Enhancement of key generation rate in QKD systems using dual branch PNR detectors.

What we believe to be a new architecture based on dual-branch photon-number-resolving (DB-PNR) detectors for the receiver in the hybrid quantum key distribution (QKD) is introduced. DB-PNR scheme empowers the receiver to detect both quadratures of the coherent state simultaneously. Our results show that using DB-PNR detectors, the key generation rate (KGR) is almost doubled as compared to homodyne detection which detects only one quadrature at a time. The mutual information is enhanced by around 0.85 bits/symbol using DB-PNR as compared to heterodyne detection. DB-PNR is also found to outperform the heterodyne detection against Eve's individual and collective attacks. PNR-based detection schemes require less local oscillator (LO) power compared to homodyne/heterodyne detection schemes and thereby, the power efficiency of the receiver is enhanced.

Influence of COVID-19 on the sustainability of livestock performance and welfare on a global scale.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently spreading worldwide. The pandemic has already had significant adverse effects on human civilization, the environment, and the ecosystem at national and global levels. Moreover, the various sectors of the food production chain, particularly agriculture and livestock, have also been significantly affected in terms of production sustainability and economic losses. The global pandemic has already resulted in a sharp drop in meat, milk, and egg production. Restrictions of movement at national and international levels, implemented as a part of control strategies by public health sectors, have negatively impacted business related to the supply of raw materials for livestock farmers and farm outputs, veterinary services, farmworkers, and animal welfare. This review highlights the significant impacts of COVID-19 on the sustainability of livestock performance, welfare on a global scale, and strategies for mitigating these adverse effects.

Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals.

The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. Multiple FCS amino acid deletions such as Δ680SPRRA684 and Δ685RSVA688 were only detected in eight and four human isolates, respectively. Surprisingly, deletion of the entire FCS motif as Δ680SPRRARSVA688 and Δ680SPRRARSVAS689 was detected only in three human isolates. On the other hand, analysis of FCS from emergent variants showed no deletions in the FCS except for spike P681del, which was detected in seven B.1.1.7 isolates from the USA. Spike Q677P was detected only once in variant, B.1.1.7, whereas Q677H was detected in all variants, i.e., B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). Structural modeling predicted that mutations or deletions at or near the FCS significantly alter the cleavage loop structure and would presumably affect furin binding. Taken together, our results show that Q677H and FCS point mutations are prevalent and may have various biological effects on the circulating variants. Therefore, we recommend urgent monitoring and surveillance of the investigated mutations, as well as laboratory assessment of their pathogenicity and transmissibility.

Genetic profiling of CAH Egyptian children: rapid guide to clinical interpretation of common mutations.

OBJECTIVES: The prevalence of CAH in Egypt is reported to be ten times more than that of the worldwide prevalence. The study aimed at genetic screening of children diagnosed with 21-alpha hydroxylase deficiency congenital adrenal hyperplasia (21OHD-CAH). In addition, the study offers a rapid and easy guide for clinical reporting of common mutations for endocrinologists. METHODS: A cohort of 174 unrelated Egyptian children with 21OHD-CAH were screened for 11 common CYP21A2 gene mutations using a strip hybridization assay, and then, bioinformatics analysis was done to report the pathogenicity of the common mutations for clinical classification. RESULTS: The most common mutations were I2 splice and p.Q318X. Deletions/conversions comprised 45.9% of the cohort, whereas 7.4% of the cases were negative for all mutations. The least positively detected point mutations were p.P453S, cluster E6, p.R483P, and p.L307FS, which were detected in fewer than 5% of cases. CONCLUSION: Strip hybridization assay is a rapid screening tool for the diagnosis of CAH. The authors hypothesized an easy and rapid scheme for clinical interpretation of the strip results to gain the highest value of the strip in diagnosis.

Cutibacterium acnes Pneumonia in an Immunocompromised Patient: A Case Report and Review of the Literature.

