ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.

MOTIVATION: Single cell segmentation is critical in the processing of spatial omics data to accurately perform cell type identification and analyze spatial expression patterns. Segmentation methods often rely on semi-supervised annotation or labeled training data which are highly dependent on user expertise. To ensure the quality of segmentation, current evaluation strategies quantify accuracy by assessing cellular masks or through iterative inspection by pathologists. While these strategies each address either the statistical or biological aspects of segmentation, there lacks a unified approach to evaluating segmentation accuracy. RESULTS: In this article, we present ESQmodel, a Bayesian probabilistic method to evaluate single cell segmentation using expression data. By using the extracted cellular data from segmentation and a prior belief of cellular composition as input, ESQmodel computes per cell entropy to assess segmentation quality by how consistent cellular expression profiles match with cell type expectations. AVAILABILITY AND IMPLEMENTATION: Source code is available on Github at: https://github.com/Roth-Lab/ESQmodel.

Contractile ring mechanosensation and its anillin-dependent tuning during early embryogenesis.

Cytokinesis plays crucial roles in morphogenesis. Previous studies have examined how tissue mechanics influences the position and closure direction of the contractile ring. However, the mechanisms by which the ring senses tissue mechanics remain largely elusive. Here, we show the mechanism of contractile ring mechanosensation and its tuning during asymmetric ring closure of Caenorhabditis elegans embryos. Integrative analysis of ring closure and cell cortex dynamics revealed that mechanical suppression of the ring-directed cortical flow is associated with asymmetric ring closure. Consistently, artificial obstruction of ring-directed cortical flow induces asymmetric ring closure in otherwise symmetrically dividing cells. Anillin is vital for mechanosensation. Our genetic analysis suggests that the positive feedback loop among ring-directed cortical flow, myosin enrichment, and ring constriction constitutes a mechanosensitive pathway driving asymmetric ring closure. These findings and developed tools should advance the 4D mechanobiology of cytokinesis in more complex tissues.

Clinical Characteristics and Treatment Outcomes of Long-Level Intramedullary Spinal Cord Tumors: A Consecutive Series of 43 Cases.

OBJECTIVE: Long-level intramedullary spinal cord tumors (LIMSCTs) cause complex treatment issues. However, LIMSCTs have rarely been analyzed separately. The authors reported a large case series of LIMSCTs and analyzed the clinical characteristics and treatment outcomes. METHODS: The medical data of patients with LIMSCTs at our institution between January 2015 and December 2019 were retrospectively reviewed. Demographics, tumor size and location, pathology, extent of resection, and neurological functional status were collected. RESULTS: A total of 43 consecutive cases were included. Twenty-three cases (53.5%) of LIMSCTs were ependymal tumors. All patients with ependymal tumors achieved gross total resection (GTR). In ependymal tumor cases, 3 cases (13%) of ependymal tumors experienced postoperative neurological deterioration, and 66% of them showed an improvement at follow-up; 25.6% were low-grade astrocytic tumors. The rates of GTR, subtotal resection (STR) and partial resection (PR) were 63.6%, 27.3%, and 9.1%, respectively. Twenty-seven percent cases showed postoperative neurological worsening, and 33% of them had an improvement at follow-up; 20.9% were high-grade astrocytic tumors. The excision rates were 44.4% for GTR, 44.4% for STR, and 11% for PR, respectively. Fifty-five percent cases showed postoperative neurological worsening, and none of them had an improvement at follow-up. CONCLUSION: In this series, all LIMSCTs were gliomas. Aggressive tumor resection did not increase the risk of long-term functional deterioration in ependymal tumors and low-grade astrocytic tumors, but in high-grade astrocytic tumors, patients had a higher risk of neurological deterioration and difficulty in recovery. In ependymal tumors and low-grade astrocytic tumors, patients can achieve long-time survival after performing aggressive tumor resection.

Potential association among posterior fossa bony volume and crowdedness, tonsillar hernia, syringomyelia, and CSF dynamics at the craniocervical junction in Chiari malformation type I.

