their curriculum vs. 4% for MO (p<0.01); 77% report receiving lectures from MO faculty, 33% from RO, and 41% from SO (p <0.01); 41% were encouraged to consider RO as a specialty, compared to 62 % for MO and 42% for SO (p < 0.01); 45% report having a clear understanding of role of MO in oncology care vs. only 25% for RO and 38% for SO (p<0.01); 41% saw MO as leaders of the multidisciplinary cancer team, 1 % for RO, and 2% for SO, 47% felt all played equal roles (p<0.01). Students have more negative perceptions of future career prospects for RO: 81% feel that job prospects for MO are strong, 55% for RO and 73% for SO (p<0.01); 54% feel strongly that jobs are available in desirable geographic locations for MO, 36% for RO, 48% for SO (p<0.01); 27% of students report concerns about the future viability of RO, 10% for MO, and 11% for SO (p<0.01).

CONCLUSION

Compared to other oncology specialties, students have less exposure to RO, less understanding of the role of RO in multidisciplinary cancer care, and more pessimism about the future job market/specialty viability. These are likely contributing factors to declining interest in RO among graduates of US medical schools. Current radiation oncologists should increase efforts to improve medical student interest and understanding of RO.

SEA-Net: Structure-Enhanced Attention Network for Limited-Angle CBCT Reconstruction of Clinical Projection Data

PURPOSE/OBJECTIVE(S)

Limited-angle CBCT (LA-CBCT) is of great clinical interest, because the scanning time and the patient dose are proportional to the scanning range of gantry rotation angles of CBCT. However, the image reconstruction for LA-CBCT remains technically challenging, which suffers from severe wedge artifacts and image distortions. This work aims to improve LA-CBCT by developing deep learning (DL) methods for real clinical CBCT projection data, which is the first feasibility study of clinical-projection-data-based LA-CBCT, to the best of our knowledge.

MATERIALS/METHODS

Targeting at real clinical projection data, we have explored various DL methods such as image/data/hybrid-domain methods and finally developed a so-called Structure-Enhanced Attention Network (SEA-Net) method that has the best image quality from clinical projection data among the DL methods we have implemented. Specifically, the proposed SEA-Net employs a specialized structure enhancement sub-network to promote texture preservation. Based on the observation that the distribution of wedge artifacts in reconstruction images is non-uniform, the spatial attention module is utilized to emphasize the relevant regions while ignores the irrelevant ones, which leads to more accurate texture restoration.

RESULTS

SEA-Net was validated in comparison with analytic (FDK), iterative (TV), image-domain DL (DDNet and FED-INet, data-domain DL (DCAR), dual-domain DL (Sam'Net), and various unrolling DL (hdNet, CTNet, FSR-Net, CasRedSCAN) methods. Among all methods, the SEA-Net had the best image reconstruction quality as quantified by root-mean-square error (RMSE), peak signal-to-noise ratio (PSNR), and structural similarity index (SSIM), for various LA-CBCT problems of 90°-180° projection data. In addition, LA-CBCT via SEA-Net provided comparable accuracy for both patient setup (quantified by image registration accuracy from planning CT (pCT) to CBCT) and dose calculation (see the table), with full-view CBCT.

CONCLUSION

We explored various DL methods and developed an image-domain-based method termed SEA-Net that provided the best image quality for clinical projection data. To the best of our knowledge, this is the first feasibility study of the real clinical-projection-data-based LA-CBCT. Moreover, LA-CBCT via SEA-Net can potentially provide comparable accuracy for patient setup and dose calculation, with full-view CBCT.

Correlation of placental pathology with the postoperative outcomes and white matter injury in preterm infants following necrotizing enterocolitis

BACKGROUND

To determine the association of placental pathologic lesions with postoperative outcomes, survival, and white matter injury (WMI) in preterm infants with NEC.

METHODS

A retrospective chart review of 107 neonates with NEC (Bell stage > IIa) from Jan 2013- June 2020 was completed. Demographic, clinical, and outcome data were compared between infants with or without placental pathologic lesions.

RESULTS

In this cohort, 59/107 (55%) infants had medical NEC, and 48 (45%) had surgical NEC. The infants had a mean gestational age of 28.1±3.7 weeks and a birth weight of 1103±647 g. Maternal vascular malperfusion (82/107, 76.6%) and acute histological chorioamnionitis (42, 39.3%) were the most common pathological placental lesions. Acute histologic chorioamnionitis with fetal inflammatory response was more common in infants with surgical NEC vs. medical NEC (35.4% vs. 15.3%; p = 0.02). The NEC Infants with WMI on brain MRI scans had a significantly higher incidence of acute histological chorioamnionitis (52% vs. 27.8%; P = 0.04). No significant differences in mortality, length of stay and postoperative outcomes in neonates with and without acute histologic chorioamnionitis with fetal inflammatory response were noted. On unadjusted logistic regression, acute histologic chorioamnionitis without fetal inflammatory response was also associated with higher odds of WMI (OR 2.81; 95% CI 1.05-7.54; p = 0.039).

CONCLUSION

Acute histological chorioamnionitis without fetal inflammatory response was associated with higher odds of WMI in infants with NEC, with no significant impact on mortality and other postoperative outcomes.

Clinical impact of analgesic-sedative agents and peri-operative clinical status on white matter brain injury in preterm infants following surgical NEC

BACKGROUND

The potential influence of exposure to analgesic-sedative agents (ASA) before, during, and after surgical NEC and peri-operative clinical status on white matter injury (WMI) in preterm infants has not been fully defined, and a comprehensive evaluation may inform future research and clinical interventions.