Cutibacterium acnes (C. acnes), known previously as Proprionebacterium acnes, is a common skin and mucous membrane colonizing bacteria. On rare occasions it has been associated with invasive infections in both immunocompetent and immunosuppressed patients. We describe the case of a 55-year-old female with a history of Sjogren's syndrome and psoriatic arthritis on TNF-alpha inhibitor therapy with etanercept. She presented with signs and symptoms of a thoracic infection with pulmonary nodules, hilar adenopathy, and bronchiectasis on thoracic computed tomography. She was diagnosed with C. acnes pneumonia based on culture growth from both endoscopic bronchial ultrasound transbronchial lymph node needle biopsy and navigational bronchoscopy transbronchial lung biopsy. Our patient noticed marked symptom relief and radiographic pulmonary parenchymal improvement with intravenous ceftriaxone provided for a six-week course. This case highlights the potential invasive disease caused by C. acnes, a common skin commensal.

Pediatric kidney transplantation in Egypt: Results of 10-year single-center experience.

Pediatric kidney transplantation is a multidisciplinary therapy that needs special consideration and experience. In this study, we aimed to present CUCH experience; over a 10-year period, as a specialized center of kidney transplantation in children. We studied 148 transplantations performed at a single center from 2009 to 2018. Pretransplant and follow-up data were collected and graft/patient survival rates were evaluated. A total of 48 patients developed at least one rejection episode during 688 patient-years of follow-up. Infections, recurrence of original disease, and malignancy were the most important encountered medical complications (20%, 2%, and 1.4%, respectively). One-year patient survival was 94.1%, while graft and patient survival was 91.9%. Graft/patient survival at 5, 7, and 9 years was 90%, 77%, and 58%, respectively. Infections were the main cause (69%) of mortality. Death with a functioning graft and CR were the main causes of graft loss (48% and 33%, respectively). Pediatric kidney transplantation in Egypt is still a challenging yet successful experience. Rejections and infections are the most frequent complications. Short-term outcomes surpass long-term ones and graft survival rates are similar to the international standard.

The long noncoding RNA sONE represses triple-negative breast cancer aggressiveness through inducing the expression of miR-34a, miR-15a, miR-16, and let-7a.

Triple-negative breast cancer (TNBC) represents an aggressive breast cancer subtype. Among young females, TNBC is the leading cause of cancer-related mortalities. Recently, long noncoding RNAs (lncRNAs) are representing a promising pool of regulators for tuning the aggressiveness of several solid malignancies. However, this still needs further investigations in TNBC. The main aim of this study is to unravel the expression pattern of sONE lncRNA and its mechanistic role in TNBC. Results showed that sONE is restrictedly expressed in TNBC patients; its expression level is inversely correlated with the aggressiveness of the disease. sONE acts as a posttranscriptional regulator to endothelial nitric oxide synthase (eNOS) and thus affecting eNOS-induced nitric oxide (NO) production from TNBC cells measured by Greiss reagent. Mechanistically, sONE is a potential tumor suppressor lncRNA in TNBC cells; repressing cellular viability, proliferation, colony-forming ability, migration, and invasion capacities of MDA-MB-231. Furthermore, sONE effects were found to be extended to affect the maestro tumor suppressor TP53 and the oncogenic transcription factor c-Myc. Knocking down of sONE resulted in a marked decrease in TP53 and increase in c-Myc and consequently altering the expression status of their downstream tumor suppressor microRNAs (miRNAs) such as miR-34a, miR-15, miR-16, and let-7a. In conclusion, this study highlights sONE as a downregulated tumor suppressor lncRNA in TNBC cells acting through repressing eNOS-induced NO production, affecting TP53 and c-Myc proteins levels and finally altering the levels of a panel of tumor suppressor miRNAs downstream TP53/c-Myc proteins.

Phylogenetic relationship of Ornithobacterium rhinotracheale isolated from poultry and diverse avian hosts based on 16S rRNA and rpoB gene analyses.

BACKGROUND: Ornithobacterium (O.) rhinotracheale is an emerging bacterial pathogen in poultry and not fully understood to date. Because of its importance particularly for the global turkey meat industry, reliable diagnostic and characterization methods are needed for early treatment and in future for better vaccine production. The host range of birds infected by O. rhinotracheale or carrying the bacterium in their respiratory tract has constantly increased raising important epidemiological and taxonomic questions for a better understanding of its diversity, ecology and transmission cycles. The purpose of this study was to introduce partial rpoB gene sequencing for O. rhinotracheale into routine diagnostics to differentiate strains isolated from poultry and more diverse avian hosts (i.e., birds of prey, corvids and pigeons) and to compare phylogenetic relationships with results from 16S rRNA gene analysis and multilocus sequence typing (MLST). RESULTS: Partial 16S rRNA gene analysis revealed a high level of homogeneity among the 65 investigated O. rhinotracheale sequences with similarity values ranging from 98.6 to 100% between sequences from non-galliform and poultry species. The corresponding rpoB gene sequences were heterogeneous and ranged in their similarity values from 85.1 to 100%. The structure of the rpoB tree was in strong correlation with previous MLST results revealing three main clusters A (poultry and birds of prey), B (poultry, birds of prey and corvids) and C (pigeons), which were clearly separated from each other. CONCLUSIONS: By using partial sequences from a single gene, the rpoB gene analysis is in good agreement with MLST results with a slight decrease in resolution to distinguish more similar strains. The present results provide strong evidence that traditional phenotypic and genetic methods may not properly represent the heterogeneous group of bacteria classified as O. rhinotracheale. From housekeeping gene analyses, it is very likely that the genus Ornithobacterium includes additional species and partial rpoB gene sequencing can be recommended as fast, cost-effective and readily available method to identify strains and differentiate between O. rhinotracheale and Ornithobacterium-like bacteria.

Multiple Introductions of Influenza A(H5N8) Virus into Poultry, Egypt, 2017.

After high mortality rates among commercial poultry were reported in Egypt in 2017, we genetically characterized 4 distinct influenza A(H5N8) viruses isolated from poultry. Full-genome analysis indicated separate introductions of H5N8 clade 2.3.4.4 reassortants from Europe and Asia into Egypt, which poses a serious threat for poultry and humans.

Interaction between avian influenza subtype H9N2 and Newcastle disease virus vaccine strain (LaSota) in chickens.

BACKGROUND: H9N2 avian influenza virus is endemic in Egyptian poultry flocks. The role of the live viral vaccines such as LaSota in exaggeration of the clinical picture of H9N2 infection under field conditions is significantly important leading to severe economic losses due to higher mortality and lower growth performance. This experiment was designed to identify the possible interaction between experimental infection with H9N2 virus and NDV live vaccine (LaSota strain) in broiler chickens. Six groups each of 20 broiler chicks were used. Three groups (G1-3) were infected with H9N2 and vaccinated with LaSota, 3 days before, at the same day or 3 days post vaccination (dpv), while the remaining groups (G4-6) were non-vaccinated infected, vaccinated non-infected and non-vaccinated non-infected. RESULTS: The highest mortality rate (37.5%) was noticed in chickens of G1 (H9N2 infected 3 days prior LaSota vaccination). Also, this bird group had the most severe clinical signs, histopathological lesions and the longest viral shedding for 9 days post infection (dpi). In the 2nd and 3rd groups, the mortality rate was the similar (31.2%) with less pronounced clinical signs, histopathological lesions and H9N2 shedding was for only 6 dpi with the least shedding quantity in chickens of G3. The control non-vaccinated infected chickens (G4) had 18.7% mortality with the least degree of clinical signs, lesions and the highest viral shedding quantity but only for 6 dpi. At 35 days of age, there was a statistical significant decrease (P < 0.05) in chicken's body weight of all H9N2 infected groups from G1 to G4 compared to non-infected control groups, G5 and G6 respectively. CONCLUSION: It was clear that laSota vaccination significantly affect H9N2 infection in broiler chickens regarding clinical signs, mortality rate, lesions, performance and viral shedding.

Isolation and genetic characterization of a novel 2.2.1.2a H5N1 virus from a vaccinated meat-turkeys flock in Egypt.

