Statistical analysis plan for the replacing protein via enteral nutrition in a stepwise approach in critically ill patients (REPLENISH) randomized clinical trial.

BACKGROUND: The optimal amount and timing of protein intake in critically ill patients are unknown. REPLENISH (Replacing Protein via Enteral Nutrition in a Stepwise Approach in Critically Ill Patients) trial evaluates whether supplemental enteral protein added to standard enteral nutrition to achieve a high amount of enteral protein given from ICU day five until ICU discharge or ICU day 90 as compared to no supplemental enteral protein to achieve a moderate amount of enteral protein would reduce all-cause 90-day mortality in adult critically ill mechanically ventilated patients. METHODS: In this multicenter randomized trial, critically ill patients will be randomized to receive supplemental enteral protein (1.2 g/kg/day) added to standard enteral nutrition to achieve a high amount of enteral protein (range of 2-2.4 g/kg/day) or no supplemental enteral protein to achieve a moderate amount of enteral protein (0.8-1.2 g/kg/day). The primary outcome is 90-day all-cause mortality; other outcomes include functional and health-related quality-of-life assessments at 90 days. The study sample size of 2502 patients will have 80% power to detect a 5% absolute risk reduction in 90-day mortality from 30 to 25%. Consistent with international guidelines, this statistical analysis plan specifies the methods for evaluating primary and secondary outcomes and subgroups. Applying this statistical analysis plan to the REPLENISH trial will facilitate unbiased analyses of clinical data. CONCLUSION: Ethics approval was obtained from the institutional review board, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia (RC19/414/R). Approvals were also obtained from the institutional review boards of each participating institution. Our findings will be disseminated in an international peer-reviewed journal and presented at relevant conferences and meetings. TRIAL REGISTRATION: ClinicalTrials.gov, NCT04475666 . Registered on July 17, 2020.

Prevalence and epidemiological trends in mortality due to COVID-19 in Saudi Arabia.

OBJECTIVES: This article describes the prevalence and epidemiological trends of COVID-19 mortality in the largest registry in the Kingdom of Saudi Arabia (KSA). STUDY DESIGN: A prospective epidemiological cohort study using data from all healthcare facilities in KSA collected between March 23, 2020, and April 30, 2022. Data on the number of daily deaths directly related to COVID-19 were gathered, analyzed, and reported. METHOD: Data analysis was carried out using national and regional crude case fatality rate and death per 100,000 population. Descriptive statistics using numbers and proportions were used to describe age, gender, nationality, and comorbidities. The mortality trend was plotted and compared with international figures. In addition, the most common comorbidities associated with mortality and the proportion of patients who received COVID-19 vaccine were reported. RESULTS: The total reported number of deaths between March 23, 2020, and April 30, 2022, was 9085. Crude case fatality rate was 1.21%, and death per 100,000 population was 25.38, which compared favorably to figures reported by several developed countries. The highest percentages of deaths were among individuals aged between 60 and 69 years, males (71%), and individuals with diabetes (60%). Only 2.8% of mortalities occur in patients who received COVID-19 vaccine. Diabetes, hypertension, and heart failure had the highest attributable risk of mortality among patients who died due to COVID-19. CONCLUSION: Case fatality rate and death per 100,000 population in KSA are among the lowest in the world due to multiple factors. Several comorbidities have been identified, namely, diabetes, hypertension, obesity, and cardiac arrhythmias.

Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe.

The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.

Prevalence and Correlates of Depressive Symptoms among Medical Students: a Cross-sectional Single-centre Study.