Objective: The characteristic morphological parameters (bony posterior fossa volume (bony-PFV), posterior fossa crowdness, cerebellar tonsillar hernia, and syringomyelia) and CSF dynamics parameters at the craniocervical junction (CVJ) in Chiari malformation type I (CMI) were measured. The potential association between these characteristic morphologies and CSF dynamics at CVJ was analyzed. Methods: A total of 46 cases of control subjects and 48 patients with CMI underwent computed tomography and phase-contrast magnetic resonance imaging. Seven morphovolumetric measures and four CSF dynamics at CVJ measures were performed. The CMI cohort was further divided into "syringomyelia" and "non-syringomyelia" subgroups. All the measured parameters were analyzed by the Pearson correlation. Results: Compared with the control, the posterior cranial fossa (PCF) area, bony-PFV, and CSF net flow were significantly smaller (P < 0.001) in the CMI group. Otherwise, the PCF crowdedness index (PCF CI, P < 0.001) and the peak velocity of CSF (P < 0.05) were significantly larger in the CMI cohort. The mean velocity (MV) was faster in patients with CMI with syringomyelia (P < 0.05). In the correlation analysis, the degree of cerebellar tonsillar hernia was correlated with PCF CI (R = 0.319, P < 0.05), MV (R = -0.303, P < 0.05), and the net flow of CSF (R = -0.300, P < 0.05). The Vaquero index was well correlated with the bony-PFV (R= -0.384, P < 0.05), MV (R = 0.326, P < 0.05), and the net flow of CSF (R = 0.505, P < 0.05). Conclusion: The bony-PFV in patients with CMI was smaller, and the MV was faster in CMI with syringomyelia. Cerebellar subtonsillar hernia and syringomyelia are independent indicators for evaluating CMI. Subcerebellar tonsillar hernia was associated with PCF crowdedness, MV, and the net flow of CSF at CVJ, while syringomyelia was associated with bony-PFV, MV, and the net flow of CSF at the CVJ. Thus, the bony-PFV, PCF crowdedness, and the degree of CSF patency should also be one of the indicators of CMI evaluation.

Basilar invagination without atlantoaxial dislocation: treatment by correction of clivus canal angle with interfacet distraction and fixation.

BACKGROUND: This study reports on the surgical technique used and clinical outcomes obtained during the treatment of basilar invagination (BI) without atlantoaxial dislocation (AAD) through the correction of the clivus canal angle (CCA) using interfacet distraction and fixation. METHODS: Nineteen cases with BI without AAD treated by the correction of the clivus canal angle were retrospectively analyzed. Pre- and postoperative computed tomography scans and three-dimensional reconstruction views were obtained to measure the size of the CCA, pB-C2 distance, and degree of BI. Chiari malformation and syringomyelia were evaluated by magnetic resonance imaging (MRI). The clinical outcomes for all patients were measured using the Japanese Orthopedic Association (JOA) scale. The CCA was corrected by using interfacet distraction and fixation techniques. The Wilcoxon test was used to compare pre- and postoperative measurements. RESULTS: All the patients were followed up for 24.95 ± 5.22 months (range 12-36 months); no patient suffered intraoperative nerve or vascular injury. Clinical symptoms improved in 17 patients (89.5%). The mean JOA score increased from 12.32 ± 1.89 to 14.37 ± 1.30 (Z = -3.655, P < 0.001). The mean CCA improved from 129.34 ± 8.52° preoperatively to 139.75 ± 8.86° postoperatively (Z = -3.824, P < 0.001). The mean pB-C2 decreased from 7.47 ± 2.21 to 5.68 ± 3.13 (Z = -3.060, P = 0.002). Syringomyelia was significantly reduced in 10 out of 13 patients by the first follow-up year. All patients achieved bony fusion. CONCLUSION: Posterior interfacet distraction and fixation to correct the CCA is a feasible and effective method for treating BI without AAD.

Application of C2 subfacetal screws for the management of atlantoaxial dislocation in patients with Klippel-Feil syndrome characterized by a narrow C2 pedicle and high-riding vertebral artery.

