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Mohamed Farah Osman Hidig,1 Mohamed Sheikh Hassan,1,2 Abdiwahid Ahmed Ibrahim,1 Bakar Ali Adam,1 Nor Osman Sidow,1 Said Abdi Mohamed1 1Department of Neurology, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia; 2Faculty of Medicine and Surgery, Mogadishu University, Mogadishu, SomoliaCorrespondence: Mohamed Farah Osman Hidig, Department of Neurology, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia, Email mfhidig@gmail.comAbstract: Emerging symmetrical limb weakness, altered sensory perception, and absent or reduced deep tendon reflexes are the hallmarks of Guillain-Barre syndrome (GBS). There are numerous studies that indicate up to two-thirds of patients with GBS may also have autonomic dysfunction. One uncommon presenting characteristic of GBS before motor weakness is evident is paralytic ileus, a sign of gastrointestinal dysautonomia. Here we describe the case of a 55-year-old man who was brought to the emergency room of our hospital with paralytic ileus, a less common symptom of early-stage GBS. The patient was initially treated with prokinetic drugs and total parenteral nutrition with no clinical improvement. The patient quickly developed ascending lower limb weakness that progressed to quadriplegia, which ultimately affected respiratory muscles, leading to respiratory failure requiring mechanical ventilation and intensive care unit hospitalization. A nerve conduction study showed demyelinating sensorimotor polyneuropathy. Analysis of cerebrospinal fluid revealed albumin-cytological dissociation. The patient was treated with intravenous immunoglobulin (IVIG) and other supportive treatments. Even though the patient’s enteral feeding support was uncomfortable due to a profound infection complicating lack of stomach emptying during the hospital stay, the patient passed away two months after being admitted. Lack of awareness about GBS gastrointestinal dysautonomia may cause delays in treatment initiation, and as a result, GBS may lead to life-threatening events. Reducing mortality and morbidity from GBS requires prompt diagnosis and treatment. This case reminds us that GBS may present as gastrointestinal dysautonomia.Keywords: Gullian-Barre syndrome, paralytic ileus, quadraparesis, intravenous immunoglobulin

Nor Osman Sidow,1,2 Abdiwahid Ahmed Ibrahim,1 Nasra Mohamud Hilowle,3 Nasra Ahmed Diblawe,3 Ridwan Mohamud Ali,4 Abdinasir Mohamed Elmi,5 Bakar Ali Adam,1 Mohamed Sheikh Hassan1 1Department of Neurology, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, Somalia; 2Faculty of Medicine and Surgery, Jazeera University, Mogadishu, Somalia; 3Department of Anesthesia and Critical Care, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, Somalia; 4Department of Emergency, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, Somalia; 5Department of Radiology, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, SomaliaCorrespondence: Abdiwahid Ahmed Ibrahim, Email drabdiwahid00@gmail.comAbstract: Cerebral sinus venous thrombosis (CSVT) is an uncommon and potentially life-threatening neurological disorder that is often missed because its clinical and radiological symptoms are not specific. Snake bites are a rare cause of cerebral venous sinus thrombosis that must be recognized and treated promptly to improve survival. Here, we present a case of a 30-year-old male patient who had cerebral venous thrombosis after snake bite in the rural area of southern Somalia. After close monitoring with anticoagulation, the condition of the patient improved and discharged from the hospital with full of consciousness. There are only a few cases reported in the literature of snake bites causing cerebral venous thrombosis.Keywords: snakebite, cerebral venous thrombosis, venom, viper, anticoagulant

Choriocarcinoma is a rare and aggressive form of gestational trophoblastic disease with a high potential for metastasis. We report the case of a 31-year-old female who presented with severe headaches, left-sided weakness, and speech difficulties. Her past medical history included a molar pregnancy, and she had elevated β-hCG levels of 200,000 mIU/mL. Imaging revealed a right frontoparietal hemorrhagic venous infarct and multiple lung metastases. Based on these findings and the patient's clinical history, a diagnosis of gestational choriocarcinoma with multiple metastases was confirmed. This case highlights the importance of considering choriocarcinoma in the differential diagnosis of young women presenting with neurological symptoms and a history of gestational trophoblastic disease. Early recognition and prompt treatment are crucial to improving outcomes in such cases.

Multiple system atrophy is a rare and quickly progressing neurological condition characterized by autonomic failure, parkinsonism, or cerebellar ataxia. It is classified into two subtypes: MSA with predominant parkinsonism (MSA-P) and MSA with predominant cerebellar ataxia (MSA-C). We are presenting here a 54-year-old male with parkinsonism, ataxia, and dysarthria. He was diagnosed with parkinson disease and was given a maximum dose of levodopa but has not responded. After a close neurological evaluation with magnetic resonance imaging of the brain, which shows atrophy of the cerebellum and a brainstem with a hot cross bun sign of the pons, suggestive of multiple system atrophy, he was diagnosed with multiple system atrophy cerebellar type, which is the first time to have this diagnosis in Somalia, which is a low-resource country.