BACKGROUND: Depressive symptoms are common among medical students. The aim of the present study was to determine the prevalence and risk factors of depressive symptoms among medical students in Sultan Qaboos University in Oman. METHOD: A cross-sectional study was conducted among a random sample selected from 1041 medical students at Sultan Qaboos University, Oman. The Patient Health Questionnaire-9 (PHQ-9) was used to screen for depressive symptoms. A logistic regression model was used to determine risk factors for depressive symptoms. RESULTS: Of 197 medical students selected, 189 (61 men and 128 women) responded. The PHQ-9 results showed that the prevalence of depressive symptoms was 41.3%. In multivariate analysis, female students were more likely than male students to develop depression (adjusted odds ratio = 2.866, p = 0.004). Medical students with a family history of depression were more likely to develop depression than those without a family history of depression (adjusted odds ratio = 4.150, p = 0.014). CONCLUSIONS: Depressive symptoms are common among medical students in Sultan Qaboos University. Risk factors for depressive symptoms are female sex and family history of depression.

Optimization of design and production strategies for novel adeno-associated viral display peptide libraries.

Libraries displaying random peptides on the surface of adeno-associated virus (AAV) are powerful tools for the generation of target-specific gene therapy vectors. However, for unknown reasons the success rate of AAV library screenings is variable and the influence of the production procedure has not been thoroughly evaluated. During library screenings, the capsid variants with the most favorable tropism are enriched over several selection rounds on a target of choice and identified by subsequent sequencing of the encapsidated viral genomes encoding the library capsids with targeting peptide insertions. Thus, a high capsid-genome correlation is crucial to obtain the correct information about the selected capsid variants. Producing AAV libraries by a two-step protocol with pseudotyped library transfer shuttles has been proposed as one way to ensure such a correlation. Here we show that AAV2 libraries produced by such a protocol via transfer shuttles display an unexpected additional bias in the amino-acid composition which confers increased heparin affinity and thus similarity to wildtype AAV2 tropism. This bias may fundamentally impair the intended use of AAV libraries, discouraging the use of transfer shuttles for the production of AAV libraries in the future.

Mutational landscape reflects the biological continuum of plasma cell dyscrasias.

We subjected 90 patients covering a biological spectrum of plasma cell dyscrasias (monoclonal gammopathy of undetermined significance (MGUS), amyloid light-chain (AL) amyloidosis and multiple myeloma) to next-generation sequencing (NGS) gene panel analysis on unsorted bone marrow. A total of 64 different mutations in 8 genes were identified in this cohort. NRAS (28.1%), KRAS (21.3%), TP53 (19.5%), BRAF (19.1%) and CCND1 (8.9%) were the most commonly mutated genes in all patients. Patients with non-myeloma plasma cell dyscrasias showed a significantly lower mutational load than myeloma patients (0.91±0.30 vs 2.07±0.29 mutations per case, P=0.008). KRAS and NRAS exon 3 mutations were significantly associated with the myeloma cohort compared with non-myeloma plasma cell dyscrasias (odds ratio (OR) 9.87, 95% confidence interval (CI) 1.07-90.72, P=0.043 and OR 7.03, 95% CI 1.49-33.26, P=0.014). NRAS exon 3 and TP53 exon 6 mutations were significantly associated with del17p cytogenetics (OR 0.12, 95% CI 0.02-0.87, P=0.036 and OR 0.05, 95% CI 0.01-0.54, P=0.013). Our data show that the mutational landscape reflects the biological continuum of plasma cell dyscrasias from a low-complexity mutational pattern in MGUS and AL amyloidosis to a high-complexity pattern in multiple myeloma. Our targeted NGS approach allows resource-efficient, sensitive and scalable mutation analysis for prognostic, predictive or therapeutic purposes.

Evaluation of the efficacy of transcricoid lignocaine as adjunctive local anaesthesia for fiberoptic bronchoscopy.

INTRODUCTION: Optimisation of patient comfort during flexible bronchoscopy is achieved with the use of intravenous sedation and vocal anaesthesia. METHODS: The effect of transcricoid lignocaine injection was investigated with regards to ease of procedure and frequency of cough. A single-blinded study was carried out and two visual analogue scales were used as markers of efficacy. Treatment groups were matched for age, gender and total dose of lignocaine administered. RESULTS: The results highlighted a significant improvement in the perceived ease of procedure (p < 0.0001) and frequency of coughing during the procedure (p < 0.0001). CONCLUSION: The findings of the study demonstrate that the use of transcricoid injection of lignocaine provided a safe adjunct for anaesthesia in flexible bronchoscopy.