METHODS

A retrospective study comparing ASA exposure before/during /after surgical NEC and peri-operative clinical status in neonates with and without WMI.

RESULTS

Infants with any WMI (grade 2-4, n = 36/67, 53.7%) had a higher number of surgical procedures receiving ASA (5 [IQR: 3, 8] vs. 3 [2, 4]; p = 0.002) and had a longer duration of hypotension during their first (48.0 hours [26.0, 48.0] vs. 15.5 [6, 48]; p = 0.009) and second surgery (20 hours [0, 48h] vs. 0 [0, 22]; p = 0.017), received more hydrocortisone (35% vs.13.3%,p = 0.04) than those without any WMI. There were no differences in fentanyl/morphine/midazolam exposure before/during/after the NEC onset in the two groups.Infants with severe WMI (19/67, 28.3%, grade 3/4) had a higher incidence of AKI (P = 0.004), surgical morbidity (p = 0.047), more surgical procedures (6.5 [3, 10] vs. 4 [2, 5]; p = 0.012), and received higher mean fentanyl doses(p = 0.03) from birth until NEC onset than those without severe WMI. The univariate associations between these factors and severe WMI remained insignificant after multivariable logistic regression.

CONCLUSION

Infants with WMI had more surgical procedures receiving ASA and had a longer duration of hypotension during surgeries. A large multicenter prospective study is needed to understand the full impact of ASA.

Efficacy of rh-PDGF-BB and Emdogain with or without DFDBA using M-MIST in the treatment of intrabony defects

Background

The versatile combination of emdogain or enamel matrix derivative (EMD), recombinant human platelet-derived growth factor-BB (rhPDGF-BB), and demineralized freeze-dried bone allograft (DFDBA) has not been utilized in the treatment of intrabony defects yet.

Aim

The present study attempted to investigate the efficacy of a combination of simple, uncomplicated nature of modified minimally invasive surgical technique (M-MIST) with EMD, rhPDGF-BB, and DFDBA in the surgical management of intrabony defects and to assess the possible favorable effects for a period of 6 months.

Patients and Methods

Thirty healthy subjects were included in the present double-blind, randomized controlled, two-arm parallel study. The test group was treated with M-MIST by using rhPDGF-BB, EMD, and DFDBA, and the control group was treated with M-MIST by using rhPDGF-BB and EMD.

Results

Differences between the mean values of primary clinical parameters including relative attachment level, probing depth, and gingival recession at baseline and those at 6 months after surgery were statistically significant in both groups. Inter-group comparison for clinical attachment level gain, probing depth reduction, and change in the position of gingival margin revealed no statistically significant differences. Inter-group comparison revealed significant differences in linear bone growth (LBG) and percentage bone fill (% BF) but no significant differences in the residual defect depth and change in the alveolar crest position.

Conclusion

The additional use of DFDBA provides superior benefits in terms of LBG and % BF in intrabony defects. This improvement might be attributed to the use of an osteoinductive scaffold.

Pituitary metastasis: From pathology to clinical and radiological considerations

PURPOSE

A review of the literature with respect to pituitary metastases (PM) with clinical and radiological considerations are summarized to facilitate clinical decision making in the management of PM METHODS: A review of literature associated with PM and tumour to tumour metastases in the English literature was reviewed and summarized RESULTS: Pituitary metastases account for 1.0-3.6% of all surgically treated pituitary lesions. Often identified in parallel with extensive disseminated disease, once diagnosed, the prognosis is generally poor, although survival is highly heterogeneous and dependent on the primary tumor histology. Within this anatomical region is also the observation of tumor-to-tumor metastases and collision tumours. Both the tumor macro- and microenvironment play central roles to the progression of disease with distinctive radiological features that may suggest a metastatic sellar lesion as opposed to a primary pituitary lesion. Surgical resection is the first line of therapy followed by adjuvant chemoradiotherapy and endocrinological evaluation for hormonal supplementation CONCLUSION: PMs are relatively rare but important oncological entities representing disseminated disease in the majority of cases. Careful consideration of the relevant clinical history and radiological features can aid the clinician differentiate between a metastatic lesion to the pituitary region and a primary pituitary tumor. While surgical resection is first line therapy, stereotactic radiosurgery in carefully selected patients is emerging as a viable alternative.

Bacterial infection, antibiotic use and COVID-19: Lessons from the intensive care unit

BACKGROUND

Empirical broad-spectrum antibiotics are frequently prescribed to patients with severe COVID-19, motivated by concern about bacterial coinfection. There is no evidence of benefit from such a strategy, while the dangers of inappropriate antibiotics are well described.

OBJECTIVES

To investigate the frequency, profile and related outcomes of infections by bacterial pathogens in patients admitted to an intensive care unit (ICU) with severe COVID-19 pneumonia.

METHODS

This was a prospective, descriptive study in a dedicated COVID-19 ICU in Cape Town, South Africa, involving all adult patients admitted to the ICU with confirmed COVID-19 pneumonia between 26 March and 31 August 2020. We collected data on patient comorbidities, laboratory results, antibiotic treatment, duration of admission and in-hospital outcome.

