Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.

Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.

Modular Oxidation of Cytosine Modifications and Their Application in Direct and Quantitative Sequencing of 5-Hydroxymethylcytosine.

Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) using 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+BF4-) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with CAPS, CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells, human normal brain, and glioblastoma DNA samples and demonstrated its superior sensitivity in analyzing the hydroxymethylome.

Cerebral syphilitic Gumma in the modern era: a report of an unusual case and brief review of recent published reports.

BACKGROUND: Cerebral syphilitic gummas are rare. However, numerous case reports on them have been published recently, consistent with the resurgence of syphilis and its accompanying atypical manifestations. We here present a patient with a cerebral syphilitic gumma and an unusual clinical course and review recent case reports. CASE PRESENTATION: A 49-year-old woman had a generalised seizure and was found by computed tomography and magnetic resonance imaging to have a brain mass that mimicked a brain abscess or malignant tumour. Further imaging with magnetic resonance spectroscopy and positron emission tomography did not contribute further to the differential diagnosis. Because treatment with ceftriaxone was ineffective, the lesion was resected. Serological tests on serum and cerebrospinal fluid were positive for syphilis and histopathological examination of the operative specimen revealed a syphilitic gumma. Antibiotic treatment is preferred over invasive interventions for cerebral syphilitic gumma. However, as in our case, radical resection is required when antibiotic treatment is ineffective. CONCLUSIONS: It has recently been reported that the prevalence of syphilis is increasing in older individuals, including in patients without HIV infection or prior treatment for early syphilis. Though advanced imaging and molecular biological techniques are often used to help make a diagnosis, they are of limited value. Because the clinical and imaging features are nonspecific, some neurosurgeons do not include cerebral syphilitic gummas in their differential diagnoses. It is vital that this possibility be considered when a patient has a tumour-like cerebral mass and serum positivity for syphilis.

Creation, effects on embryo quality, and clinical outcomes of a new embryo culture medium with 31 optimized components derived from human oviduct fluid: A prospective multicenter randomized trial.

Purpose: Our aim is to make an ideal embryo culture medium close to human oviduct fluid (HOF) components, and to evaluate the quality of this medium with embryo quality and clinical outcomes in assisted reproductive technology (ART) by a prospective randomized controlled trial (RCT). Methods: Study I: HOF was collected laparoscopically from patients (n = 28) with normal pelvic findings. According to HOF analysis results, the new medium "HiGROW OVIT®" (OVIT) was designed. Study II: Embryos (2 pronuclei (2PN) = 9633) were assigned from 1435 patients. The blastulation rate (BR), good BR (gBR), utilized (transferred/cryo-preserved) BR (uBR), pregnancy rate (PR), and miscarriage rate (MR) were compared between the OVIT and control groups by RCT. Results: The novel medium 'OVIT' was produced according to 31 HOF components. The concentrations of essential amino acids (e-AAs) were lower in OVIT than in current media, yet the opposite was true for ne-AA concentrations. gBR and uBR were higher in the OVIT group than in the control group. In the older female group, gBT and uBR were significantly higher in the OVIT group. Conclusions: The novel medium 'OVIT' was produced according to HOF data. The OVIT had significantly better embryo quality and clinical outcomes than the current media.

Survival case of rhinocerebral and pulmonary mucormycosis due to Cunninghamella bertholletiae during chemotherapy for acute myeloid leukemia: a case report.