Mohamed Sheikh Hassan,1,2 Ahmet Bakir,1 Nor Osman Sidow,1 Umut Erkok,3 Said Abdirahman Ahmed,4 Maryan Dahir Abshir,5 Ayhan Ayhan Köksal6 1Department of Neurology, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia; 2Faculty of Medicine and Surgery, Mogadishu University, Mogadishu, Somalia; 3Department of Gynecology and Obstetrics, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia; 4Department of Cardiology, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia; 5Department of Medical Laboratory, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia; 6University of Health Sciences, Istanbul Başakşehir Cam and Sakura City Hospital, Istanbul, TurkiyeCorrespondence: Mohamed Sheikh Hassan, Mogadishu Somalia Turkish Training and Research Hospital, Mogadishu, Somalia, Email dr.m.qalaf@gmail.comIntroduction: Spontaneous Intracerebral hemorrhage (ICH) in young patients is less common and not well studied compared to ICH in older patients. The etiology, risk factors and outcome of ICH in young patients may have regional and ethnic differences. The study aims to investigate the clinical characteristics, risk factors, etiology and outcome of spontaneous intracerebral hemorrhage in young adults in Somalia.Methods: The study enrolled 168 young patients with ICH (16– 50 years) admitted to the neurology department of a tertiary hospital from 2019 to 2022. The information about the demographic details, documented ICH risk factors, etiology and patients’ clinical status were retrieved. The etiology of ICH was determined based on clinical, laboratory and radiological findings. Intra-hospital survival status and associated factors were assessed.Results: The mean age of the patients was 35± 8.6 years. 99 (59%) of patients were male while 69 (41%) were females. Hypertension 48 (29%) was the most common risk factor, followed by substance abuse. Hypertensive hemorrhage was the most common etiology of ICH 60 (35.7%), followed by cerebral venous thrombosis (CVT) 5(15%), substance abuse 23 (13.7%) and arteriovenous malformation (AVM) in 10 (6%). AVM, CVT, cavernoma, eclampsia, substance abuse and cryptogenic etiology were more common in the 2nd and 3rd decades whereas hypertension was more common in the 4th and 5th decade. Intrahospital mortality was 28% in this study. Factors predicting intrahospital mortality were hematoma volume of greater than 30mL, thrombolytic etiology, brainstem ICH location, substance abuse related etiology, presence of associated mass effect, low GCS score on admission, high systolic blood pressure on admission, and the presence of chronic renal failure.Conclusion: In this study, hypertension, substance abuse, CVT and vascular malformation are the leading causes of ICH in young adults. Intracerebral hemorrhage in the young has different spectrum of etiologies and factors associated with short-term mortality compared to older patients.Keywords: intracerebral hemorrhages, young patients, etiology, outcome

Said Abdi Mohamed,1 Nor Osman Sidow,1,2 Bakar Ali Adam,1 Mohamed Sheikh Hassan,1,3 Abdiwahid Ahmed Ibrahim,1 Mohamed Farah Osman,1 Abdulkadir Ahmed,1 Abdullahi Ali Roble4 1Department of Neurology, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, Somalia; 2Faculty of Medicine and Surgery, Jazeera University, Mogadishu, Somalia; 3Faculty of Medicine and Surgery, Mogadishu University, Mogadishu, Somalia; 4Department of Ophthalmology, Mogadishu-Somalia Turkey Recep Tayyip Erdoğan Training and Research Hospital, Mogadishu, SomaliaCorrespondence: Nor Osman Sidow, Tel +252618300616, Email ziidoow113@gmail.comAbstract: Sturge-Weber syndrome is a rare, sporadic, progressive neurocutaneous condition that presents with congenital hamartomatous malformations, epilepsy, and a variety of facial symptoms. We discussed a rare case of an eighteen-year-old female child who came to our neurology department with status epilepticus, mental impairment, and a port-wine in the lateral left side of her face. We diagnosed Sturge-Weber syndrome after a thorough neurological and radiological evaluation. The purpose of presenting this case is to illustrate both the characteristic presentation and the complications associated with managing Sturge-Weber syndrome.Keywords: sturge-weber, seizure, port-wine

Key Clinical Message Here, we are presenting a young previous healthy child with seizures and right side hemiparesis for 6 months. After blood work and an MRI brain with IV contrast, it is confirmed that the child has large cerebral tuberculoma. The child is improved with TB treatment and surgery.

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.