RESULTS

We included 363 patients, who collectively had 1 199 blood cultures, 308 tracheal aspirates and 317 urine cultures performed. We found positive cultures for pathogens in 20 patients (5.5%) within the first 48 hours of ICU admission, while 73 additional patients (20.1%) had positive cultures later during their stay. The most frequently isolated pathogens at all sites were Acinetobacter baumannii (n=54), Klebsiella species (n=13) and coagulase-negative staphylococci (n=9). Length of ICU stay (p&lt;0.001) and intubation (p&lt;0.001) were associated with positive cultures on multivariate analysis. Disease severity (p=0.5), early antibiotic use (p=0.5), diabetes mellitus (p=0.1) and HIV (p=0.9) were not associated with positive cultures. Positive cultures, particularly for tracheal aspirates (p&lt;0.05), were associated with longer ICU length of stay and mortality. Early empirical antibiotic use was not associated with mortality (odds ratio 2.5; 95% confidence interval 0.95 - 6.81).

CONCLUSIONS

Bacterial coinfection was uncommon in patients at the time of admission to the ICU with severe COVID-19. Avoiding early empirical antibiotic therapy is therefore reasonable. Strategies to avoid coinfection and outbreaks in hospital, such as infection prevention and control, as well as the strict use of personal protective equipment, are important to improve outcomes.

Duration and frequency of drainage and flooding events interactively affect soil biogeochemistry and N flux in subtropical peat soils

With the demand for restoration and future prediction of climate change effects, subtropical peatlands are expected to be subjected to hydrologic regimes with variable duration and frequency of drained and flooded conditions, but knowledge of their interactive effects on soil biogeochemistry and emission of greenhouse gases including nitrous oxide (N₂O) is largely limited. The objective of this study was to investigate how the duration and frequency of drainage and flooding events interactively influence soil biogeochemical properties and denitrification and related net N₂O production rates following rewetting. Surface soils are susceptible to different hydrologic regimes. Significantly higher pH, extractable organic carbon (ext. OC), ammonium (NH₄⁺-N), denitrification enzyme activity (DEA), but lower nitrate (NO₃^--N), microbial biomass C and N were observed when the peat soils were under flooded conditions compared to drained conditions. Two-week and four-week drainage or flooding duration did not result in statistically significant differences in soil biogeochemical properties. A 24-week prolonged drainage led to an accumulation of NO₃^--N and a significantly lower pH. Soil microbial biomass and fungal:bacterial abundance likely increased with the frequency of drainage-flooding cycles. Significant differences in denitrification and net N₂O production rates following reflooding were mainly found in the surface soils. Structural equation modeling indicated that hydroperiod and water-filled pore space (WFPS) prior to reflooding is likely to control denitrification and net N₂O production through its regulation of NO₃^--N and activity of microorganisms involved in denitrification while higher drainage-flooding frequency decreases the availability of organic C and NO₃^--N for denitrification. Our results also suggest high NO₃^--N and low pH within peat soils caused by prolonged drainage likely leads to a significant N₂O emission pulse following reflooding. For peat soils subjected to frequent drainage-flooding cycles, N₂O emission pulses following reflooding would decrease with time, attributing to the loss of substrates for denitrification.

Soil phosphorus forms and storage in stormwater treatment areas of the Everglades: Influence of vegetation and nutrient loading

Stormwater treatment areas (STAs) are an integral component of the Everglades restoration strategies to reduce phosphorus (P) loads from adjacent agricultural and urban areas. The overall objective of this study was to determine the forms and distribution of P in floc and soils along the flow-path of two parallel flow-ways (FWs) in STA-2 with emergent aquatic vegetation (EAV) and submerged aquatic vegetation (SAV), respectively, to assess their stability and potential for long term storage. In EAV high organic matter accretion supported low bulk density and high P concentrations in floc and soil, while high mineral matter accretion in SAV resulted in high bulk density and low P concentrations. Approximately 25-30% of the total P is identified as highly reactive P (HRP) pools, 50-60% in moderately reactive P (RP) forms, and 15-20% in the non-reactive P (NRP) pool. Within HRP and RP pools, a large proportion of P in the SAV areas was inorganic while organic P was more dominant in the EAV areas. Enrichment of total P (especially in HRP and RP pools) found in the upstream areas of both FWs resulted from the P loading into FWs over time, and the surplus P conditions can potentially support flux into the water column. In EAV FW, approximately 45% of the P retained was recovered in floc and RAS and remaining was possibly retained in the above and below ground biomass and incorporated into subsurface soils. In SAV FW, all of the P retained was recovered in floc and soils suggesting P retention in plants was not significant. For STAs to continue to function effectively and meet the desired outflow TP concentrations, management strategies should be aimed to promote P limiting conditions within the system to avoid release of P from floc and soils to water column and potential downstream transport.

Influence of select bioenergy by-products on soil carbon and microbial activity: A laboratory study

Concerns about the negative impacts of crop biomass removal on soil ecological functions have led to questioning the long-term sustainability of bioenergy production. To offset this potential negative impact, use of organic C rich by-products from the bioenergy industries have been proposed as a means to replenish soil C in degraded soils. However, the impact of these by-products application on soil carbon dynamics is not fully understood. We measured biogeochemical changes in soil organic C following a three-year field application of two by-products, biochar (BC) and fermentation-by product (FBP), of bioenergy industry processes in an elephant grass [Pennisetum purpureum (L.) Schum.] field. There was a significant increase in overall soil organic C (SOC) observed in BC (270%) treated plots, however the higher labile SOC (51%) content was present in FBP treated plots. Solid-state ¹³C NMR spectroscopy further revealed increased aromatic and alkyl groups in BC amended soils which lend to its significantly higher hydrophobicity index, HI (2.13) compared with FBP amended soils (HI = 0.8). Initial biogeochemical responses of amended soils to drought conditions were also investigated during a short-term experiment with drying and rewetting of soils. Increased concentrations of extractable C and higher stimulation of microbial activities (respiration and enzyme activities) in FBP amended soils were measured. Overall, our results reveal different impacts of the two soil amendments, where FBP soil application can affect the labile SOC availability, and stimulate rapid microbial response in drought affected soils, and biochar soil application lowers the labile SOC and microbial stimulation facilitating C sequestration over time.

