Automated Identification of Germline de novo Mutations in Family Trios: A Consensus-Based Informatic Approach.

Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well as methods for the analysis of the data they generate, with putative solutions often involving ad hoc filters and visual inspection of identified variants. Here, we present a purely informatic method for the identification of DNVs by analyzing short-read genome sequencing data from proband-parent trios. Our method evaluates variant calls generated by three genome sequence analysis pipelines utilizing different algorithms-GATK HaplotypeCaller, DeepTrio and Velsera GRAF-exploring the assumption that a requirement of consensus can serve as an effective filter for high-quality DNVs. We assessed the efficacy of our method by testing DNVs identified using a previously established, highly accurate classification procedure that partially relied on manual inspection and used Sanger sequencing to validate a DNV subset comprising less confident calls. The results show that our method is highly precise and that applying a force-calling procedure to putative variants further removes false-positive calls, increasing precision of the workflow to 99.6%. Our method also identified novel DNVs, 87% of which were validated, indicating it offers a higher recall rate without compromising accuracy. We have implemented this method as an automated bioinformatics workflow suitable for large-scale analyses without need for manual intervention.

Effects of Orange Oil Aromatherapy on Pain and Anxiety During Invasive Interventions in Patients With Hematopoietic Stem Cell Transplants.

Invasive interventions, such as peripheral intravenous cannula, port needle placement, and blood collection, are often required for both inpatient and outpatient follow-up patients with hematological malignancies and hematopoietic stem cell transplants. This prospective, randomized controlled experimental study assessed the effect of orange oil inhalation used in aromatherapy on pain and anxiety levels in invasive interventions with hematological malignancies and hematopoietic stem cell transplants. It was conducted prospectively with 80 patients with hematological malignancies who were treated in the adult bone marrow transplant unit and adult hematology service of a private hospital between May 2021 and April 2022. The orange oil inhalation used in aromatherapy was applied to patients in the intervention group. The Visual Analog Scale (VAS) and State-Trait Anxiety Inventory (STAI) were used for data collection. Regarding the personal characteristics of the patients, 42.5% were ≥61 years old, 60% were men, and 85% were married. VAS pain scores of the intervention group were statistically lower than those of the control group (P < .001). However, there was no statistically significant difference in the STAI scores of groups (P >.05). The study results show that orange oil inhalation has been determined to reduce pain during invasive interventions.

The effect of endometriosis on anxiety and the Quality of Life in women.

This descriptive and cross-sectional study was conducted with 420 women. The data were collected by using the "Descriptive Information Form", "SF-36 Quality of Life Scale (QoLS)" and "State Anxiety Inventory (SAI)". The data were evaluated with Mann-Whitney U-test, Student's t-test and Pearson correlation analysis. Endometriosis had been diagnosed in 12.1% of the women. The score medians obtained by the women with endometriosis from the pain and physical role difficulty sub-dimensions of the QoLS were found to be significantly lower than those obtained by women without endometriosis. The presence of endometriosis was found not to affect the state anxiety in the women. A weak or moderately significant negative relationship was found between the number and onset time of the symptoms and certain sub-dimensions of the QoLS in the women with endometriosis.

Clinical and Genetic Spectrum of Myotonia Congenita in Turkish Children.

BACKGROUND: Myotonia congenita is the most common form of nondystrophic myotonia and is caused by Mendelian inherited mutations in the CLCN1 gene encoding the voltage-gated chloride channel of skeletal muscle. OBJECTIVE: The study aimed to describe the clinical and genetic spectrum of Myotonia congenita in a large pediatric cohort. METHODS: Demographic, genetic, and clinical data of the patients aged under 18 years at time of first clinical attendance from 11 centers in different geographical regions of Türkiye were retrospectively investigated. RESULTS: Fifty-four patients (mean age:15.2 years (±5.5), 76% males, with 85% Becker, 15% Thomsen form) from 40 families were included. Consanguineous marriage rate was 67%. 70.5% of patients had a family member with Myotonia congenita. The mean age of disease onset was 5.7 (±4.9) years. Overall 23 different mutations (2/23 were novel) were detected in 52 patients, and large exon deletions were identified in two siblings. Thomsen and Becker forms were observed concomitantly in one family. Carbamazepine (46.3%), mexiletine (27.8%), phenytoin (9.3%) were preferred for treatment. CONCLUSIONS: The clinical and genetic heterogeneity, as well as the limited response to current treatment options, constitutes an ongoing challenge. In our cohort, recessive Myotonia congenita was more frequent and novel mutations will contribute to the literature.