A 42-year-old man diagnosed with acute myeloid leukemia complained of progressive swelling of the right side of his face with pain 11 days after the third cycle of consolidation therapy with high-dose arabinosylcytosine-cytarabine. Head and neck magnetic resonance imaging showed a mass lesion in his right maxillary sinus with parapharyngeal involvement, which included the right masseter muscle, intraorbital involvement, and an abscess in his brain. Chest computed tomography revealed peribronchial small nodules in his right upper lobe and a necrotic tumor in his right lower lobe. Molds identified as Cunninghamella bertholletiae were isolated from the necrotic ulcer. According to these results, chemotherapy for leukemia was discontinued. High-dose liposomal amphotericin (10 mg/kg/day) was initiated. Because renal dysfunction occurred, the dosage was decreased to 6 mg/kg and combined with 150 mg/day micafungin. Debridement of necrotic tissue in the right maxillary sinus and establishment of the fenestration between the sinus and oral cavity were performed. Subsequently, brain and lung lesions were surgically removed. Rhinocerebral mucormycosis was successfully treated without relapse over 3 years by a 112-day course of intravenous anti-fungal therapy and 223-day course of terbinafine and partial surgical removal, respectively, to maintain masticatory and ocular functions. To our knowledge, there has been no other report of a long-term survival case of rhinocerebral mucormycosis due to C. bertholletiae.

Effect of Mechanical Thrombectomy Without vs With Intravenous Thrombolysis on Functional Outcome Among Patients With Acute Ischemic Stroke: The SKIP Randomized Clinical Trial.

IMPORTANCE: Whether intravenous thrombolysis is needed in combination with mechanical thrombectomy in patients with acute large vessel occlusion stroke is unclear. OBJECTIVE: To examine whether mechanical thrombectomy alone is noninferior to combined intravenous thrombolysis plus mechanical thrombectomy for favorable poststroke outcome. DESIGN, SETTING, AND PARTICIPANTS: Investigator-initiated, multicenter, randomized, open-label, noninferiority clinical trial in 204 patients with acute ischemic stroke due to large vessel occlusion enrolled at 23 hospital networks in Japan from January 1, 2017, to July 31, 2019, with final follow-up on October 31, 2019. INTERVENTIONS: Patients were randomly assigned to mechanical thrombectomy alone (n = 101) or combined intravenous thrombolysis (alteplase at a 0.6-mg/kg dose) plus mechanical thrombectomy (n = 103). MAIN OUTCOMES AND MEASURES: The primary efficacy end point was a favorable outcome defined as a modified Rankin Scale score (range, 0 [no symptoms] to 6 [death]) of 0 to 2 at 90 days, with a noninferiority margin odds ratio of 0.74, assessed using a 1-sided significance threshold of .025 (97.5% CI). There were 7 prespecified secondary efficacy end points, including mortality by day 90. There were 4 prespecified safety end points, including any intracerebral hemorrhage and symptomatic intracerebral hemorrhage within 36 hours. RESULTS: Among 204 patients (median age, 74 years; 62.7% men; median National Institutes of Health Stroke Scale score, 18), all patients completed the trial. Favorable outcome occurred in 60 patients (59.4%) in the mechanical thrombectomy alone group and 59 patients (57.3%) in the combined intravenous thrombolysis plus mechanical thrombectomy group, with no significant between-group difference (difference, 2.1% [1-sided 97.5% CI, -11.4% to ∞]; odds ratio, 1.09 [1-sided 97.5% CI, 0.63 to ∞]; P = .18 for noninferiority). Among the 7 secondary efficacy end points and 4 safety end points, 10 were not significantly different, including mortality at 90 days (8 [7.9%] vs 9 [8.7%]; difference, -0.8% [95% CI, -9.5% to 7.8%]; odds ratio, 0.90 [95% CI, 0.33 to 2.43]; P > .99). Any intracerebral hemorrhage was observed less frequently in the mechanical thrombectomy alone group than in the combined group (34 [33.7%] vs 52 [50.5%]; difference, -16.8% [95% CI, -32.1% to -1.6%]; odds ratio, 0.50 [95% CI, 0.28 to 0.88]; P = .02). Symptomatic intracerebral hemorrhage was not significantly different between groups (6 [5.9%] vs 8 [7.7%]; difference, -1.8% [95% CI, -9.7% to 6.1%]; odds ratio, 0.75 [95% CI, 0.25 to 2.24]; P = .78). CONCLUSIONS AND RELEVANCE: Among patients with acute large vessel occlusion stroke, mechanical thrombectomy alone, compared with combined intravenous thrombolysis plus mechanical thrombectomy, failed to demonstrate noninferiority regarding favorable functional outcome. However, the wide confidence intervals around the effect estimate also did not allow a conclusion of inferiority. TRIAL REGISTRATION: umin.ac.jp/ctr Identifier: UMIN000021488.

