Machine Learning Analysis Using RNA Sequencing to Distinguish Neuromyelitis Optica from Multiple Sclerosis and Identify Therapeutic Candidates.

This study aims to identify RNA biomarkers distinguishing neuromyelitis optica (NMO) from relapsing-remitting multiple sclerosis (RRMS) and explore potential therapeutic applications leveraging machine learning (ML). An ensemble approach was developed using differential gene expression analysis and competitive ML methods, interrogating total RNA-sequencing data sets from peripheral whole blood of treatment-naïve patients with RRMS and NMO and healthy individuals. Pathway analysis of candidate biomarkers informed the biological context of disease, transcription factor activity, and small-molecule therapeutic potential. ML models differentiated between patients with NMO and RRMS, with the performance of certain models exceeding 90% accuracy. RNA biomarkers driving model performance were associated with ribosomal dysfunction and viral infection. Regulatory networks of kinases and transcription factors identified biological associations and identified potential therapeutic targets. Small-molecule candidates capable of reversing perturbed gene expression were uncovered. Mitoxantrone and vorinostat-two identified small molecules with previously reported use in patients with NMO and experimental autoimmune encephalomyelitis-reinforced discovered expression signatures and highlighted the potential to identify new therapeutic candidates. Putative RNA biomarkers were identified that accurately distinguish NMO from RRMS and healthy individuals. The application of multivariate approaches in analysis of RNA-sequencing data further enhances the discovery of unique RNA biomarkers, accelerating the development of new methods for disease detection, monitoring, and therapeutics. Integrating biological understanding further enhances detection of disease-specific signatures and possible therapeutic targets.

Comparison of four surgical methods for pediatric forearm double diaphyseal fractures: a retrospective analysis.

OBJECTIVE: One of the most frequent fractures in children is a double forearm fracture. They make up 26% of children's long bone fractures in the upper extremities and their incidence has increased in recent years. In this study, pediatric patients with double forearm fractures were treated using plate screw, intramedullary K-wire (I-KW), intramedullary titanium elastic nails (TENs), and hybrid fixation (HF) to compare the radiographic and functional results. PATIENTS AND METHODS: The printed and digital medical records were retrospectively examined from our hospital's archives after receiving consent from the regional ethics committee. Legal guardians of the patients, who were under the age of 18, gave their informed consent. Based on the surgical procedure used, the patients were split into 4 groups. Double plating was the D-P group, hybrid fixation method was the HF group, intramedullary elastic titanium nail was the TEN group, and intramedullary K-wire was the I-KW group. The study comprised 78 patients in total, with 19 patients in the HF group, 21 patients in the TEN group, 20 patients in the I-KW group, and 18 patients in the D-P group. RESULTS: When the mean operating times of the four approaches were compared, a substantial difference was found. The D-P group's mean operating time (65.2±4.9 minutes) was noticeably longer than those of the other groups (p<0.001). The HF group's mean operating time was 55.93.4 min longer than that of the TENs and I-KW groups, which was statistically significant (p<0.001). In comparison to the other groups, the D-P group's mean intraoperative fluoroscopy time was considerably shorter (6±3 sec) (p<0.001). When compared to the D-P group, it was considerably higher in the HF group (12±2 sec) (p<0.001). In comparison to the TENs (20±4 sec) and I-KW groups (19±5 sec), it was significantly lower in the HF group (p<0.001). In comparison to the HF group, the D-P group's tourniquet use lasted much longer (p<0.001). The TENs and I-KW groups did not use a tourniquet because a mini-incision was made. The D-P group's mean blood loss (110±10 ml) was substantially larger than that of the other groups (p<0.001) in the mean blood loss data. In comparison to the TENs (40±5 ml) and I-KW (40±5 ml) groups, the mean blood loss in the HF group (90±10 ml) was considerably larger (p<0.001). All patients received an above-elbow postoperative cast. The HF group (2 weeks) and the D-P group (2 weeks) experienced significantly less postoperative immobility than the TENs and I-KW groups (4.4 weeks, p<0.001). CONCLUSIONS: The four fixation techniques used in the current study for juvenile diaphyseal double forearm fractures produced positive clinical and functional outcomes. The hybrid fixation technique was discovered to be comparable to the other techniques and even beneficial in some ways. So, a safe and efficient treatment option for juvenile diaphyseal double forearm fractures is hybrid fixation.

Association between Expanded Disability Status Scale score and dietary antioxidant capacity in patients with multiple sclerosis.

Multiple sclerosis (MS), a neuroinflammation that results in neurodegeneration, is the most prevalent central nervous system inflammatory disease in young people. A diet rich in antioxidants is known to decrease the production/activity of pro-inflammatory cytokines and have a positive impact on the prognosis of MS. The purpose of this study was to assess if dietary antioxidant capacity is related to Expanded Disability Status Scale (EDSS) scores in patients with MS. Patients with MS (n=220; 137 women and 83 men) were asked to complete a questionnaire on diet. According to the EDSS score, patients were split into two groups (group 1: EDSS ≤5 and group 2: EDSS >5). Analyzed risk variables were antioxidant levels and demographic data. A nutritional database tool (BeBiS 4 software, Germany) created for the evaluation of Turkish foods was used to examine the questionnaire findings. Age, vitamin A, retinol, vitamin D, vitamin E, and vitamin C were significantly different between groups (P<0.05). The levels of vitamins A, D, E, C, and retinol were significantly correlated, according to Pearson's correlation analysis. Receiver operator characteristic curve analysis revealed that vitamin A, vitamin D, and vitamin C levels were discriminating variables in group 2 patients (EDSS >5). The current study has shown that antioxidant levels obtained by EDSS may be useful in determining illness severity and treatment success of patients with MS. Further clinical trials have been initiated in MS patients with more effective antioxidants.

Association between Expanded Disability Status Scale score and dietary antioxidant capacity in patients with multiple sclerosis

Multiple sclerosis (MS), a neuroinflammation that results in neurodegeneration, is the most prevalent central nervous system inflammatory disease in young people. A diet rich in antioxidants is known to decrease the production/activity of pro-inflammatory cytokines and have a positive impact on the prognosis of MS. The purpose of this study was to assess if dietary antioxidant capacity is related to Expanded Disability Status Scale (EDSS) scores in patients with MS. Patients with MS (n=220; 137 women and 83 men) were asked to complete a questionnaire on diet. According to the EDSS score, patients were split into two groups (group 1: EDSS ≤5 and group 2: EDSS >5). Analyzed risk variables were antioxidant levels and demographic data. A nutritional database tool (BeBiS 4 software, Germany) created for the evaluation of Turkish foods was used to examine the questionnaire findings. Age, vitamin A, retinol, vitamin D, vitamin E, and vitamin C were significantly different between groups (P<0.05). The levels of vitamins A, D, E, C, and retinol were significantly correlated, according to Pearson's correlation analysis. Receiver operator characteristic curve analysis revealed that vitamin A, vitamin D, and vitamin C levels were discriminating variables in group 2 patients (EDSS >5). The current study has shown that antioxidant levels obtained by EDSS may be useful in determining illness severity and treatment success of patients with MS. Further clinical trials have been initiated in MS patients with more effective antioxidants.

Identification of Iguania Ancestral Syntenic Blocks and Putative Sex Chromosomes in the Veiled Chameleon (Chamaeleo calyptratus, Chamaeleonidae, Iguania).

The veiled chameleon (Chamaeleo calyptratus) is a typical member of the family Chamaeleonidae and a promising object for comparative cytogenetics and genomics. The karyotype of C. calyptratus differs from the putative ancestral chameleon karyotype (2n = 36) due to a smaller chromosome number (2n = 24) resulting from multiple chromosome fusions. The homomorphic sex chromosomes of an XX/XY system were described recently using male-specific RADseq markers. However, the chromosomal pair carrying these markers was not identified. Here we obtained chromosome-specific DNA libraries of C. calyptratus by chromosome flow sorting that were assigned by FISH and sequenced. Sequence comparison with three squamate reptiles reference genomes revealed the ancestral syntenic regions in the C. calyptratus chromosomes. We demonstrated that reducing the chromosome number in the C. calyptratus karyotype occurred through two fusions between microchromosomes and four fusions between micro-and macrochromosomes. PCR-assisted mapping of a previously described Y-specific marker indicates that chromosome 5 may be the sex chromosome pair. One of the chromosome 5 conserved synteny blocks shares homology with the ancestral pleurodont X chromosome, assuming parallelism in the evolution of sex chromosomes from two basal Iguania clades (pleurodonts and acrodonts). The comparative chromosome map produced here can serve as the foundation for future genome assembly of chameleons and vertebrate-wide comparative genomic studies.

The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs.

Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S-28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.

Longitudinal assessment and stability of long non-coding RNA gene expression profiles measured in human peripheral whole blood collected into PAXgene blood RNA tubes.

OBJECTIVE: Long non-coding RNAs (lncRNAs) are emerging as novel biomarkers for a variety of chronic conditions including autoimmune disease. PAXgene Blood RNA tubes are routinely used in clinical research and molecular diagnostic development to capture RNA profiles in peripheral whole blood. While the stability of mRNA expression profiles captured using PAXgene tubes has been documented previously, no previous work has determined the stability of lncRNA expression profiles observed in PAXgene tubes stored at - 80 °C. Here we sought to determine the effects on lncRNA expression profiles following - 80 °C storage of total RNA templates, cDNA synthesized using fresh or frozen total RNA template, and the impact of freeze-thaw cycles on both total RNA and cDNA obtained from PAXgene tubes. RESULTS: We find that storage of whole blood in PAXgene tubes, total RNA and cDNA for up to 1 year at - 80 °C or up to ten total RNA or cDNA freeze-thaw cycles do not significantly alter lncRNA expression profiles compared to baseline. As monthly expression profiles were determined, some month to month lncRNA expression variability was observed. However, all monthly observations fell within the 95% confidence interval calculated at baseline.

PD-1 up-regulation on CD4+ T cells promotes pulmonary fibrosis through STAT3-mediated IL-17A and TGF-ß1 production.

Pulmonary fibrosis is a progressive inflammatory disease with high mortality and limited therapeutic options. Previous genetic and immunologic investigations suggest common intersections between idiopathic pulmonary fibrosis (IPF), sarcoidosis, and murine models of pulmonary fibrosis. To identify immune responses that precede collagen deposition, we conducted molecular, immunohistochemical, and flow cytometric analysis of human and murine specimens. Immunohistochemistry revealed programmed cell death-1 (PD-1) up-regulation on IPF lymphocytes. PD-1+CD4+ T cells with reduced proliferative capacity and increased transforming growth factor-ß (TGF-ß)/interleukin-17A (IL-17A) expression were detected in IPF, sarcoidosis, and bleomycin CD4+ T cells. PD-1+ T helper 17 cells are the predominant CD4+ T cell subset expressing TGF-ß. Coculture of PD-1+CD4+ T cells with human lung fibroblasts induced collagen-1 production. Strikingly, ex vivo PD-1 pathway blockade resulted in reductions in TGF-ß and IL-17A expression from CD4+ T cells, with concomitant declines in collagen-1 production from fibroblasts. Molecular analysis demonstrated PD-1 regulation of the transcription factor STAT3 (signal transducer and activator of transcription 3). Chemical blockade of STAT3, using the inhibitor STATTIC, inhibited collagen-1 production. Both bleomycin administration to PD-1 null mice or use of antibody against programmed cell death ligand 1 (PD-L1) demonstrated significantly reduced fibrosis compared to controls. This work identifies a critical, previously unrecognized role for PD-1+CD4+ T cells in pulmonary fibrosis, supporting the use of readily available therapeutics that directly address interstitial lung disease pathophysiology.

Evaluation of serum transforming growth factor ß1 and C-reactive protein levels in migraine patients.

BACKGROUND AND PURPOSE: Migraine is a frequent form of head-ache. Although many mechanisms describing onset of migraine with and without visual aura have been suggested, the aetiology of migraine headaches is still not clear. Neurogenic inflammation may play a key role in the development of migraine headaches. We evaluated the discriminative power of serum levels of C-reactive protein (CRP) and transforming growth factor beta 1 (TGF-ß1) in patients who presented to our clinic with migraine headaches with or without visual aura. MATERIAL AND METHODS: We designed a prospective case-control study of 51 patients with migraine (27 with migraine with aura and 24 with migraine without aura; all had headache) and compared them with 27 healthy subjects during the study period. Demographic and clinical characteristics recorded were age, sex, marital status, occupation, characteristics of headache, laboratory values, and serum CRP and TGF-ß1 levels. Statistical analyses used Student t-test, the χ2 test, and ANOVA followed by the post-hoc Bonferroni test for multiple comparisons. Receiver operator characteristic (ROC)-curve analysis for CRP and TGF-ß1 was also conducted. RESULTS: There was no difference between the groups in terms of demographic characteristics, marital status, and socioeconomic status. Statistically, white blood cell levels, serum glucose levels, triglyceride levels, high-density lipoprotein levels, and serum CRP and TGF-ß1 were significantly higher in patients with migraine (p < 0.05). The ROC curve results in this study identified that CRP and TGF-ß1 may discriminate patients who have different types of migraine headache. CONCLUSIONS: This study suggests that serum CRP and TGF-ß1 levels may be diagnostic factors to differentiate migraine patients with and without aura. These findings show that neurogenic inflammation may have a role in the aetiology of migraines.

Serum cytokine and pro-brain natriuretic peptide (BNP) levels in patients with migraine.

OBJECTIVE: Although migraine has been related with an increased risk for ischemic stroke and cardiovascular events, there is insufficient data for role of pro-brain natriuretic peptide (pro-BNP) in migraine. In present case-control study, serum levels of pro-inflammatory (TNF-alpha, IL-1beta and IL-6) and anti-inflammatory cytokines (IL-2, and IL-10) of migraine patients were investigated to determine the role of cytokines and pro-BNP in migraine. PATIENTS AND METHODS: Sixty-four consecutive newly diagnosed migraine patients and 34 healthy controls were enrolled. Serum TNF-alpha, IL-1beta, IL-2, IL-6, IL-10 and pro-BNP levels were measured by using a chemiluminescence assay. RESULTS: Migraine patients had significantly higher concentrations of IL-1beta and IL-6 compared with the healthy controls (for IL-1beta; 5.73 +/- 1.44 vs. 4.90 +/- 1.40 pg/mL, respectively, p = 0.006; for IL-6; 3.1 +/- 1.44 vs. 2.40 +/- 0.22 pg/mL, respectively, p = 0.007). The mean IL-10 levels were found to be significantly lower in migraine patients (3.38 +/- 2.93 pg/mL) than controls (6.76 +/- 1.48 pg/mL) (p = 0.007). There were no differences in TNF-alpha (27.2 +/- 48.1 vs. 15.4 +/- 0.7) and IL-2 (1017 +/- 661 vs. 1153 +/- 228) levels between patients with migraine and healthy controls. Migraine patients had higher concentrations of pro-BNP compared with healthy controls (27.0 +/- 28.0 versus 13.2 +/- 8.6, p = 0.006). CONCLUSIONS: Migraine patients have higher serum IL-1beta and IL-6 levels, and lower IL-10 levels than healthy subjects. These findings support that cytokines may be related to neurogenic inflammation in the pathogenesis of migraine. Also, increased pro-BNP may indicate to preclinical cardiac involvement in patients with migraine.

Inheritance of a translocation between chromosomes 12 and 16 in a family with recurrent miscarriages and a newborn with Down syndrome carrying the same translocation.

Reciprocal translocation carriers have reduced fertility, increased risk of spontaneous abortion or unbalanced karyotype in their offspring. Here, we report the inheritance of a translocation between chromosomes 12 and 16 in a family with recurrent miscarriages and a newborn with Down syndrome carrying the same translocation. Chromosomal analysis from fetal amniotic fluid and peripheral blood lymphocytes from the family were performed at the Cukurova university hospital in Turkey. We assessed a family in which the translocation between chromosomes 12 and 16 segregates; one of the eight progenies with the karyotype 47,XY,+21,t(12;16)(q24;q24) was heterozygote for the translocation and presented with Down syndrome. His mother is phenotypically normal, one brother and one sister were also carrying the same translocation. Apparently, this rearrangement occurred due to the unbalanced chromosome segregation of the mother [t(12;16)(q24;q24)mat]. This case will enable us to explain the behavior of segregation patterns and the mechanism for each type oftranslocation from carrier to carrier and their effects on reproduction and numerical aberrations. The t(12;16) is also associated with fetal wastage and may play a role in the etiology of the family's miscarriages. These findings can be used in clinical genetics and may be used as an effective tool for reproductive guidance and genetic counseling.