A study into efficacy of omalizumab therapy in patients with severe persistent allergic asthma at a tertiary referral centre for asthma in Ireland.

BACKGROUND: Asthma is a chronic airway disease characterized by airway inflammation, bronchial hyperresponsiveness and airflow obstruction. Patients with persistent symptoms despite maximum standard treatment as per Global Initiative of Asthma guidelines are considered to have severe persistent asthma. Omalizumab is a recombinant humanized monoclonal antibody licenced for use as an add-on therapy in these patients. AIM: To assess the clinical benefit amongst responders to omalizumab therapy at a tertiary referral centre. METHODS: This was a retrospective audit assessing the effect of omalizumab therapy on asthma control, frequency of exacerbation and hospitalization rates over 6 months before and after therapy. RESULTS: The study included 30 responders (14 females). There was a reduction in exacerbation and hospitalization rates following initiation of omalizumab, 73 and 91%, respectively (P-value < 0.0001). The number of exacerbations decreased from 3.48 ± 2.20 to 0.93 ± 0.83 and the mean number of admissions decreased from 1.07 ± 1.1 to 0.1 ± 0.40 over the study duration (P < 0.001). There was 73% reduction in the weekly need for rescue salbutamol therapy with mean of 30.33 ± 6.49 puffs to 8.23 ± 1.51 puffs after omalizumab therapy (P < 0.0001). Seventy-nine per cent of patients were able to reduce their maintenance oral corticosteroid therapy. CONCLUSION: Overall, responders to omalizumab therapy are less likely to experience an asthma exacerbation and hospitalization. They were also more likely to reduce maintenance corticosteroid therapy and the need for rescue reliever therapy. These data suggest that omalizumab has proven effective in improving health outcomes for a cohort of carefully selected patients with severe allergic asthma in Ireland.

Eosinophil peroxidase induces the expression and function of acid-sensing ion channel-3 in allergic rhinitis: in vitro evidence in cultured epithelial cells.

BACKGROUND: Acid-sensing ion channels (ASIC) are a family of acid-activated ligand-gated cation channels. As tissue acidosis is a feature of inflammatory conditions, such as allergic rhinitis (AR), we investigated the expression and function of these channels in AR. OBJECTIVES: The aim of the study was to assess expression and function of ASIC channels in the nasal mucosa of control and AR subjects. METHODS: Immunohistochemical localization of ASIC receptors and functional responses to lactic acid application were investigated. In vitro studies on cultured epithelial cells were performed to assess underlying mechanisms of ASIC function. RESULTS: Lactic acid at pH 7.03 induced a significant rise in nasal fluid secretion that was inhibited by pre-treatment with the ASIC inhibitor amiloride in AR subjects (n = 19). Quantitative PCR on cDNA isolated from nasal biopsies from control and AR subjects demonstrated that ASIC-1 was equally expressed in both populations, but ASIC-3 was significantly more highly expressed in AR (P < 0.02). Immunohistochemistry confirmed significantly higher ASIC-3 protein expression on nasal epithelial cells in AR patients than controls (P < 0.01). Immunoreactivity for EPO+ eosinophils in both nasal epithelium and submucosa was more prominent in AR compared with controls. A mechanism of induction of ASIC-3 expression relevant to AR was suggested by the finding that eosinophil peroxidase (EPO), acting via ERK1/2, induced the expression of ASIC-3 in epithelial cells. Furthermore, using a quantitative functional measure of epithelial cell secretory function in vitro, EPO increased the air-surface liquid depth via an ASIC-dependent chloride secretory pathway. CONCLUSIONS: This data suggests a possible mechanism for the observed association of eosinophils and rhinorrhoea in AR and is manifested through enhanced ASIC-3 expression.