Expression of Human ß-defensin 2 (hBD-2) in Pichia Pastoris and Investigation of Its Binding Efficiency with ACE-2.

COVID-19 is a disease that have affected the entire world, and it continues to spread with new variants. A patient's innate immune system plays a critical role in the mild and severe transition of COVID-19. Antimicrobial peptides (AMPs), which are important components of the innate immune system, are potential molecules to fight pathogenic bacteria, fungi, and viruses. Human ß-defensin 2 (hBD-2), a 41-amino-acid antimicrobial peptide, is one of the defensins inducibly expressed in the skin, lungs, and trachea in humans. In this study, it was aimed to investigate the interaction of hBD-2 produced recombinantly in Pichia pastoris with the human angiotensin-converting enzyme 2 (ACE-2) under in vitro conditions. First, hBD-2 was cloned in P. pastoris X-33 via the pPICZαA vector, a yeast expression platform, and its expression was confirmed by SDS-PAGE, western blotting, and qRT-PCR. Then, the interaction between recombinant hBD-2 and ACE-2 proteins was revealed by a pull-down assay. In light of these preliminary experiments, we suggest that the recombinantly produced hBD-2 may be protective against SARS-CoV-2 and be used as a supplement in treatment. However, current findings need to be supported by cell culture studies, toxicity analyses, and in vivo experiments.

Pediatric-Onset Chronic Inflammatory Demyelinating Polyneuropathy: A Multicenter Study.

BACKGROUND: To evaluate the clinical features, demographic features, and treatment modalities of pediatric-onset chronic inflammatory demyelinating polyneuropathy (CIDP) in Turkey. METHODS: The clinical data of patients between January 2010 and December 2021 were reviewed retrospectively. The patients were evaluated according to the Joint Task Force of the European Federation of Neurological Societies and the Peripheral Nerve Society Guideline on the management of CIDP (2021). In addition, patients with typical CIDP were divided into two groups according to the first-line treatment modalities (group 1: IVIg only, group 2: IVIg + steroid). The patients were further divided into two separate groups based on their magnetic resonance imaging (MRI) characteristics. RESULTS: A total of 43 patients, 22 (51.2%) males and 21 (48.8%) females, were included in the study. There was a significant difference between pretreatment and post-treatment modified Rankin scale (mRS) scores (P < 0.05) of all patients. First-line treatments include intravenous immunoglobulin (IVIg) (n = 19, 44.2%), IVIg + steroids (n = 20, 46.5%), steroids (n = 1, 2.3%), IVIg + steroids + plasmapheresis (n = 1, 2.3%), and IVIg + plasmapheresis (n = 1, 2.3%). Alternative agent therapy consisted of azathioprine (n = 5), rituximab (n = 1), and azathioprine + mycophenolate mofetil + methotrexate (n = 1). There was no difference between the pretreatment and post-treatment mRS scores of groups 1 and 2 (P > 0.05); however, a significant decrease was found in the mRS scores of both groups with treatment (P < 0.05). The patients with abnormal MRI had significantly higher pretreatment mRS scores compared with the group with normal MRI (P < 0.05). CONCLUSIONS: This multicenter study demonstrated that first-line immunotherapy modalities (IVIg vs IVIg + steroids) had equal efficacy for the treatment of patients with CIDP. We also determined that MRI features might be associated with profound clinical features, but did not affect treatment response.

Palliative Care in Patients with Hematological Malignancies.

Palliative care is an attempt to improve the quality of life of patients and their relatives who have lost the chance of a cure. Interventions to improve the quality of life of patients include physical, mental, and psychosocial problems. It is known that symptoms such as pain, fatigue, loss of appetite, and feeling unwell, which often cause deterioration in quality of life, are improved with palliative care support. It is seen that palliative care support, which is mostly recommended in the end-of-life period of patients with solid tumors, is not recommended for patients with hematological malignancies. In fact, patients with hematological malignancies face physical, mental, and economic difficulties due to the intense treatment protocols required for their disease and the side effects of the treatments. Compared to patients with solid tumors, patients with hematological malignancies have a higher frequency of hospitalization and intensive care unit admission. For these reasons, our aim is to define the palliative care needs of patients with hematologic malignancies, understand the barriers to palliative care and end-of-life care, and offer solutions to improve the quality of life and care of patients with hematologic malignancies.

Age- and gender-related radiological changes of the cervical spine: A study with largest magnetic resonance imaging database of 5672 consecutive patients.

Background: The morphological features of the cervical spine are an essential issue. This retrospective study aimed to investigate the structural and radiological changes in the cervical spine. Materials and Methods: A total of 250 patients with neck pain but no apparent cervical pathology were selected from a database of 5672 consecutive patients undergoing magnetic resonance imaging (MRI). MRIs were directly examined for cervical disc degeneration. These include Pfirrmann grade (Pg/C), cervical lordosis angle (A/CL), Atlantodental distance (ADD), the thickness of transverse ligament (T/TL), and position of cerebellar tonsils (P/CT). The measurements were taken at the positions of T1- and T2-weighted sagittal and axial MRIs. To evaluate the results, patients were divided into seven age groups (10-19, 20-29, 30-39, 40-49, 50-59, 60-69, 70, and over). Results: In terms of ADD (mm), T/TL (mm), and P/CT (mm), there was no significant difference among age groups (P > 0.05). However, in terms of A/CL (degree) values, a statistically significant difference was observed among age groups (P < 0.05). Conclusions: Intervertebral disc degeneration was more severe in males than in females as age increased. For both genders, cervical lordosis, decreased significantly as age increased. T/TL, ADD, and P/CT did not significantly differ with age. The present study indicates that structural and radiological changes are possible reasons for cervical pain at advanced ages.

Effects of four antibiotics on Pseudomonas aeruginosa motility, biofilm formation, and biofilm-specific antibiotic resistance genes expression.

The aim of this study was to determine the effects of 4 antibiotics (tobramycin, fosfomycin, ciprofloxacin, and piperacillin/tazobactam) against Pseudomonas aeruginosa motility, biofilm formation, and biofilm resistance gene expression changes using different methods including microscopy, microdilution, crystal violet staining, and qRT-PCR. Although the antibiotics reduced swarming motility, they inhibited biofilm formation to a greater extent than the minimum inhibitory concentration (MIC) value. The qRT-PCR results showed that the antibiotics, other than fosfomycin, decreased the expression levels of the selected biofilm resistance genes (ndvB, tssC1, PA5033 and PA2070) in the biofilm structure compared to planktonic cells. Furthermore, it was found that there was an increase in the expression levels of biofilm resistance genes in the antibiotic application groups compared to the biofilm structure that was not treated with antibiotics. These results showed for the first time that the treatment of antibiotics at sub-MIC concentrations increases the expression levels of biofilm-specific resistance genes and contributes to resistance and motility.

De novo Pure Partial Trisomy 6p Associated with Facial Dysmorphism, Developmental Delay, Brain Anomalies, and Primary Congenital Hypothyroidism.

Introduction: Partial trisomy 6p is a rare chromosomal anomaly, characterized by low birth weight, developmental delay, craniofacial abnormalities, feeding difficulties, congenital heart defects, and renal abnormalities. Some of the partial trisomy 6p cases reported in the literature included partial monosomy of another chromosome. This is often due to the fact that one of the parents is a balanced translocation carrier, thereby making it difficult to determine the genotype-phenotype relationship. Pure partial trisomy 6p cases are even rarer and may occur as a result of a marker chromosome, tandem or inverted duplication, and interchromosomal insertion. Case Presentation: In this study, we evaluated the physical characteristics and genetic data of a 2-year-old girl with developmental delay and facial dysmorphic features. Dysmorphology assessment revealed the presence of a prominent forehead, short and narrow palpebral fissures, blepharoptosis, convex nasal ridge, hemangioma on the left eyelid, high-arched palate, retromicrognathia, and low-set ears. The patient‧s G-banded karyotype was 46,XX,der(2)t(2;6)(q37.3;p22.1). Upon SNP-array analysis, aimed to determine the origin of the extra chromosomal material detected in chromosome 2 of the patient, there was a de novo 27.5-Mb duplication at 6p, arr[GRCh37] 6p25.3p22.1(204,909_27,835,272)×3, interpreted to be pathogenic. Conclusion: We present this case report to clarify the clinical findings of a rare chromosomal anomaly, discuss the genes that may be related to the phenotype and contribute to the literature in terms of knowledge regarding genotype-phenotype correlation.

Shared Biological Pathways and Processes in Patients with Intellectual Disability: A Multicenter Study.