OBJECTIVE: This study aims to investigate the clinical application and feasibility of C2 subfacetal screws in patients with Klippel-Feil syndrome (KFS), narrow C2 pedicles, and high-riding vertebral arteries (HRVAs). METHODS: The clinical data of seven patients with KFS, atlantoaxial dislocation, narrow C2 pedicles, and HRVAs treated with C2 subfacetal screws were analyzed in this retrospective study. The internal height, isthmus height, and pedicle width of C2 vertebra were measured using preoperative computed tomography (CT). Subfacetal screws were inserted for 7 patients (12 sides). The position and length of the screws were observed using postoperative CT. Intraoperative dura mater and vertebral artery (VA) injuries were recorded. Bone fusion was observed using follow-up CT. RESULTS: The internal height was 10.5 ± 3.2 mm, the isthmus height was 3.7 ± 1.8 mm, the pedicle width was 3.0 ± 1.4 mm, and the screw length was 19.7 ± 1.5 mm. All patients had HRVAs and narrow pedicles. No injury to the dura mater and vertebral artery (VA) occurred in this group of patients. Bone fusion was achieved in all patients during follow-up. CONCLUSIONS: In patients with KFS, HRVA, and a narrow C2 pedicle, there is sufficient space below the C2 articular surface for screw insertion. When the pedicle is narrow and the C2 pedicle screw is not suitable for placement due to possible injury to the VA, subfacetal screws are a feasible alternative.

Spinal intradural schwannoma presenting with acute subarachnoid hemorrhage: a case report and review of published reports.

Acute subarachnoid hemorrhage (SAH) presentation is a very rare occurrence in spinal schwannomas. We report a case of lumbar schwannoma in a patient presenting first with acute SAH. A 40-year-old man was referred to our department 7 days after the sudden onset of headache, neck pain, and fever. SAH was suspected; however, head computed tomography (CT) findings were normal. A lumbar puncture indicated blood-stained cerebrospinal fluid (CSF). Moreover, the CSF pressure changed from 200 mmH2O to 90 mmH2O after drainage of 10 mL of CSF indicating a blockage of CSF. Subsequent magnetic resonance imaging (MRI) confirmed an intradural tumor with SAH, which also caused blockage of the CSF circulation. The patient underwent immediate surgery and fully recovered. In conclusion, the early diagnosis and total removal of the tumor and blood clot significantly improved the patient's outcome. There is a high index of suspicion for spinal tumors resulting in SAH when there is a CSF pressure change after lumbar puncture in an SAH patient.

Surgical management of a huge intramedullary ependymoma from oblongata to T4: A case report.

INTRODUCTION AND IMPORTANCE: Huge intramedullary tumor is a rare condition. Surgical management of such huge ependymoma is technically challenging. We reported one case of 300 mm long intramedullary spinal cord ependymoma from oblongata to T4, which was satisfactorily en bloc gross total resected and the cervical spine alignment was successfully maintained by laminoplasty. CASE PRESENTATION: A 30-year-old man presented to our service with two-year progressive neck pain combined with bilateral sense disorders of both the upper and lower extremities. The neurological grade was ASIA D. Repeat MRI imaging demonstrated a "medulla oblongata to T4" intramedullary spinal cord tumor complicated with cervical physiological curvature loss. CLINICAL DISCUSSION: Laminectomies were made at the C1-T4 level by a milling cutter. The tumor was gently separated bilaterally. The ventral part of the tumor was separated from the cranial and the caudal ends until reaching the middle site of the tumor. The whole tumor was isolated en bloc. Titanium miniplates were used bilaterally to fix both sides of the laminoplasty section on each level. At the 2-year postoperative follow-up, the muscle strength of both the upper and lower limbs were grade Ⅳ. No tumor recurrence was detected. CONCLUSION: The total removal of an intramedullary ependymoma should be recommended as soon as the diagnosis is made, regardless of its extension. Long-level laminoplasty could be an effective alternative option to maintain the proper spine alignment.