Abstract Background The physiological function of eukaryotic DNA occurs in the context of nucleosomal arrays that can expose or obscure defined segments of the genome. Certain DNA sequences are capable of strongly positioning a nucleosome in vitro, suggesting the possibility that favorable intrinsic signals might reproducibly structure chromatin segments. As high-throughput sequencing analyses of nucleosome coverage in vitro and in vivo have become possible, a vigorous debate has arisen over the degree to which intrinsic DNA:nucleosome affinities orchestrate the in vivo positions of nucleosomes, thereby controlling physical accessibility of specific sequences in DNA. Results We describe here the in vivo consequences of placing a synthetic high-affinity nucleosome-positioning signal, the 601 sequence, into a DNA plasmid vector in mice. Strikingly, the 601 sequence was sufficient to position nucleosomes during an early phase after introduction of the DNA into the mice (when the plasmid vector transgene was active). This positioning capability was transient, with a loss of strong positioning at a later time point when the transgenes had become silent. Conclusions These results demonstrate an ability of DNA sequences selected solely for nucleosome affinity to organize chromatin in vivo, and the ability of other mechanisms to overcome these interactions in a dynamic nuclear environment.

Abstract Background Otopetrin 1 (Otop1) encodes a multi-transmembrane domain protein with no homology to known transporters, channels, exchangers, or receptors. Otop1 is necessary for the formation of otoconia and otoliths, calcium carbonate biominerals within the inner ear of mammals and teleost fish that are required for the detection of linear acceleration and gravity. Vertebrate Otop1 and its paralogues Otop2 and Otop3 define a new gene family with homology to the invertebrate Domain of Unknown Function 270 genes (DUF270; pfam03189). Results Multi-species comparison of the predicted primary sequences and predicted secondary structures of 62 vertebrate otopetrin, and arthropod and nematode DUF270 proteins, has established that the genes encoding these proteins constitute a single family that we renamed the Otopetrin Domain Protein (ODP) gene family. Signature features of ODP proteins are three "Otopetrin Domains" that are highly conserved between vertebrates, arthropods and nematodes, and a highly constrained predicted loop structure. Conclusion Our studies suggest a refined topologic model for ODP insertion into the lipid bilayer of 12 transmembrane domains, and highlight conserved amino-acid residues that will aid in the biochemical examination of ODP family function. The high degree of sequence and structural similarity of the ODP proteins may suggest a conserved role in the intracellular trafficking of calcium and the formation of biominerals.

Abstract Background As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on variation due to shared selective pressures. In comparative sequence analysis, for example, sequence similarity is often used to illuminate important regions of the genome, but if the comparison is between closely related species, then similarity is the rule rather than the interesting exception. Furthermore, and perhaps worse yet, the contribution of a divergent third species may be masked by the strong similarity between the other two. Here we propose a remedy that weighs the contribution of each species according to its phylogenetic placement. Results We first solve the problem of summarizing data related by phylogeny, and we explain why an average should operate on the entire evolutionary trajectory that relates the data. This perspective leads to a new approach in which we define the average in terms of the phylogeny, using the data and a stochastic model to obtain a probability on evolutionary trajectories. With the assumption that the data evolve according to a Brownian motion process on the tree, we show that our evolutionary average can be computed as convex combination of the species data. Thus, our approach, called the BranchManager, defines both an average and a novel taxon weighting scheme. We compare the BranchManager to two other methods, demonstrating why it exhibits desirable properties. In doing so, we devise a framework for comparison and introduce the concept of a representative point at which the average is situated. Conclusion The BranchManager uses as its representative point the phylogenetic center of mass, a choice which has both intuitive and practical appeal. Because our average is intrinsic to both the dataset and to the phylogeny, we expect it and its corresponding weighting scheme to be useful in all sorts of studies where interspecies data need to be combined. Obvious applications include evolutionary studies of morphology, physiology or behaviour, but quantitative measures such as sequence hydrophobicity and gene expression level are amenable to our approach as well. Other areas of potential impact include motif discovery and vaccine design. A Java implementation of the BranchManager is available for download, as is a script written in the statistical language R.

Abstract Background Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task. Results The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics. Conclusions The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available http://mendel.stanford.edu/sidowlab/downloads.html.

We report a case of new-onset atrial fibrillation with rapid ventricular response in a 37-year-old malewho presented to the emergency department. This patient was not admitted to the hospital or placed onobservation, but rather placed on a cellular outpatient 12-lead telemetry (COTLT) device with emergencyresponse capabilities and discharged home. We define a new modality that allows these patients tobe managed via telemedicine and receive care similar to that which would be rendered in a hospital orobservation unit.

Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic.

We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the mutational spectrum between the mouse and rat lineages, with the net effect being a relative increase in GC content in the rat genome. Our estimate for the neutral point substitution rate separating the two rodents is 0.196 substitutions per site, and 0.65 substitutions per site for the tree relating all three mammals. Small insertions and deletions of 1-10 bp in length ("microindels") occur at approximately 5% of the point substitution rate. Inferred regional correlations in evolutionary rates between lineages and between types of sites support the idea that rates of evolution are influenced by local genomic or cell biological context. No substantial correlations between rates of point substitutions and rates of microindels are found, however, implying that the influences that affect these processes are distinct. Finally, we have identified those regions in the human genome that are evolving slowly, which are likely to include functional elements important to human biology. At least 5% of the human genome is under substantial constraint, most of which is noncoding.