Pleural fluid analysis: standstill or a work in progress?

Pleural fluid analysis yields important diagnostic information in pleural effusions in combination with clinical history, examination, and radiology. For more than 30 years, the initial and most pragmatic step in this process is to determine whether the fluid is a transudate or an exudate. Light's criteria remain the most robust in separating the transudate-exudate classification which dictates further investigations or management. Recent studies have led to the evaluation and implementation of a number of additional fluid analyses that may improve the diagnostic utility of this method. This paper discusses the current practice and future direction of pleural fluid analysis in determining the aetiology of a pleural effusion. While this has been performed for a few decades, a number of other pleural characteristics are becoming available suggesting that this diagnostic tool is indeed a work in progress.

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload.

Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge. Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.

Serratia marcescens-contaminated baby shampoo causing an outbreak among newborns at King Abdulaziz University Hospital, Jeddah, Saudi Arabia.

During November 2008 to January 2009, 11 babies in the neonatal intensive care (NICU) and three babies in the nursery were infected with Serratia marcescens at King Abdulaziz University Hospital in Saudi Arabia. Overall, fifteen infections were identified among 11 newborns in the NICU: septicaemia (five cases), purulent conjunctivitis (three), urinary tract infection (two), meningitis (two) and cellulitis (one). Three newborns in the nursery had three infections: purulent conjunctivitis (two cases) and omphalitis (one). Thirteen of 14 babies recovered fully but one died from S. marcescens meningitis and septicaemia. All infections were traced to intrinsically contaminated baby shampoo introduced to the units five days before the first reported case. The outbreak terminated following withdrawal of the shampoo product.

Temperature influences the population structure of nitrite-oxidizing bacteria in activated sludge.

Activated sludge from the municipal waste water treatment plant in Hamburg was seeded with mineral nitrite medium and incubated at 10°C, 17°C and 28°C. Dominant lithoautotrophic nitrite-oxidizing bacteria have been identified by electron microscopy, denaturing and temperature gradient gel electrophoresis and PCR with genus-specific primer pairs. The results have revealed the existence of three different genera of nitrite-oxidizing bacteria, namely Nitrospira, Nitrobacter and a novel cold-adapted nitrite oxidizer. As shown by electron microscopy members of the novel genus coexisted in activated sludge together with Nitrospira. A temperature-dependent shift in the population structure was demonstrated by cultivation-based approaches. The novel nitrite oxidizer was enriched at temperatures of 10°C and 17°C. Representatives of Nitrospira were able to grow in a broad temperature range between 10°C and 28°C and members of Nitrobacter were enriched during incubations at 17°C and 28°C. By subsequent 16S rDNA sequencing, the cold-adapted nitrite oxidizer was shown to be closely related to the betaproteobacterium 'Candidatus Nitrotoga arctica'. These findings demonstrated that the population structure of nitrite-oxidizing bacteria in activated sludge is more complex than previously thought and responds strongly to long-term temperature changes.

Physiological and phylogenetic characterization of a novel lithoautotrophic nitrite-oxidizing bacterium, 'Candidatus Nitrospira bockiana'.

A new isolate of a lithoautotrophic nitrite-oxidizing bacterium was obtained from internal corrosion deposits from a steel pipeline of the Moscow heating system. The organism oxidized nitrite as the sole energy source and fixed carbon dioxide as the only carbon source. The cells were extremely pleomorphic: loosely wound spirals, slightly curved and even straight rods were detected, as well as coccoid cells. The highest rate of nitrite consumption (1.5 mM nitrite as substrate) was measured at 42 degrees C, with a temperature range of 28-44 degrees C. In enrichment cultures with Nocardioides sp. as an accompanying organism, optimal oxidation of 5.8 mM nitrite occurred at 45 degrees C, with a range of 28-48 degrees C. Neither pyruvate nor yeast extract stimulated nitrification. Organotrophic growth was not observed. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel isolate represents a new sublineage of the genus Nitrospira. On the basis of physiological, chemotaxonomic and molecular characteristics, the name 'Candidatus Nitrospira bockiana' is proposed.