Long-level intramedullary spinal cord astrocytoma complicated with spine scoliosis: Report of two cases.

INTRODUCTION AND IMPORTANCE: Long-level intramedullary astrocytomas complicated with spine scoliosis are rare. Surgical treatment of such tumors becomes more complicated and challenging when spinal scoliosis is present. However, studies describing the treatment of long segmental intramedullary spinal cord astrocytomas complicated with severe spine scoliosis have been rarely reported. CASE PRESENTATION: Two cases of long-level intramedullary astrocytomas complicated with severe spine scoliosis were surgically treated with one-stage operation of tumor resection and scoliosis correction in this report. Case 1: A 16-year-old boy presented to our hospital with a five-month progressive paresthesia, weakness of the left lower limb, and a long-time abnormal body appearance. MRI showed a T4-T12 intramedullary tumor combined with spinal scoliosis. Case 2: A 14-year-old boy presented at our service with a 6-year history of visible spine scoliosis and a 1-year progressive motor disability of bilateral lower limbs. Spine MRI indicated a long-level abnormal syringomyelia signal from C4 to L1 and there was irregular enhancement after intravenous contrast medium administration at C7-T2 and T9-T12 level. DISCUSSION: We performed a laminectomy over the whole length of the tumor and corrected the scoliosis with trans-pedicle screws. The patients exhibited a long-time tumor free with largely neurological function preservation. One-stage operation did not generate severe short- or long-term complications. The correction of the scoliosis prevented the progression of the spinal deformity and facilitated the recovery of normal life. CONCLUSION: This case report demonstrates that the one-stage resection of long-level intramedullary astrocytoma and correction of the complicated scoliosis might be a feasible option.

Anterior cervical transvertebral approach for resection of an intraspinal ventral lesion: illustrative case.

BACKGROUND: The anterior cervical corpectomy and fusion approach has been reported for the removal of ventral cervical tumors. However, the normal cervical vertebral body and the adjacent intervertebral discs have to be sacrificed. In this paper, the authors describe a novel anterior cervical transvertebral approach for the resection of cervical intraspinal ventral lesions. OBSERVATIONS: A patient presented with an anteriorly placed extramedullary cyst. An anterior cervical transvertebral open-window and close-window approach was designed and applied to resect an intraspinal ventral enterogenous cyst. With this novel technique, a square was cut through the whole vertebral body at the four sides. After the cyst resection, the bone block was restored and fixed with a titanium miniplate. The lesion was totally resected, and the compression of the spinal cord was relieved. The physiological function of the cervical spine was kept intact after the operation. There was no postsurgical complication. The cervical alignment was normal at the 1-year postoperative follow-up. LESSONS: The anterior cervical transvertebral open-window and close-window approach was developed and confirmed to be effective for the resection of cervical intraspinal lesions. The cervical physiological structure and function can be restored with this new technique.

A modified microsurgical interfacet release and direct distraction technique for management of congenital atlantoaxial dislocation: technical note.

Various techniques have been used for management of congenital atlantoaxial dislocation. Recently, the reduction of atlantoaxial dislocation through a single posterior approach has attracted more and more attention. Here, we present a modified technique including direct interfacet release and distraction between C1 and C2 by a specially designed distractor, posterior internal fixation and bone graft fusion. The illustrated technique was performed in 15 consecutive patients, and the outcomes were recorded and analyzed. Follow-up ranged from 12 to 26 months. Clinical symptoms improved in 14 patients (93.3%) and were stable in 1 patient (6.7%). Radiologically, 60-100% reduction was achieved in 13 patients (86.6%). Bone fusion was obtained in all patients at 12 months after the operation. The two-tailed Wilcoxon signed-rank test was used to analyze the preoperative and postoperative Japanese Orthopedic Association scores (JOA), atlas-dens interval (ADI), and cervicomedullary angle (CMA) (P < 0.001). Our results suggested that this direct interfacet release and distraction technique with a specially designed C1-2 distractor can provide a definite effective C1-2 facet distraction and odontoid process restoration through a single posterior approach.