Psychometric evaluation of a measure of factors influencing hand hygiene behaviour to inform intervention

BACKGROUND

Although the hand hygiene (HH) procedure is simple, the related behaviour is complex and is not readily understood, explained or changed. There is a need for practical tools to provide data that can guide healthcare managers and practitioners not only on the 'what' (the standards that must be met), but also the 'how' (guidance on how to achieve the standards).

AIM

To develop a valid questionnaire to evaluate attitudes to the factors that influence engagement in HH behaviour that can be readily completed, administered and analysed by healthcare professionals to identify appropriate intervention strategies. Construct validity was assessed using confirmatory factor analysis, predictive validity was assessed through comparison with self-reported HH behaviour, and convergent validity was assessed through direct unit-level observation of HH behaviour.

METHODS

The Capability, Opportunity, Motivation-Behaviour (COM-B) model was used to design a 25-item questionnaire that was distributed to intensive care unit (ICU) personnel in Ireland. Direct observation of HH behaviour was carried out at two ICUs.

FINDINGS

In total, 292 responses to the survey (response rate 41.0%) were included in the analysis. Confirmatory factor analysis resulted in a 17-item questionnaire. Multiple regression revealed that a model including capability, opportunity and motivation was a significant predictor of self-reported behavioural intention [F(3,209)=22.58, P<0.001]. However, the opportunity factor was not found to make a significant contribution to the regression model.

CONCLUSION

The COM-B HH questionnaire is reliable and valid, and provides data to support the development and evaluation of HH interventions that meet the needs of specific healthcare units.

Is there a role for perfusion imaging in assessing treatment response following ablative therapy of small renal masses-A systematic review

Aims

Ablation therapies are an innovative nephron-sparing alternative to radical nephrectomy for early stage renal cancers, although determination of treatment success is challenging. We aimed to undertake a systematic review of the literature to determine whether assessment of tumour perfusion may improve response assessment or alter clinical management when compared to standard imaging.

Material and Methods

Two radiologists performed independent primary literature searches for perfusion imaging in response assessment following ablative therapies (radiofrequency ablation and cryotherapy) focused on renal tumours.

Results

5 of 795 articles were eligible, totaling 110 patients. The study designs were heterogeneous with different imaging techniques, perfusion calculations, reference standard and follow-up periods. All studies found lower perfusion following treatment, with a return of ‘high grade’ perfusion in the 7/110 patients with residual or recurrent tumour. One study found perfusion curves were different between successfully ablated regions and residual tumour.

Conclusions

Studies were limited by small sample size and heterogeneous methodology. No studies have investigated the impact of perfusion imaging on management. This review highlights the current lack of evidence for perfusion imaging in response assessment following renal ablation, however it suggests that there may be a future role. Further prospective research is required to address this.

Direct-acting antiviral treatment for hepatitis C virus infection and risk of incident liver cancer: a retrospective cohort study

BACKGROUND

Eradication of hepatitis C virus (HCV) infection via interferon-based treatment lowers hepatocellular carcinoma risk; some research suggests this effect extends to interferon-free treatment.

AIMS

The objective of this retrospective cohort study was to examine the association of direct-acting antiviral (DAA) exposure with risk of incident liver cancer in real-world data.

METHODS

From United States administrative claims data through March 31, 2017, we identified 30 183 adult HCV patients exposed to DAAs. For comparison, we identified contemporary adult HCV patients without evidence of HCV treatment (N = 137 502), and historical HCV patients treated with interferon prior to the introduction of DAAs (N = 12 948). Included patients had at least 12 months of prior enrolment and no evidence of prior liver cancer at baseline. Hazard ratios (HRs) estimating risk of incident liver cancer associated with DAA treatment were calculated using Cox proportional hazards methods.

RESULTS

Relative to untreated HCV patients, DAA-treated patients were older, more likely to be male, and more likely to have cirrhosis at baseline. After adjustment, DAA treatment was associated with a significantly reduced risk of liver cancer relative to no treatment (adjusted HR = 0.84, 95% CI: 0.73-0.96), and relative to interferon-based treatment in the pre-DAA era (HR = 0.69, 95% CI: 0.59-0.81).

CONCLUSIONS

In this large, population-based study, DAA-based treatment was associated with a reduced risk of incident liver cancer relative to both no HCV treatment and to interferon-based treatment in the pre-DAA era. As additional follow-up time of DAA-treated patients accrues, we anticipate that the long-term benefits of DAA treatment will become more apparent.