Impact of Coronavirus Disease 2019 on Time Delay and Functional Outcome of Mechanical Thrombectomy in Tokyo, Japan.

OBJECTIVES: An association has been reported between delays in the onset-to-door (O2D) time for mechanical thrombectomy (MT) and outbreaks of coronavirus disease 2019 (COVID-19). However, the association between other MT time courses or functional outcomes and COVID-19 outbreaks remains unclear. We compared the time courses of stroke pathways or functional outcomes in 2020 (the COVID-19 era) with those in 2019 (the pre-COVID-19 era) in Tokyo, Japan. MATERIALS AND METHODS: This retrospective observational study used data from the Tokyo-tama-REgistry of Acute endovascular Thrombectomy (TREAT), a multicenter registry of MT for acute large vessel occlusion in the Tokyo Metropolitan Area. Patients who had undergone acute MT from January 2019 to December 2020 were included. Patients were classified by the year they had undergone MT (2019 or 2020). RESULTS: In total, 477 patients were analyzed. O2D time was significantly longer in 2020 (146.0 min) than in 2019 (105.0 min; p = 0.034). No significant difference in door-to-puncture time (D2P) time or modified Rankin Scale (mRS) score 0-2 at 90 days was seen between 2019 and 2020. In the subgroup analysis, O2D time was significantly longer in the first half of 2020 compared with 2019. Multivariable logistic regression analysis revealed that the year 2020 was a independent predictor of longer O2D time, but not for mRS score 0-2 at 90 days. CONCLUSIONS: Although O2D time was significantly longer in the COVID-19 compared with the pre-COVID-19 era, D2P may not be significantly delayed and functional outcomes may not be different, despite the COVID-19 pandemic.

Intracranial growing teratoma syndrome observed at 44 months after initial treatment; a case presentation and literature review.

Intracranial growing teratoma syndrome (iGTS) is rare phenomenon which is observed in non-germinomatous germ cell tumor (NGGCT) after chemotherapy. The clinical features of iGTS are rapidly increasing in size compared with relapse, no elevation of tumor marker in spite of tumor regrowth, multiple cystic lesions in cranial imaging, and histopathologically diagnosed as mature teratoma. Here we present a 14-year-old man with iGTS which was revealed at 44 months after initial chemotherapy. He was diagnosed as pineal immature teratoma by histopathological specimen, and we performed chemotherapy and radiation therapy. After this treatment, we found growing cystic lesion in tumor removal cavity at 26 months after surgery. The histopathological findings showed dermoid cyst in first salvage surgery. Following this result, we observed him without adjuvant chemotherapy. However he had continuous headache, abnormal eye movement at 44 months after initial treatment. Cranial MRI showed regrowing cyst. In second salvage surgery, mature teratoma was demonstrated on histopathological specimen, and we diagnosed as iGTS. Although most reported iGTSs show rapid increasing after initial chemotherapy, few reported cases show regrowth at chronic phase as our case. In long-term follow-up of germ cell tumor, iGTS is important as differential diagnosis.

Minimal Tissue Reaction after Chronic Subdural Electrode Implantation for Fully Implantable Brain-Machine Interfaces.