BACKGROUND: Although the underlying genetic causes of intellectual disability (ID) continue to be rapidly identified, the biological pathways and processes that could be targets for a potential molecular therapy are not yet known. This study aimed to identify ID-related shared pathways and processes utilizing enrichment analyses. METHODS: In this multicenter study, causative genes of patients with ID were used as input for Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. RESULTS: Genetic test results of 720 patients from 27 centers were obtained. Patients with chromosomal deletion/duplication, non-ID genes, novel genes, and results with changes in more than one gene were excluded. A total of 558 patients with 341 different causative genes were included in the study. Pathway-based enrichment analysis of the ID-related genes via ClusterProfiler revealed 18 shared pathways, with lysine degradation and nicotine addiction being the most common. The most common of the 25 overrepresented DO terms was ID. The most frequently overrepresented GO biological process, cellular component, and molecular function terms were regulation of membrane potential, ion channel complex, and voltage-gated ion channel activity/voltage-gated channel activity, respectively. CONCLUSION: Lysine degradation, nicotine addiction, and thyroid hormone signaling pathways are well-suited to be research areas for the discovery of new targeted therapies in ID patients.

Pregnancy outcomes following maternal macrolide use: A systematic review and meta-analysis.

To determine whether gestational use of all or specific macrolides (azithromycin, clarithromycin, roxithromycin or erythromycin) lead to an increase in rates of overall major congenital malformations, organ-specific malformations, and other adverse pregnancy outcomes in infants. PubMed/MEDLINE, Cochrane Central Register of Controlled Trials and Reprotox® databases were searched. Dichotomous outcomes or calculated log odds ratios and standard errors from observational studies are combined using the random-effects method in Review Manager 5.3. No significant increased risks for major congenital malformation (OR 1.06 [95% CI 0.99, 1.13]) and congenital heart defect (OR 1.05 [95% CI 0.92, 1.19]) following all macrolides use during the first trimester were detected. Prenatal azithromycin use was associated with a significantly increased risk of major congenital malformations in the analysis of cohort studies (OR 1.21 [95% CI 1.08-1.36]). This significance was also present in the sensitivity analysis. There were no statistically significant associations between the risk of organ specific malformations and all or specific macrolide exposures except for the decreased risk in hypospadias following erythromycin use in the meta-analysis of case-control studies (OR 0.38 [95% CI 0.18, 0.81]. Also, a significant 1.5-fold increased risk for spontaneous abortion following macrolide use was detected. A slight yet significantly increased rate of major congenital malformation with azithromycin exposure during pregnancy may be associated with maternal confounders. Nevertheless, level II ultrasound can be suggested following maternal azithromycin use during the first trimester. Future studies should take into account the inclusion of a disease-matched control group and accurate classification of the malformations.

Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis.

Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based toolkits for NGS read alignment and variant calling, methods to curate genomic variants and subsequently construct genome graphs remain an understudied problem that inevitably determines the effectiveness of the overall bioinformatics pipeline. In this study, we discuss obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and demonstrate this approach on the whole-genome samples of African ancestry. Our results show that population-specific graphs, as more representative alternatives to linear or generic graph references, can achieve significantly lower read mapping errors and enhanced variant calling sensitivity, in addition to providing the improvements of joint variant calling without the need of computationally intensive post-processing steps.

An investigation of the effects of chronic zonisamide, sultiam, lacosamide, clobazam, and rufinamide anti-seizure medications on foliculogenesis in ovarian tissue in prepubertal non-epileptic rats.

We aimed to determine the morphological and histological effects of zonisamide, sultiam, lacosamide, clobazam, and rufinamide on ovarian folliculogenesis in rats. Sixty female Wistar rats were divided into six experimental groups as control, zonisamide, sultiam, lacosamide, clobazam, and rufinamide groups; control solution and drugs were administered by gavage for 90 days. The number of healthy follicles in the control group was significantly higher than in the anti-medication groups (p < 0.001), and the number of corpus luteum was significantly lower (p < 0.001). There was a significant difference in the number of TUNEL positive apoptotic follicles between the control and drug groups (p < 0.001). With EGF, IGF-1, and GDF-9 staining, a very strong immunoreaction was observed in the ovarian multilaminar primary follicle granulosa cells and oocytes in the control group compared to the drug group (p < 0.001). Long-term anti-seizure medication with zonisamide, sultiam, lacosamide, clobazam, and rufinamide from prepubertal to adulthood causes apoptosis and disruption of folliculogenesis in the ovarian follicles of nonepileptic rats.

The effectiveness and tolerability of clobazam in the pediatric population: Adjunctive therapy and monotherapy in a large-cohort multicenter study.