BACKGROUND: Vaccination of poultry to control highly pathogenic avian influenza virus (HPAIV) H5N1 is used in several countries. HPAIV H5N1 of clade 2.2.1 which is endemic in Egypt has diversified into two genetic clades. Clade 2.2.1.1 represents antigenic drift variants in vaccinated commercial poultry while clade 2.2.1.2 variants are detected in humans and backyard poultry. Little is known about H5N1 infection in vaccinated turkeys under field conditions. CASE PRESENTATION: Here, we describe an HPAI H5N1 outbreak in a vaccinated meat-turkey flock in Egypt. Birds were vaccinated with inactivated H5N2 and H5N1 vaccines at 8 and 34 days of age, respectively. At 72nd day of age (38 days post last vaccination), turkeys exhibited mild respiratory signs, cyanosis of snood and severe congestion of the internal organs. Survivors had a reduction in feed consumption and body gain. A mortality of ~29% cumulated within 10 days after the onset of clinical signs. Laboratory diagnosis using RT-qPCRs revealed presence of H5N1 but was negative for H7 and H9 subtypes. A substantial antigenic drift against different serum samples from clade 2.2.1.1 and clade 2.3.4.4 was observed. Based on full genome sequence analysis the virus belonged to clade 2.2.1.2 but clustered with recent H5N1 viruses from 2015 in poultry in Israel, Gaza and Egypt in a novel subclade designated here 2.2.1.2a which is distinct from 2014/2015 2.2.1.2 viruses. These viruses possess 2.2.1.2 clade-specific genetic signatures and also mutations in the HA similar to those in clade 2.2.1.1 that enabled evasion from humoral immune response. Taken together, this manuscript describes a recent HPAI H5N1 outbreak in vaccinated meat-turkeys in Egypt after infection with a virus representing novel distinct 2.2.1.2a subclade. CONCLUSIONS: Infection with HPAIV H5N1 in commercial turkeys resulted in significant morbidity and mortality despite of vaccination using H5 vaccines. The isolated virus showed antigenic drift and clustered in a novel cluster designated here 2.2.1.2a related to viruses in poultry in Israel, Gaza and Egypt. Enforcement of biosecurity and constant update of vaccine virus strains may be helpful to protect vaccinated birds and prevent spillover infection to neighbouring countries.

Levels of cystatin C in low- and high-flux hemodialysis in children with end-stage renal disease.

BACKGROUND: Cystatin-C (CyC) is a middle molecule that is freely filtered at the glomerulus and almost completely reabsorbed by the proximal tubules. The aim of this study was to evaluate serum CyC and its reduction ratio as a biomarker for assessing the adequacy of the hemodialysis (HD) sessions in children with end-stage renal disease on maintenance HD. We also compared levels of CyC in patients on low-flux HD (LFH) and high-flux HD (HFH). METHODS: Forty patients were included in the study and divided into two groups, with one group (16 patients) receiving HFH and the other group receiving LFH (24 patients) (high-flux and low-flux polysulfone filters, respectively). Before and after each dialysis session serum CyC and beta-2-microglobulin (B2M) levels were measured using an ELISA technique, and routine laboratory tests were performed for each patient. RESULTS: Pre-dialytic levels of CyC were significantly lower in the patients receiving HFH than in those receiving LFH (7.33 ± 1.35 vs. 9.73 ± 0.93, respectively; p < 0.0001). In the HFH group, post-dialytic levels of serum CyC were significantly lower than pre-dialytic levels (4.49 ± 0.71 vs. 7.33 ± 1.35, respectively; p < 0.0001). The reduction ratio (RR) of CyC was significantly higher in the HFH group than in the LFH group (38.2 ± 3.91 vs. -6.49 ± 5.05, respectively; p < 0.0001). Serum CyC level significantly correlated with B2M, urea and creatinine levels in both the LFH and HFH groups, whereas its RR significantly correlated with the RRs of urea, creatinine, and B2M in the HFH group. CONCLUSION: The results of our study emphasize the role of CyC as a good marker for assessing the adequacy of HD sessions in children on HFH and show that the CyC RR may be used as an index of middle-molecule toxin clearance following HFH sessions.

Evaluation of rumen-protected choline additive to diet on productive performance of male Zaraibi growing goats during hot summer season in Egypt.