Influence of Vegetation on Long-term Phosphorus Sequestration in Subtropical Treatment Wetlands

Sustainable operation of a treatment wetland depends on its continued treatment of influent water to achieve desired outflow water quality targets. Water treatment or nutrient reduction is attained by a combination of biotic and abiotic processes. We studied one of the world's largest treatment wetlands established to revive the Florida Everglades from impacts of excessive phosphorus (P) inputs. Phosphorus retained in the treatment wetlands is sequestered within the accumulated material via biotic and abiotic pathways that are influenced by the existing wetland vegetation. Recently accreted soils (RAS) provide a major sink for stored P, and long-term P removal efficiency of treatment wetlands is governed by the stability of accreted P because more stable P pools are less susceptible to mobilization and loss. We quantified reactive P (extracted with acid and alkali) and nonreactive P (not extracted with acid and alkali) pools in wetland soils by using an operationally defined P fractionation scheme and assessed the effect of emergent vs. submerged vegetation communities on stability of sequestered P. Reactive P comprised 63 to 79% of total P in wetland soils without a clear difference between two vegetation groups. The quantities of reactive P forms (inorganic vs. organic P) were significantly different between two vegetation types. A higher proportion of reactive P was stored as organic P in flocculent detrital organic matter (floc) and RAS under emergent vegetation (46-47% total P) in comparison with submerged vegetation (21-34% total P). The dominant P removal pathway in the submerged vegetation system was associated with calcium whereas plant uptake and peat burial appeared to be the main pathway in the emergent vegetation system.

Safety and efficacy of sofosbuvir-based direct-acting antiviral regimens for hepatitis C virus genotypes 1-4 and 6 in Myanmar: Real-world experience

This open-label, clinical experience investigated the safety and efficacy of direct-acting antiviral (DAA) hepatitis C virus (HCV) therapy in Myanmar; 344 patients completed treatment between June 2015 and May 2016. Patients with HCV genotypes 1-4 and 6 received one of four treatments: (i) Peg-interferon (PEG-IFN)+sofosbuvir (SOF)+ribavirin (RBV) for 12 weeks, (ii) SOF+RBV for 24 weeks, (iii) ledipasvir (LDV)+SOF for 12 weeks or (iv) daclatasvir (DCV)+SOF+RBV for 12 or 24 weeks. Genotype 3 was most common (n=133, 38.7%), followed by genotype 6 (n=122, 35.5%) and genotype 1 (n=86, 25%). Overall, 91% of patients achieved sustained virologic response (SVR); 99% in group 1, (n=148/149), 90% in group 2 (n=95/106), 78% in group 3 (n=65/83) and 100% in group 4 (n=6/6). In group 3, SVR rates were 96.8% in genotype 1 (n=30/31) and 64.1% in genotype 6 (n=25/39). Multivariable regression analysis identified advanced fibrosis (F3-4) (OR=.16 CI: 0.05-0.57, P=.005), genotype 6 (OR=.35, CI: 0.16-0.79, P=.012) and diabetes (OR=.29, CI: 0.12-0.71, P=.007) as negative independent predictors of response. Adverse events were mild with all-oral therapy.

CONCLUSION

DAA therapy ±PEG-IFN achieved high SVR rates. Genotype 6 patients had a low SVR to 12 weeks of LDV and SOF raising the need for other regimens, RBV or longer treatment duration in this population.

Effect of viral suppression on hepatic venous pressure gradient in hepatitis C with cirrhosis and portal hypertension

Portal hypertension is a predictor of liver-related clinical events and mortality in patients with hepatitis C and cirrhosis. The effect of interferon-free hepatitis C treatment on portal pressure is unknown. Fifty patients with Child-Pugh-Turcotte (CPT) A and B cirrhosis and portal hypertension (hepatic venous pressure gradient [HVPG] >6 mm Hg) were randomized to receive 48 weeks of open-label sofosbuvir plus ribavirin at Day 1 or after a 24-week observation period. The primary endpoint was sustained virologic response 12 weeks after therapy (SVR12) in patients who received ≥1 dose of treatment. Secondary endpoints included changes in HVPG, laboratory parameters, and MELD and CPT scores. A subset of patients was followed 48 weeks posttreatment to determine late changes in HVPG. SVR12 occurred in 72% of patients (33/46). In the 37 patients with paired HVPG measurements at baseline and the end of treatment, mean HVPG decreased by -1.0 (SD 3.97) mm Hg. Nine patients (24%) had ≥20% decreases in HVPG during treatment. Among 39 patients with pretreatment HVPG ≥12 mm Hg, 27 (69%) achieved SVR12. Four of the 33 (12%) patients with baseline HVPG ≥12 mm Hg had HVPG <12 mm Hg at the end of treatment. Of nine patients with pretreatment HVPG ≥12 mm Hg who achieved SVR12 and completed 48 weeks of follow-up, eight (89%) had a ≥20% reduction in HVPG, and three reduced their pressure to <12 mm Hg. Patients with chronic HCV and compensated or decompensated cirrhosis who achieve SVR can have clinically meaningful reductions in HVPG at long-term follow-up. (EudraCT 2012-002457-29).

Acute Kidney Injury in Cirrhosis: Baseline Serum Creatinine Predicts Patient Outcomes

OBJECTIVES

The International Ascites Club (IAC) recently defined Stage 1 acute kidney injury (AKI) for cirrhosis as an acute increase in serum creatinine (SCr) by ≥0.3 mg/dl or by ≥50% in <48 h from a stable value within 3 months. The baseline SCr may influence AKI risk and patient outcomes. The objective of this study is to determine in cirrhosis whether the baseline SCr has any effect on the in-hospital AKI course and patient survival.

METHODS

North American Consortium for the Study of End-Stage Liver Disease is a consortium of tertiary-care hepatology centers prospectively enroling non-elective cirrhotic inpatients. Patients with different baseline SCr levels (≤0.5, 0.51-1.0, 1.01-1.5, >1.5 mg/dl) were evaluated for the development of AKI, and compared for AKI outcomes and 30-day survival.