Assessment of the environmental impact of landfill sites with open combustion located in arid regions by combined chemical and ecotoxicological studies.

Two different waste disposal sites in Jordan were investigated in order to determine the environmental situation in context with waste disposal techniques. One landfill, located at Marka/Amman, had been closed about 25 years ago and covered with soil. Here, the waste had been actively open combusted and openings in the cover, still emitting smoke, indicated that waste was still smoldering inside the landfill's body. The second disposal site close to Ekeeder/Irbid is still operated. On this ground, the solid waste is not intentionally burned, although spontaneous fires frequently come up. Samples of waste, soil, and entrained dust were collected and analyzed. From the solid samples, respectively, their eluates, sum parameters, ecotoxicological effects as well as contents of elements/heavy metals and organic pollutants (PAH, PCDD/F) were determined. In general, the Ekeeder-samples were low-contaminated. The investigation of the Marka-samples showed higher contamination of the site's center, clearly being influenced by combustion processes. A significant contamination of the landfill's vicinity by its emissions could not be derived from the analytical data. Ecotoxicological investigations, applying a bio-test battery, revealed correlations with the sum parameters but not with the trace pollutants. Thus, the Marka-samples with the highest measured values of sum parameters caused adverse effects on three different test species, whereas other samples from Marka and Ekeeder had small or no effects. The results of these investigations depict the influence of different disposal techniques on the contamination situation of a landfill and they shall contribute to assess the conditions of other disposal sites in (semi)arid regions.

Storage of organochlorine pesticides in human adipose tissues of Jordanian males and females.

Adipose tissue of 50 human patients (5-96, years old) were taken and analysed by gas chromatography equipped with electron capture detector (63Ni) for determination of storage levels of HCH's (alpha, beta, and gamma-hexachlorcyclohexanes), DDT and its metabolites DDE and DDD, the cyclodiens (heptachlor, heptachlorepoxide, dieldrin, aldrin and endrin) and HCB (hexachlorbenzene). The data is reported according to age groups and sexes. The results show relatively moderate concentrations of all studied pesticides and that Jordanian men are more exposed to DDT and HCH's than women.

Dioxins and furans in the Jordanian environment. Part 2: Levels of PCDD and PCDF in human milk samples from Jordan.

Thirty individual human milk samples were gathered from five main towns in Jordan. They were mixed to six pooled samples and analyzed for PCDD and PCDF. All examined samples were contaminated with 1,2,3,4,6,7,8-HeptaCDD (3.2-96.0 ng/kg fat) and OctaCDD (29.0-147 ng/kg fat). The calculated TEQ (BGA)-values range between 0.26 and 60.32 ng TEQ/kg fat, which are all above the calculated tolerable concentration of 0.19 ng TEQ/kg milk fat.

Catecholamines in Drosophila melanogaster (wild type and ebony mutant) decuticalarized retinas and brains.

The concentrations of catecholamines were determined in the decuticalarized retinas and brains at different ages in wildtype and ebony Drosophila melanogaster using the HPLC-technique with an electrochemical detector. L-Dopa, dopamine (DA), alpha-methyldopa (alpha-MD) and unidentified compounds X1, X2 and X3 were found in decuticalarized retinas and brains of wildtype and ebony at different ages. Retinas and brains of the mutant ebony have higher concentrations of L-Dopa, DA and alpha-MD than the wildtype. In both wildtype and ebony, the concentrations of X1, X2 and X3 were found to be higher in decuticalarized retinas than in brains. The identity and importance of X1, X2 and X3 are still unknown.