There is a growing interest in the use of electrocorticographic (ECoG) signals in brain-machine interfaces (BMIs). However, there is still a lack of studies involving the long-term evaluation of the tissue response related to electrode implantation. Here, we investigated biocompatibility, including chronic tissue response to subdural electrodes and a fully implantable wireless BMI device. We implanted a half-sized fully implantable device with subdural electrodes in six beagles for 6 months. Histological analysis of the surrounding tissues, including the dural membrane and cortices, was performed to evaluate the effects of chronic implantation. Our results showed no adverse events, including infectious signs, throughout the 6-month implantation period. Thick connective tissue proliferation was found in the surrounding tissues in the epidural space and subcutaneous space. Quantitative measures of subdural reactive tissues showed minimal encapsulation between the electrodes and the underlying cortex. Immunohistochemical evaluation showed no significant difference in the cell densities of neurons, astrocytes, and microglia between the implanted sites and contralateral sites. In conclusion, we established a beagle model to evaluate cortical implantable devices. We confirmed that a fully implantable wireless device and subdural electrodes could be stably maintained with sufficient biocompatibility in vivo.

The Endometriosis Fertility Index Is Useful for Predicting the Ability to Conceive without Assisted Reproductive Technology Treatment after Laparoscopic Surgery, Regardless of Endometriosis.

OBJECTIVE: The endometriosis fertility index (EFI) is a novel index for predicting pregnancy after surgery. We investigated the utility of the EFI for predicting the ability to conceive without assisted reproductive technology (ART) treatment after laparoscopic surgery. METHODS: From July 2011 through December 2012, we recruited 133 infertile patients who underwent laparoscopy, and the EFI was calculated. After surgery, 55 of 133 achieved pregnancy without ART treatment. We evaluated the factors that predicted a naturally successful pregnancy and compared them between the pregnant and non-pregnant subjects. RESULTS: On a univariate linear regression analysis, we found that a younger age, shorter duration of infertility, and higher EFI were positively associated with a successful pregnancy without ART after laparoscopic surgery (p < 0.05). According to 50th percentile EFI, the cutoff EFI predicting a successful pregnancy without ART was 7, the pregnancy rate in the high-EFI group (EFI; 8-10) was significantly higher than that in the low-EFI group (EFI ≤7; p < 0.05), but the duration to natural conception after surgery was similar between the 2 groups. CONCLUSION: The EFI possesses greater predictive power for a successful pregnancy with natural intercourse or intrauterine insemination in infertile patients, regardless of endometriosis, than the Revised-American Society of Reproductive Medicine classification.

New Prediction Score for Hematoma Expansion and Neurological Deterioration after Spontaneous Intracerebral Hemorrhage: A Hospital-Based Retrospective Cohort Study.

OBJECTIVE: To ensure hematoma expansion and neurological deterioration in the management of acute spontaneous intracerebral hemorrhage, accurate prediction is crucial for initial assessment on admission. We conducted this study to develop a new clinical prediction score using only noncontrast computed tomography image and simply measurable variables. METHODS: This study was a retrospective cohort analysis. The study took place in a single academic medical center in Japan. Development of the prediction score was conducted based on patients who presented between October 2010 and June 2015, using univariate and multivariate logistic regression. We then validated the results in a second cohort between July 2015 and April 2017. The primary outcome was hematoma expansion and the secondary outcome was neurological deterioration up to 14 days after onset. RESULTS: In total, 622 patients were included in the analysis after excluding unsuitable cases. Of these, 457 patients were included in the development cohort and 165 were included in the validation cohort, with 10.8% meeting the criteria for hematoma expansion and 8.8% showing neurological deterioration. In the multivariate analysis, predictors of expansion or deterioration were as hematoma heterogeneity on computed tomography, niveau formation, peripheral edema, hematoma volume of more than 30 mL, and anticoagulant use. We then created the HEAVN score based on the univariate regression coefficients. The C-statistics for the hematoma expansion scores were .81 and .80 in the development and validation cohorts, respectively. Similar results were obtained for neurological deterioration. CONCLUSIONS: The HEAVN score is simple and useful for predicting hematoma expansion and neurological deterioration based on imaging and background data.

Specific Factors to Predict Large-Vessel Occlusion in Acute Stroke Patients.

