The various malformations of the aerodigestive tract collectively known as esophageal atresia/tracheoesophageal fistula (EA/TEF) constitute a rare group of birth defects of largely unknown etiology. Previous studies have identified a small number of rare genetic variants causing syndromes associated with EA/TEF. We performed a pilot exome sequencing study of 45 unrelated simplex trios (probands and parents) with EA/TEF. Thirteen had isolated and 32 had nonisolated EA/TEF; none had a family history of EA/TEF. We identified de novo variants in protein-coding regions, including 19 missense variants predicted to be deleterious (D-mis) and 3 likely gene-disrupting (LGD) variants. Consistent with previous studies of structural birth defects, there is a trend of increased burden of de novo D-mis in cases (1.57-fold increase over the background mutation rate), and the burden is greater in constrained genes (2.55-fold, p = 0.003). There is a frameshift de novo variant in EFTUD2, a known EA/TEF risk gene involved in mRNA splicing. Strikingly, 15 out of 19 de novo D-mis variants are located in genes that are putative target genes of EFTUD2 or SOX2 (another known EA/TEF gene), much greater than expected by chance (3.34-fold, p value = 7.20e−5). We estimated that 33% of patients can be attributed to de novo deleterious variants in known and novel genes. We identified APC2, AMER3, PCDH1, GTF3C1, POLR2B, RAB3GAP2, and ITSN1 as plausible candidate genes in the etiology of EA/TEF. We conclude that further genomic analysis to identify de novo variants will likely identify previously undescribed genetic causes of EA/TEF.

Many application problems are formulated as nonlinear binary programming models which are hard to be solved using exact algorithms especially in large dimensions. One of these practical applications is to optimally distribute protective materials for the newly emerged COVID-19. It is defined for a decision-maker who wants to choose a subset of candidate hospitals comprising the maximization of the distributed quantities of protective materials to a set of chosen hospitals within a specific time shift. A nonlinear binary mathematical programming model for the problem is introduced with a real application case study; the case study is solved using a novel discrete binary gaining-sharing knowledge-based optimization algorithm (DBGSK). The solution algorithm proposes a novel binary adaptation of a recently developed gaining-sharing knowledge-based optimization algorithm (GSK) to solve binary optimization problems. GSK algorithm is based on the concept of how humans acquire and share knowledge through their life span. Discrete binary version of GSK named novel binary gaining-sharing knowledge-based optimization algorithm (DBGSK) depends mainly on two binary stages: binary junior gaining-sharing stage and binary senior gaining-sharing stage with knowledge factor 1. These two stages enable DBGSK for exploring and exploitation of the search space efficiently and effectively to solve problems in binary space.

SummaryCongenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

Stress triggered concurrent microbial/parasitic infections are prevalent in earthen pond based farmed Nile tilapia Oreochromis niloticus. In the current study, a total of thirty five O. niloticus were collected from a commercial fish farm with a history of severe mortalities at Port Said, Egypt. Nile tilapia samples were subjected to bacteriological, parasitological and pathological examinations. Twenty one Enterococcus fecalis and 15 Streptococcus agalactiae isolates were presumptively identified utilizing the semi-automated API 20 Strept test kit. The identities of the retrieved bacteria were confirmed by the sequencing of 16 S rRNA gene. Moribund O. niloticus were found to be heavily infected by one or both of Centrocestus formosanus encysted metacercariae (EMC) and/or Myxobolus tilapiae spores presenting a unique form of synergistic and/or symbiotic relationship. The identities of both parasites were confirmed through morphological and molecular characterization. Variable circulatory, degenerative, necrotic and proliferative changes were also noticed in hematopoietic organs. Interestingly, multiple myxobolus spores and EMC were noticed in some histological sections. It was obvious that the current concurrent bacterial and parasitic infections are triggered by the deleterious effects of some stressing environmental conditions. The unfavorable climatic conditions (high temperature and high relative humidity) recorded at the surge of mortalities are probable predisposing stress factors.