OBJECTIVE: To evaluate the effectiveness and tolerability of clobazam therapy in the pediatric population in terms of seizure semiology, epileptic syndromes, and etiological subgroups. METHODS: A retrospective cohort study was conducted consisting of 1710 epileptic children from eight centers in seven geographic regions of Turkey. The initial efficacy of clobazam therapy was evaluated after three months of treatment. The long-term effectiveness of the drug, overall seizure outcomes, and overall therapeutic outcomes were evaluated during 12 months of therapy. RESULTS: Analysis of initial efficacy after the first three months of clobazam therapy showed that 320 (18.7 %) patients were seizure-free, 683 (39.9 %) had > 50 % seizure reductions, and 297 (17.4 %) had < 50 % seizure reductions. A positive response (seizure-free and >50 % seizure reduction) was determined for focal-onset (62.3 %) seizures, epileptic spasms (61.5 %), and generalized onset seisures (57.4). The highest positive response rate among the epileptic syndromes was for self-limited epilepsy with centrotemporal spikes (SeLECTS). The highest negative response rate was for developmental and/or epileptic encephalopathies (DEEs). Magnetic resonance imaging (MRI) revealed a structural etiological diagnosis in 25.8 % of the cohort. A higher positive response rate was observed at MRI in patients with sequelae lesions than in those with congenital lesions. The seizure recurrence rate was higher in the patient group with epilepsy with genetic and metabolic causes, in individuals with more than one seizure type, and in those using three or more antiseizure drugs. CONCLUSIONS: This cohort study provides additional evidence that clobazam is an effective and well-tolerable drug with a high seizure-free rate (18.7 %), a significant seizure reduction rate (57.3 %), and with excellent overall therapeutic outcomes with a low seizure relapse rate and considerable reversible benefits in the pediatric population.

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Molecular mechanisms involved in pre-eclampsia through expressional regulation of endothelin-1.

INTRODUCTION: Preeclampsia (PE) is a condition affecting 2-8% of all pregnancies and is a leading cause of perinatal morbidity and mortality. In our study; we aim to investigate the differences in endothelin-1 (ET-1) at both tissue and blood level in the placenta, umbilical cord, and maternal blood obtained from different experimental groups and the changes in the contraction response of umbilical arteries in order to explain how PE affects mother and fetus. METHODS: Umbilical cord and placenta samples were obtained from normotensive controls (n = 10) and patients with preeclampsia (n = 10), aged 20-39 years, who delivered by cesarean section at term (between 37 and 39 weeks). All samples were investigated with isolated tissue bath, histopathological, immunohistochemical and real-time PCR methods. RESULTS: ET-1 messenger RNA expression levels and immunoreactivity were found significantly higher in the PE group while microRNA-1 and microRNA-125b (miR-125b) levels were significantly decreased in placenta compared to control. miR-125b levels were found significantly higher in maternal and umbilical cord blood samples of the PE group. The enlargement in intervillous space, decrease in villous branching, increase in syncytial knots and smaller lumen areas in umblicard cord vessels were also observed. In tissue bath experiments, there were no significant differences in ET-1 responses between groups. DISCUSSION: We tried to evaluate molecular mechanisms of PE pathogenesis through expressional regulation and contraction response of ET-1. Although quite abundant work in this field has previously highlighted the importance of ET-1 system, further work is needed to determine the molecular mechanisms underlying expressional regulation of ET-1 in PE.

An Investigation of Changing Attitudes and Behaviors and Problematic Internet Use in Children Aged 8 to 17 Years During the COVID-19 Pandemic.

PURPOSE: To examine the effects of the COVID-19 pandemic on the lifestyle, habits, and behavioral differences in children, and their changing internet use habits. METHODS: The research was planned as a cross-sectional study involving 4892 children aged 8 to 17 years attending schools in the city center of Trabzon, Turkey. Children's daily living activities, social habits, mood and temperament changes, and internet use were investigated before and during the pandemic. In terms of problematic internet use, internet addiction rates were evaluated using the validated Turkish-language version of the Parent-Child Internet Addiction Scale (PCIAT-20). RESULTS: The children's mean age was 13 ± 2.45 years, and 17.1% (n = 837) exhibited problematic internet use features on the PCIAT-20. Problematic internet use was higher in boys and in children older than 13 years. The presence of COVID-19 infection among members of the household, quarantine measures, attending private schools, the mother's occupation, the time spent by the mother and father on their mobile phones, and high parental education levels were associated with a high level of internet addiction. Families also described significant changes in their children's temperament and character compared with the pre-pandemic period. CONCLUSION: The prevalence of problematic internet use increased during the COVID-19 pandemic compared with previous studies from Turkey. Children were also more introverted, irritable, and pessimistic during the pandemic.