Twenty Zaraibi goat bucks were used in this experiment which lasted 3 months during summer season of Egypt. The animals were divided randomly into two equal groups. The first group was kept without treatment as control while in the second group, rumen-protected choline (RPC) at the level of 20 g/buck/day was added to the concentrate feed mixture at the morning feeding. RPC additives to diet of Zaraibi goat bucks during the period of hot summer season increased (P < 0.01) total gain and average daily gain compared to the control group. RPC increased (P < 0.05) dry matter intake and feed conversion while water intake was not affected by RPC additives. RPC increased (P < 0.05) red and white blood cell (RBC × 106, WBC × 103) counts and hemoglobin concentration and hematocrit percentage. RPC increased total protein (P < 0.05), globulin, and γ-globulin (P < 0.01). On the other hand, total lipids, total cholesterol, and triglyceride concentrations decreased (P < 0.05 and P < 0.05) while phospholipids, glucose, and choline concentrations increased (P < 0.01) due to RPC supplementation. RPC increased (P < 0.01) thyroxin and triiodothyronine, increased (P < 0.05) testosterone levels, and decreased (P < 0.01) cortisol level compared with control bucks. It is concluded that dietary RPC at the rate of 20 g daily is required for growing male goats, especially, under heat stress conditions of summer season in Egypt and showed the best results concerning the growth, feed conversion, blood metabolites, and economic efficiency.

Caudal extradural catheterization in pediatric renal transplant and its effect on perioperative hemodynamics and pain scoring: a prospective randomized study.

PURPOSE: 'Hockey stick incision' used in renal transplant is large enough to cause severe postoperative morbidity especially in pediatric recipients. Although epidural analgesia is known to be effective in pain control, the resulting sympathectomy might affect hemodynamics interfering with the transplant process. In our study, we evaluated the feasibility and safety of inserting an epidural catheter to the thoracic level via the caudal route, and the effect of using epidural local anesthetics at low concentrations on hemodynamics. METHODS: After approval from the ethical committee at Kasr Al Ainy University Hospital and consent from parents/legal guardians, sixty patients aged 3-12 years who were scheduled for renal transplant were randomly divided into two equal groups. Group I (epidural group) received continuous caudal epidural bupivacaine 0.125 % with fentanyl together with intravenous (IV) fentanyl and paracetamol. Group II (control group) received only IV fentanyl and paracetamol. Intraoperative data included heart rate (HR), mean arterial blood pressure (MAP) and central venous pressure (CVP). Postoperative variables included HR, MAP, CVP, pain score and complications. RESULTS: Threading failure via the caudal route occurred in 6.67 % of cases. Intraoperative differences in hemodynamics and CVP were not clinically significant between groups. Postoperative HR, MAP, and CVP were generally higher in the control group. Pain control was more satisfactory and postoperative complications were less in the epidural group. CONCLUSION: Caudal epidural anesthesia in pediatric renal transplant is a valuable addition to general anesthesia as it provides stable perioperative hemodynamics, excellent postoperative analgesia and is associated with fewer complications than narcotic-dependent analgesia. CLINICAL TRIAL REGISTRATION NUMBER: NCT02037802.

Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.

BACKGROUND: Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type. RESULTS: We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro). CONCLUSION: Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

Juvenile systemic lupus erythematosus: onset patterns and short-term outcome in Egyptian children, a single-center experience.

OBJECTIVE: The objective of this article is to define disease onset pattern and understand the response to therapy in children with systemic lupus erythematosus (SLE) in Egypt. METHODS: A prospective cohort of 41 Egyptian children diagnosed with SLE was analyzed. SLE Disease Activity Index (SLEDAI) score was used to record disease activity at onset, and renal biopsy was performed to define the stage of lupus nephritis. Response to therapy over a follow-up period ranging from 10 to 50 months was evaluated. RESULTS: The mean age at diagnosis was 12.12 ± 3.45 years. Thirty-six (87.8%) patients were females. Most patients had multiple manifestations at onset. The most common presenting symptoms were pallor and fever (51.2% and 43.9%, respectively). Lupus nephritis was found in 27 (65.9%) children. International Society of Nephrology (ISN) classes I and III were the most common findings on renal biopsy. Neuropsychiatric manifestations were present at disease onset in 19 patients (46.3%) with a bad prognostic course. At diagnosis, high SLEDAI scores were recorded (mean: 29.95 ± 2.06). The mean renal SLEDAI score was 10.2 ± 4. At follow-up 16 (39.02%) patients were in complete remission, 10 (24.39%) were in partial remission, two (4.87%) had active disease, five (12.9%) had relapsed, four (9.75%) had died and four (9.75%) patients were lost to follow-up. CONCLUSIONS: Egyptian children with SLE appear to have severe disease on presentation with high SLEDAI scores and high prevalence of lupus nephritis, but respond well to therapy with a favorable short-term prognosis.