BackgroundThe African Surgical OutcomeS-2 (ASOS-2) trial tested an enhanced postoperative surveillance intervention to reduce postoperative mortality in Africa. We undertook a concurrent evaluation to understand the process of intervention delivery.
Methods
Mixed-methods process evaluation, including field notes, interviews, and post-trial questionnaire responses. Qualitative analysis used the framework method with subsequent creation of comparative case studies, grouping hospitals by intervention fidelity. A post-trial questionnaire was developed using initial qualitative analyses. Categorical variables were summarised as count (%) and continuous variables as median (inter-quartile range [IQR]). Odds ratios (OR) were used to rank influences by impact on fidelity.
Results
The dataset included eight in-depth case studies, and 96 questionnaire responses (response rate 67%) plus intervention fidelity data for each trial site. Overall, 57% (n=55/96) of hospitals achieved intervention delivery using an inclusive definition of fidelity. Delivery of the ASOS-2 interventions and data collection presented a significant burden to the investigators, outstripping limited resources. The influences most associated with fidelity were: surgical staff enthusiasm for the trial (OR=3.0; 95% confidence interval [CI], 1.3–7.0); nursing management support of the trial (OR=2.6; 95% CI, 1.1–6.5); performance of a dummy run (OR=2.6; 95% CI, 1.1–6.1); nursing colleagues seeing the value of the intervention(s) (OR=2.1; 95% CI, 0.9–5.7); and site investigators' belief in the effectiveness of the intervention (OR=3.2; 95% CI, 1.2–9.4).
Conclusions
ASOS-2 has proved that coordinated interventional research across Africa is possible, but delivering the ASOS-2 interventions was a major challenge for many investigators. Future improvement science efforts must include better planning for intervention delivery, additional support to investigators, and promotion of strong inter-professional teamwork.
Clinical trial registration
ClinicalTrials gov NCT03853824.

A field experiment was carried out to evaluate the effects of different biochars on grain yield and phytoavailability and uptake of macro- and micro-nutrients by rice and wheat grown in a paddy soil in a rotation. Soil was treated with i) maize raw (un-washed) biochar (MRB), ii) maize water-washed biochar (MWB), iii) wheat raw biochar (WRB) or iv) wheat water-washed biochar (WWB) and untreated soil was used as control (CF). Inorganic fertilizers were applied to all soils while biochar treated soils received 20 ton ha−1 of designated biochar before rice cultivation in rice-wheat rotation. The WRB significantly (P < 0.05) increased rice grain yield and straw by up to 49%, compared to the CF. Biochar addition, particularly WRB, significantly increased the availability of N, P, K and their content in the grain (26–37%) and straw (22–37%) of rice and wheat. Also, the availability and grain content of Fe, Mn, Zn, and Cu increased significantly after biochar addition, particularly after the WRB, due to WRB water dissolved C acting as a carrier for micronutrients in soil and plant. However, the water-washing process altered biochar properties, particularly the water extractable C, which decreased its efficiency. Both wheat- and maize-derived biochars, particularly the WRB, are recommended to improve nutrients availability and to improve grain yield in the rice-wheat rotation agro-ecosystem. These results shed light on the importance of crop straw transformation into an important source for soil C and nutrients necessary for sustainable management of wheat-rice agro-ecosystem. However, with the current and future alternative energy demands, the decision on using crop biomass for soil conservation or for bioenergy becomes a challenge reliant on regulatory and policy frameworks.

This work reports, for first time, on optically-driven white light emission from samarium-doped yttrium aluminum garnet ceramic, Sm-doped YAG. Nanocrystalline Sm-doped YAG sample has been prepared via co-precipitation method then transformed to bulk ceramic by sintering process using Spark Plasma Sintering (SPS) technique. X-ray diffraction (XRD) and high resolution transmission electron microscopy (HRTEM) are used to characterize the crystal structure of the nanocrystals. The micro-grains of the obtained ceramic have been demonstrated by scanning electron microscope (SEM). Photoluminescence (PL) and cathodoluminescence (CL) spectroscopies have been performed on the ceramic sample. It is found that the PL spectral features are strongly dependent on the excitation wavelength. Remarkable PL spectral overlapping between bluish-green band and reddish-orange lines related to host defects/impurities and Sm ions, respectively, has been obtained. In addition, controlling the relative PL spectral contributions from the host-related emission and Sm ions has been achieved by changing the excitation wavelengths. This led to manipulate the emission color coordinates as investigated by chromaticity diagram. Moreover, under certain excitation wavelengths, an intense white emission is observed with a naked eye. The origin of the white emission has been discussed in light of specific PL spectral overlapping from the host and Sm ion contributions. This work emphasizes on the role played by the host defects/impurities in the optical properties of ceramic materials that can be exploited in several lighting applications.

{The Acute Kidney Outreach to Reduce Deterioration and Death trial was a large pilot study for a cluster-randomized trial of acute kidney injury (AKI) outreach.An observational control (before) phase was conducted in two teaching hospitals (9 miles apart) and their respective catchment areas. In the intervention (after) phase, a working-hours AKI outreach service operated for the intervention hospital/area for 20 weeks, with the other site acting as a control. All AKI alerts in both hospital and community patients were screened for inclusion. Major exclusion criteria were patients who were at the end of life, unlikely to benefit from outreach, lacking mental capacity or already referred to the renal team. The intervention arm included a model of escalation of renal care to AKI patients, depending on AKI stage. The 30-day primary outcome was a combination of death, or deterioration, as shown by any need for dialysis or progression in AKI stage. A total of 1762 adult patients were recruited; 744 at the intervention site during the after phase.A median of 3.0 non-medication recommendations and 0.5 medication-related recommendations per patient were made by the outreach team a median of 15.7 h after the AKI alert. Relatively low rates of the primary outcomes of death within 30 days (11–15\%) or requirement for dialysis (0.4–3.7\%) were seen across all four groups. In an exploratory analysis, at the intervention hospital during the after phase, there was an odds ratio for the combined primary outcome of 0.73 (95\% confidence interval 0.42–1.26; P = 0.26).An AKI outreach service can provide standardized specialist care to those with AKI across a healthcare economy. Trials assessing AKI outreach may benefit from focusing on those patients with ‘mid-range’ prognosis, where nephrological intervention could have the most impact.}

Background Pneumonia is a common and severe complication of abdominal surgery, it is associated with increased length of hospital stay, healthcare costs, and mortality. Further, pulmonary complication rates have risen during the SARS-CoV-2 pandemic. This study explored the potential cost-effectiveness of administering preoperative chlorhexidine mouthwash versus no-mouthwash at reducing postoperative pneumonia among abdominal surgery patients. Methods A decision analytic model taking the South African healthcare provider perspective was constructed to compare costs and benefits of mouthwash versus no-mouthwash-surgery at 30 days after abdominal surgery. We assumed two scenarios: (i) the absence of COVID-19; (ii) the presence of COVID-19. Input parameters were collected from published literature including prospective cohort studies and expert opinion. Effectiveness was measured as proportion of pneumonia patients. Deterministic and probabilistic sensitivity analyses were performed to assess the impact of parameter uncertainties. The results of the probabilistic sensitivity analysis were presented using cost-effectiveness planes and cost-effectiveness acceptability curves. Results In the absence of COVID-19, mouthwash had lower average costs compared to no-mouthwash-surgery, $3,675 (R 63,770) versus $3,958 (R 68,683), and lower proportion of pneumonia patients, 0.029 versus 0.042 (dominance of mouthwash intervention). In the presence of COVID-19, the increase in pneumonia rate due to COVID-19, made mouthwash more dominant as it was more beneficial to reduce pneumonia patients through administering mouthwash. The cost-effectiveness acceptability curves shown that mouthwash surgery is likely to be cost-effective between $0 (R0) and $15,000 (R 260,220) willingness to pay thresholds. Conclusions Both the absence and presence of SARS-CoV-2, mouthwash is likely to be cost saving intervention for reducing pneumonia after abdominal surgery. However, the available evidence for the effectiveness of mouthwash was extrapolated from cardiac surgery; there is now an urgent need for a robust clinical trial on the intervention on non-cardiac surgery.

The steroidogenesis capacity and adaptive response of follicular granulosa cells (GCs) to heat stress were assessed together with the underlying regulating molecular mechanisms in Egyptian buffalo. In vitro cultured GCs were exposed to heat stress treatments at 39.5, 40.5, or 41.5 °C for the final 24 h of the culture period (7 days), while the control group was kept under normal conditions (37 °C). Comparable viability was observed between the control and heat-treated GCs at 39.5 and 40.5 °C. A higher release of E2, P4 and IGF-1 was observed in the 40.5 °C group compared with the 39.5 or 41.5 °C groups. The total antioxidant capacity was higher in response to heat stress at 39.5 °C. At 40.5 °C, a significant upregulation pattern was found in the expression of the stress resistance transcripts (SOD2 and NFE2L2) and of CPT2. The relative abundance of ATP5F1A was significantly downregulated for all heat-treated groups compared to the control, while TNFα was downregulated in GCs at 39.5 °C. Expression analyses of stress-related miRNAs (miR-1246, miR-181a and miR-27b) exhibited a significant downregulation in the 40.5 °C group compared to the control, whereas miR-708 was upregulated in the 39.5 and 40.5 °C groups. In conclusion, buffalo GCs exhibited different adaptive responses, to the different heat stress conditions. The integration mechanism between the molecular and secretory actions of the GCs cultured at 40.5 °C might provide possible insights into the biological mechanism through which buffalo GCs react to heat stress.

The steroidogenesis capacity and adaptive response of follicular granulosa cells (GCs) to heat stress were assessed together with the underlying regulating molecular mechanisms in Egyptian buffalo. In vitro cultured GCs were exposed to heat stress treatments at 39.5, 40.5, or 41.5 °C for the final 24 h of the culture period (7 days), while the control group was kept under normal conditions (37 °C). Comparable viability was observed between the control and heat-treated GCs at 39.5 and 40.5 °C. A higher release of E2, P4 and IGF-1 was observed in the 40.5 °C group compared with the 39.5 or 41.5 °C groups. The total antioxidant capacity was higher in response to heat stress at 39.5 °C. At 40.5 °C, a significant upregulation pattern was found in the expression of the stress resistance transcripts ( and ) and of . The relative abundance of was significantly downregulated for all heat-treated groups compared to the control, while was downregulated in GCs at 39.5 °C. Expression analyses of stress-related miRNAs (miR-1246, miR-181a and miR-27b) exhibited a significant downregulation in the 40.5 °C group compared to the control, whereas miR-708 was upregulated in the 39.5 and 40.5 °C groups. In conclusion, buffalo GCs exhibited different adaptive responses, to the different heat stress conditions. The integration mechanism between the molecular and secretory actions of the GCs cultured at 40.5 °C might provide possible insights into the biological mechanism through which buffalo GCs react to heat stress.

BACKGROUND: To evaluate the relationship between superficial, deep foveal avascular zone (FAZ) and foveal cyst areas in eyes with cystoid macular oedema (CMO) associated with gyrate atrophy of the choroid and retina (GA).

METHODS: This is a retrospective collaborative multicenter study of optical coherence tomography-angiography (OCTA) images in GA. Superficial and deep FAZ and foveal cyst were measured using Image J by two independent experts. Values were corrected for myopia magnification. These values were compared with age-matched controls from normative data.

RESULTS: Twenty-three eyes from 12 patients with GA and CMO were included in the study. The mean ± standard deviation age was 22 ± 19.7 years, mean Snellen spectacle-corrected visual acuity of 20/70 with mean myopia of 5.7 ± 4.1 dioptres. Qualitatively, no focal occlusion of superficial and deep capillary plexus was noted. Mean superficial FAZ area (0.484 ± 0.317 mm), deep FAZ area (0.626 ± 0.452 mm), and foveal cyst area (0.630 ± 0.503 mm) were significantly larger than superficial and deep FAZ areas in controls of same age range (p < 0.001). Macular cyst area correlated with superficial FAZ area (R = 0.59; p = 0.0057) and more strongly with deep FAZ area (R = 0.69; p < 0.001).

CONCLUSIONS: The superficial and deep FAZ area in GA-associated CMO were noted to be significantly larger than in controls. It seems that RPE dysfunction leads to foveal cyst enlargement displacing the capillary plexus with resultant enlarged superficial and deep FAZ area.

n/a

Nephropathic cystinosis is a rare disease caused by mutations of the CTNS gene that encodes for cystinosin, a lysosomal cystine/H+ symporter. The disease is characterized by early-onset chronic kidney failure and progressive development of extra-renal complications related to cystine accumulation in all tissues. At the cellular level, several alterations have been demonstrated, including enhanced apoptosis, altered autophagy, defective intracellular trafficking, and cell oxidation, among others. Current therapy with cysteamine only partially reverts some of these changes, highlighting the need to develop additional treatments. Among compounds that were identified in a previous drug-repositioning study, disulfiram (DSF) was selected for in vivo studies. The cystine depleting and anti-apoptotic properties of DSF were confirmed by secondary in vitro assays and after treating mice with 200 mg/kg/day of DSF for 3 months. However, at this dosage, growth impairment was observed. Long-term treatment with a lower dose (100 mg/kg/day) did not inhibit growth, but failed to reduce cystine accumulation, caused premature death, and did not prevent the development of renal lesions. In addition, DSF also caused adverse effects in cystinotic zebrafish larvae. DSF toxicity was significantly more pronounced in mice and zebrafish compared to wild-type animals, suggesting higher cell toxicity of DSF in cystinotic cells.