BACKGROUND: The effectiveness of thrombectomy for acute ischemic stroke has been established, and earlier treatment produces better outcomes. If possible to identify large-vessel occlusion (LVO) at the prehospital phase, eligible patients can be shipped directly to a hospital that can perform thrombectomy. The purpose of this study was to determine factors that are specific to LVO and can be known before hospital arrival. METHODS: The subjects were stroke patients during the period between July 2014 and June 2016, who had a National Institutes of Health Stroke Scale (NIHSS) score of 8 or higher and came to our hospital within 6 hours of onset. These patients were divided into an LVO group and a non-LVO group, and background factors, mode of onset, individual NIHSS item scores, and blood pressure at the time of the visit were retrospectively investigated. The selected factors were compared with LVO prediction scales reported in the past. RESULTS: There were 196 stroke patients who had NIHSS scores of 8 or higher and arrived at the hospital within 6 hours. Of these 196 patients, 56 had LVO. This LVO group included a significantly higher number of patients with the 2 items of atrial fibrillation (odds ratio [OR], 11.5: 95% confidence interval [CI], 4.04-32.9; P < .0001) and systolic blood pressure of 170 mm Hg or lower (OR, 2.99: 95% CI, 1.33-6.71, P = .008). These 2 items predicted LVO equally to existing LVO prediction scales. CONCLUSIONS: The 2 items of atrial fibrillation and systolic blood pressure of 170 mm Hg or lower were significantly correlated with LVO.

Three timescales in prism adaptation.

It has been proposed that motor adaptation depends on at least two learning systems, one that learns fast but with poor retention and another that learns slowly but with better retention (Smith MA, Ghazizadeh A, Shadmehr R. PLoS Biol 4: e179, 2006). This two-state model has been shown to account for a range of behavior in the force field adaptation task. In the present study, we examined whether such a two-state model could also account for behavior arising from adaptation to a prismatic displacement of the visual field. We first confirmed that an "adaptation rebound," a critical prediction of the two-state model, occurred when visual feedback was deprived after an adaptation-extinction episode. We then examined the speed of decay of the prism aftereffect (without any visual feedback) after repetitions of 30, 150, and 500 trials of prism exposure. The speed of decay decreased with the number of exposure trials, a phenomenon that was best explained by assuming an "ultraslow" system, in addition to the fast and slow systems. Finally, we compared retention of aftereffects 24 h after 150 or 500 trials of exposure: retention was significantly greater after 500 than 150 trials. This difference in retention could not be explained by the two-state model but was well explained by the three-state model as arising from the difference in the amount of adaptation of the "ultraslow process." These results suggest that there are not only fast and slow systems but also an ultraslow learning system in prism adaptation that is activated by prolonged prism exposure of 150-500 trials.

Modulation of error-sensitivity during a prism adaptation task in people with cerebellar degeneration.

Cerebellar damage can profoundly impair human motor adaptation. For example, if reaching movements are perturbed abruptly, cerebellar damage impairs the ability to learn from the perturbation-induced errors. Interestingly, if the perturbation is imposed gradually over many trials, people with cerebellar damage may exhibit improved adaptation. However, this result is controversial, since the differential effects of gradual vs. abrupt protocols have not been observed in all studies. To examine this question, we recruited patients with pure cerebellar ataxia due to cerebellar cortical atrophy (n = 13) and asked them to reach to a target while viewing the scene through wedge prisms. The prisms were computer controlled, making it possible to impose the full perturbation abruptly in one trial, or build up the perturbation gradually over many trials. To control visual feedback, we employed shutter glasses that removed visual feedback during the reach, allowing us to measure trial-by-trial learning from error (termed error-sensitivity), and trial-by-trial decay of motor memory (termed forgetting). We found that the patients benefited significantly from the gradual protocol, improving their performance with respect to the abrupt protocol by exhibiting smaller errors during the exposure block, and producing larger aftereffects during the postexposure block. