RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

Structural characteristics are essential for the functioning of many noncoding RNAs and cis‐regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome‐wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild‐type. These local regions are approximated in a “screening mode” that is intended for genome‐wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed‐up of several orders of magnitude over shuffling‐based approaches. On a data set comprising 501 SNPs associated with human‐inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs. RNAsnp is available at http://rth.dk/resources/rnasnp .     

Preparation and characterisation of PHT-loaded chitosan lecithin nanoparticles for intranasal drug delivery to the brain

The use of nanoparticles (NPs) for intranasal (IN) drug delivery to the brain represents a hopeful strategy to enhance brain targeting of anti-epileptic drugs. In the present work, chitosan–lecithin NPs loaded with phenytoin (PHT), were prepared using the nano-precipitation method. The spherical nature of the NPs and their stability were confirmed using scanning and transmission electron microscopy, while the average dynamic size and zeta potential were measured using dynamic light scattering. The encapsulation efficiency of PHT was higher than 60% for all prepared NPs. Release studies showed that the amount of released PHT was directly related to the amount of chitosan used. The optimum preparation, L₁₀C_i⁺ was administered via the IN route, and the levels of PHT in the brain were measured in three-time points. Two experimental controls were given via the intraperitoneal (IP) and IN routes. The highest PHT amount reaching 1.01 ± 0.55% for L₁₀C_i⁺, which was associated with a sustained release of PHT. These preliminary findings show that the IN delivery of PHT-loaded NPs is very promising for managing epilepsy. The direct nose-to-brain approach increases the safety margins of PHT, while the sustained release could improve patient compliance in a clinical setting.

The use of nanoparticles (NPs) for intranasal (IN) drug delivery to the brain represents a hopeful strategy to enhance brain targeting of anti-epileptic drugs.     

Increased presence of anti-HLA antibodies early after allogeneic granulocyte colony-stimulating factor-mobilized peripheral blood hematopoietic stem cell transplantation compared with bone marrow transplantation

We have recently shown that the use of allogeneic granulocyte colony-stimulating factor (G-CSF)-mobilized peripheral blood hematopoietic stem cell transplantation (PBHSCT), as compared with bone marrow transplantation (BMT), is associated with increased titers of antibodies (Abs) directed against red blood cell ABO antigens. To further evaluate the influence of a G-CSF-mobilized PBHSCT graft on alloimmune Ab responses, we examined the frequency of anti-HLA Abs after transplantation in the setting of the same randomized study, comparing PBHSCT with BMT in adults. Anti-HLA Ab presence was determined by complement-dependent cytotoxicity assay (CDC) and flow cytometry in the recipient before and 30 days after transplantation as well as in the donor before graft donation. The use of PBHSCT was significantly associated with increased detection of anti-HLA immunoglobulin G (IgG) Abs early after transplantation as evidenced by flow cytometry (11 of 24 versus 4 of 27 transplant recipients, P =.03) and, less so, by CDC (5 of 24 versus 1 of 27 transplant recipients, P =.09). The difference between PBHSCT and BMT was further heightened when analysis was restricted to anti-HLA IgG Ab-negative donor/recipient pairs. In such a setting, early anti-HLA Ab was never detected after BMT but was repeatedly detected after PBHSCT (flow cytometry, 6 of 18 versus 0 of 17 transplant recipients, P =.02; CDC, 4 of 23 versus 0 of 26 transplant recipients, P =.04). Importantly, the PBHSCT-associated increase in anti-HLA Ab detection was observed despite a reduction in the median number of platelet-transfusion episodes per patient in PBHSC transplant versus BM transplant recipients (3 platelet-transfusion episodes [range, 1-21] in PBHSCT group vs 6 platelet-transfusion episodes [range, 3-33] in the BMT group; P =.02). In conclusion, this study strongly suggests that G-CSF-mobilized PBHSCT results in an increased incidence of circulating anti-HLA Abs and further confirms that the use of such a graft alters alloimmune Ab responses.     

Role of endoscopic ultrasound in pediatric patients: A single tertiary center experience and review of the literature

BACKGROUND Although endoscopic ultrasound(EUS) is now widely available and has an established role in adults, the utility of EUS and EUS-guided fine needle aspiration(EUS-FNA) in pediatrics is insufficiently described compared to adults and is supported by only a few studies.AIM To report the experience of a single tertiary center in the use of EUS and EUS-FNA in a pediatric population and to further assess its safety, feasibility, and clinical impact on management.METHODS A retrospective study of 13 children(aged 18 years or younger) identified from our medical database was conducted. A retrospective review of demographic data, procedure indications, EUS findings, and the clinical impact of EUS on the subsequent management of these patients was performed.RESULTS During the 4-year study period, a total of 13(1.7%) pediatric EUS examinations out of 749 EUS procedures were performed in our unit. The mean age of these 8 females and 5 males was 15.6 years(range: 6-18). Six of the 13 EUS examinations were pancreatobiliary(46.1%), followed by mediastinal 2/13(15.4%), peri-gastric 2/13(15.4%), abdominal lymphadenopathy 1/13(7.7%), tracheal 1/13(7.7%) and rectal 1/13(7.7%). Overall, EUS-FNA was performed in 7 patients(53.8%) with a diagnostic yield of 100%. The EUS results had a significant impact on clinical care in 10/13(77%) cases. No complications occurred in these patients during or after any of the procedures.CONCLUSION EUS and EUS-FNA in the pediatric population are safe, feasible, and have a significant clinical impact on the subsequent management; thus avoiding invasive and unnecessary procedures.     

Diagnosing peripheral neuropathy in South‐East Asia: A focus on diabetic neuropathy

Burning and stabbing pain in the feet and lower limbs can have a significant impact on the activities of daily living, including walking, climbing stairs and sleeping. Peripheral neuropathy in particular is often misdiagnosed or underdiagnosed because of a lack of awareness amongst both patients and physicians. Furthermore, crude screening tools, such as the 10‐g monofilament, only detect advanced neuropathy and a normal test will lead to false reassurance of those with small fiber mediated painful neuropathy. The underestimation of peripheral neuropathy is highly prevalent in the South‐East Asia region due to a lack of consensus guidance on routine screening and diagnostic pathways. Although neuropathy as a result of diabetes is the most common cause in the region, other causes due to infections (human immunodeficiency virus, hepatitis B or C virus), chronic inflammatory demyelinating polyneuropathy, drug‐induced neuropathy (cancer chemotherapy, antiretrovirals and antituberculous drugs) and vitamin deficiencies (vitamin B₁, B₆, B₁₂, D) should be actively excluded.