RESULTS

653 hospitalized cirrhotics (56.7±10years, 64% men, 30% with infection) were included. The incidence of AKI was 47% of enrolled patients. Patients with higher baseline SCr were more likely to develop AKI, with significantly higher delta and peak SCr (P<0.001) than the other groups, more likely to have a progressive AKI course (P<0.0001), associated with a significantly reduced 30-day survival (P<0.0001). Multivariate logistic regression showed that the delta SCr during an AKI episode to be the strongest factor impacting AKI outcomes and survival (P<0.001), with a delta SCr of 0.70 mg/dl having a 68% sensitivity and 80% specificity for predicting 30-day mortality.

CONCLUSIONS

Admitted cirrhotic patients with higher baseline SCr are at higher risk for in-hospital development of AKI, and more likely to have AKI progression with reduced survival. Therefore, such patients should be closely monitored and treated promptly for their AKI.

Chronic hepatitis C and chronic kidney disease: Advances, limitations and unchartered territories

Over the past few years, treatment options for chronic hepatitis C virus (HCV) infection have evolved dramatically. The current approved interferon-free direct-acting antiviral (DAA) regimens have been shown to be safe and effective with sustained virologic response (SVR) rates of >90% in most patients. Unique issues yet remain such as the challenges in patients with impaired renal function or decompensated cirrhosis. Patients with stages 4-5 chronic kidney disease (CKD) have a higher prevalence of HCV infection compared with the general population. Chronic HCV in those on dialysis and in kidney transplant recipients is associated with higher morbidity and mortality than uninfected patients. The HCV-infected population is also at risk of developing extrahepatic manifestations associated with altered immune system function and chronic inflammation with cryoglobulinaemic vasculitis being the most common of these manifestations. Therefore, patients with CKD stages 4-5 have to be considered priority patients for HCV therapy. New antiviral therapies have the potential to improve outcomes in this vulnerable patient population, including those on haemodialysis. Recently published studies conducted in kidney transplant recipients have demonstrated successful outcomes. It is thus essential that we carefully select the most appropriate DAA regimen and the best time for treatment in the context of kidney transplantation or cryoglobulinaemic vasculitis. While sofosbuvir, the only approved nucleotide NS5B inhibitor, has been the backbone of most pangenotypic therapeutic regimens, it has a limitation in those with advanced kidney disease. The currently approved regimens for those with stage 4/5 CKD, while effective, have challenges in that they apply to genotype 1/4 and may require RBV for genotype 1a. Globally, genotype 3 is a common infection, and thus, this group with CKD presents a huge unmet need for effective therapies. As therapy of HCV in renal transplant recipients has been highly successful, it provides an opportunity to expand the use of HCV-infected organs in solid organ transplantation.

Evaluation of Ageratum conyzoides in field scale constructed wetlands (CWs) for domestic wastewater treatment

Ageratum conyzoides were evaluated in field scale subsurface flow constructed wetlands (CWs) to quantify its nitrogen (N) and phosphorus (P) uptake and compare with wetland plants (Pistia stratiotes, Typha latifolia and Canna indica). The two-field scale subsurface flow CWs, located in the International Crops Research Institute for Semi-Arid Tropics, received wastewater from an urban colony. The CW1 and CW2 had the same dimensions (length:10 m, width:3 m, total depth:1.5 m and sand and gravel:1 m), similar flow rates (3 m³/d), hydraulic loading rates (HLRs-10 cm/d) and hydraulic retention time (HRT-5 days) from July 2014-August 2015. The vegetation in both CWs consisted of Pistia stratiotes, Typha latifolia, Canna indica, and Ageratum conyzoides, respectively. The CW1 (% reduction with respect to concentrations) reduced total suspended solids (TSS) (68%), NH₄-N (26%), NO₃-N (30%), soluble reactive P (SRP) (20%), chemical oxygen demand (COD) (45%) and fecal coliforms (71%), while the CW2 (%-reduction with respect to concentrations) reduced TSS (63%), NH₄-N (32%), NO₃-N (26%), SRP (35%), COD (39%) and fecal coliforms (70%). Ageratum conyzoides can be used in combination with Pistia stratiotes, Typha latifolia and Canna indica to enhance removal of excessive N, P and fecal coliforms from domestic wastewater.

Ledipasvir-sofosbuvir and sofosbuvir plus ribavirin in patients with chronic hepatitis C and bleeding disorders

INTRODUCTION

Chronic hepatitis C virus (HCV) infection is prevalent among patients with inherited bleeding disorders and is a leading cause of mortality in those with haemophilia.

AIM

We evaluated the efficacy and safety of ledipasvir-sofosbuvir and sofosbuvir plus ribavirin in patients with chronic HCV genotype 1-4 infection and an inherited bleeding disorder.

METHODS

Ledipasvir-sofosbuvir was administered for 12 weeks to patients with genotype 1 or 4 infection and for 12 or 24 weeks to treatment-experienced cirrhotic patients with genotype 1 infection. Patients with genotype 2 and 3 infection received sofosbuvir plus ribavirin for 12 and 24 weeks respectively.

RESULTS

The majority of the 120 treated patients had a severe bleeding disorder (55%); overall, 65% of patients had haemophilia A and 26% of patients had haemophilia B; 22% were HIV coinfected. Sustained virologic response at 12 weeks posttreatment was 99% (98/99) in patients with genotype 1 or 4 infection; 100% (5/5) in treatment-experienced cirrhotic patients with genotype 1 infection; 100% (10/10) in patients with genotype 2 infection; and 83% (5/6) in patients with genotype 3 infection. There were no treatment discontinuations due to adverse events (AEs). The most frequent non-bleeding AEs were fatigue, headache, diarrhoea, nausea and insomnia. Bleeding AEs occurred in 22 patients, of which all but one were considered unrelated to treatment.

CONCLUSION

Treatment with ledipasvir-sofosbuvir for patients with HCV genotype 1 or 4 infection or sofosbuvir plus ribavirin for patients with genotype 2 or 3 infection was highly effective and well tolerated among those with inherited bleeding disorders.

All-oral direct-acting antiviral therapy in HCV-advanced liver disease is effective in real-world practice: observations through HCV-TARGET database

BACKGROUND

Chronic hepatitis C virus therapy in patients with advanced liver disease remains a clinical challenge. HCV-TARGET collects data in patients treated at tertiary academic and community centres.

AIM

To assess efficacy of all-oral HCV therapy in advanced liver disease.

METHODS

Between December 2013 and October 2014, 240 patients with a MELD score of ≥10 initiated HCV treatment with an all-oral regimen. Data from the 220 patients who completed 12-week follow-up were analysed.

RESULTS

Genotype 1 (GT1) patients had higher sustained virological response (SVR) when treated with sofosbuvir plus simeprevir ± ribavirin than with sofosbuvir plus ribavirin (66-74% vs. 54%); GT1b vs GT1a (84% vs. 64%). SVR for GT2 was 72% with sofosbuvir plus ribavirin, while GT3 patients had a substantially lower response (35%). A decrease in MELD score was not clearly related to SVR over the short course of follow-up although some had improvements in MELD score, serum bilirubin and albumin. A predictor of virological response was albumin level while negative predictors were elevated bilirubin level and GT1a. Most patients with GT1 were treated with approximately 12-week duration of sofosbuvir and simeprevir ± ribavirin therapy while GT2 and GT3 patients were treated with approximately 12 and 24 weeks of sofosbuvir plus ribavirin respectively.

CONCLUSIONS

All-oral therapies are effective among patients with advanced liver disease with high levels of success in GT2 and GT1b, and may serve to reduce the severity of liver disease after SVR. Treatment for GT3 patients remains an unmet need. Clinical trial number: NCT01474811.

Review article: safety and tolerability of direct-acting anti-viral agents in the new era of hepatitis C therapy

BACKGROUND

Direct-acting anti-virals (DAAs) licensed to treat chronic HCV infection have revolutionised treatment algorithms by drastically mitigating side effects while enhancing efficacy relative to interferon-based therapy.

AIM

To review adverse events (AEs) uniquely associated with DAA therapy across a broad spectrum of patient populations.

METHODS

Searches of PubMed and FDA surveillance studies were undertaken to complete an exhaustive review. Search terms included 'DAAs', 'safety', and 'tolerability'.

RESULTS

While DAAs are remarkably well tolerated, they are accompanied by unique AEs. Simeprevir, an NS3/4A protease inhibitor, has been known, albeit infrequently, to cause mild hyperbilirubinemia and photosensitivity reactions; and paritaprevir boosted with ritonavir causes bilirubin and ALT elevations. Asunaprevir, another protease inhibitor, infrequently causes elevated transaminase levels. NS5A and NS5B inhibitors are well tolerated, although sofosbuvir is contraindicated in patients with severe renal impairment. Ribavirin co-administered in certain treatment regimens has been associated with cough, rash and haemolytic anaemia.

CONCLUSIONS

With the impending reality of a more tolerable interferon-sparing regimen, the future of DAA therapy offers shorter treatment duration, simplified disease management, and a patient-centred regimen. With advantages come drawbacks, including development of resistance to therapy and accessibility to this expensive treatment. DAA therapy continues to advance at a brisk pace with a promising trend for higher tolerability, even in difficult-to-treat subgroups such as those with cirrhosis, nonresponders to prior therapy, and transplant recipients. Subgroup-specific contraindications and safety-related limitations are active areas of research. Concerted research efforts and continuing advances lend hope to the goal of rendering HCV a routinely curable disease.

Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers

The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development.

Effectiveness of Simeprevir Plus Sofosbuvir, With or Without Ribavirin, in Real-World Patients With HCV Genotype 1 Infection

BACKGROUND & AIMS

The interferon-free regimen of simeprevir plus sofosbuvir was recommended by professional guidelines for certain patients with hepatitis C virus (HCV) genotype 1 infection based on the findings of a phase 2 trial. We aimed to evaluate the safety and efficacy of this regimen in clinical practice settings in North America.

METHODS

We collected demographic, clinical, and virologic data, as well as reports of adverse outcomes, from sequential participants in HCV-TARGET--a prospective observational cohort study of patients undergoing HCV treatment in routine clinical care settings. From January through October 2014, there were 836 patients with HCV genotype 1 infection who began 12 weeks of treatment with simeprevir plus sofosbuvir (treatment duration of up to 16 weeks); 169 of these patients received ribavirin. Most patients were male (61%), Caucasian (76%), or black (13%); 59% had cirrhosis. Most patients had failed prior treatment with peginterferon and ribavirin without (46%) or with telaprevir or boceprevir (12%). The primary outcome was sustained virologic response (SVR), defined as the level of HCV RNA below quantification at least 64 days after the end of treatment (beginning of week 12 after treatment--a 2-week window). Logistic regression models with inverse probability weights were constructed to adjust for baseline covariates and potential selection bias.

RESULTS

The overall SVR rate was 84% (675 of 802 patients, 95% confidence interval, 81%-87%). Model-adjusted estimates indicate patients with cirrhosis, prior decompensation, and previous protease inhibitor treatments were less likely to achieve an SVR. The addition of ribavirin had no detectable effects on SVR. The most common adverse events were fatigue, headache, nausea, rash, and insomnia. Serious adverse events and treatment discontinuation occurred in only 5% and 3% of participants, respectively.

CONCLUSIONS

In a large prospective observational cohort study, a 12-week regimen of simeprevir plus sofosbuvir was associated with high rates of SVR and infrequent treatment discontinuation. ClinicalTrials.gov: NCT01474811.

Soil and phosphorus accretion rates in sub-tropical wetlands: Everglades Stormwater Treatment Areas as a case example

Wetlands are known to serve as sinks for particulate matter and associated nutrients and contaminants. Consequently rate of soil accretion is critical for continued performance of wetlands to provide ecosystem services including water quality improvement and reduce excess contaminant loads into downstream waters. Here we demonstrate a new technique to determine rate of soil accretion in selected subtropical treatment wetlands located in southern USA. We also report changes in soil accretion rates and subsequent phosphorus (P) removal efficiency with increasing operational history of these treatment wetlands. Utilizing discernible signatures preserved within the soil depth profiles, 'change points' (CP) that corresponded to specific events in the life history of a wetland were determined. The CP was observed as an abrupt transition in the physico-chemical properties of soil as a manifestation of prevailing historical conditions (e.g. startup of treatment wetlands in this case). Vertical depth of CP from the soil surface was equivalent to the depth of recently accreted soil (RAS) and used for soil accretion rate calculations. Annual soil and P accretion rates determined using CP technique (CPT) in studied wetlands ranged from 1.0±0.3 to 1.7±0.8 cm yr(-1) and 1.3±0.6 to 3.3±2 g m(-2) yr(-1), respectively. There was no difference in RAS depth between emergent and submerged aquatic vegetation communities found at the study location. Our results showed that soil and P accretion rates leveled off after 10 yr of treatment wetlands' operation. On comparison, soil accretion rates and RAS depth determined by CPT were commensurate with that measured by other techniques. CPT can be easily used where a reliable record of wetland establishment date or some significant alteration/perturbation is available. This technique offers a relatively simple alternative to determine vertical accretion rates in free-water surface wetlands.

Evaluation of Legacy Phosphorus Storage and Release from Wetland Soils

To better manage legacy phosphorus (P) in watersheds, reliable techniques to predict P storage and release from uplands, ditches, streams, and wetlands must be developed. Techniques such as the P saturation ratio (PSR) and the soil P storage capacity (SPSC), originally developed for upland soils, are hypothesized to be applicable to wetland soils as well. Surface soils were collected from eight beef ranches within the Lake Okeechobee Watershed, FL, to obtain a threshold PSR value and to evaluate the use of PSR and SPSC for identifying legacy P storage and release from wetland soils. Water-soluble P (WSP) was determined for all soils; the equilibrium P concentration (EPC) was determined for selected soils through the generation of Langmuir isotherms. The threshold PSR for wetland soils, calculated from P, Fe, and Al in a Mehlich 1 solution, was determined to be 0.1; SPSC, calculated using the threshold PSR, was found to be related to WSP. When SPSC was positive, WSP and EPC were minimal. However, both WSP and EPC increased once SPSC became negative. Organic matter (OM) varied from 0.4 to 90 g kg for both positive and negative SPSC, suggesting that OM in wetland soils does not have any effect on P retention and release below the threshold PSR. Moreover, when a wetland or drainage ditch is heavily P impacted, it could be a P source; wetland vegetation may no longer be able to assimilate additional P, resulting in P loss from the soil. This study suggests that the PSR-SPSC concept could be a valuable tool for evaluating legacy P release from wetlands.

HOI-02 induces apoptosis and G2-M arrest in esophageal cancer mediated by ROS

Reactive oxygen species (ROS) are chemically reactive molecules that perform essential functions in living organisms. Accumulating evidence suggests that many types of cancer cells exhibit elevated levels of ROS. Conversely, generation of ROS has become an effective method to kill cancer cells. (E)-3-hydroxy-3-(4-(4-nitrophenyl)-2-oxobut-3-en-1-yl) indolin-2-one, which is an NO2 group-containing compound designated herein as HOI-02, generated ROS and, in a dose-dependent manner, decreased esophageal cancer cell viability and inhibited anchorage-independent growth, followed by apoptosis and G2-M arrest. Moreover, results of an in vivo study using a patient-derived xenograft mouse model showed that HOI-02 treatment suppressed the growth of esophageal tumors, without affecting the body weight of mice. The expression of Ki-67 was significantly decreased with HOI-02 treatment. In addition, the phosphorylation of c-Jun, and expression of p21, cleaved caspase 3, and DCFH-DA were increased in the HOI-02-treated group compared with the untreated control group. In contrast, treatment of cells with (E)-3-(4-(4-aminophenyl)-2-oxobut-3-en-1-yl)-3-hydroxyindolin-2-one, which is an NH2 group-containing compound designated herein as HOI-11, had no effect. Overall, we identified HOI-02 as an effective NO2 group-containing compound that was an effective therapeutic or preventive agent against esophageal cancer cell growth.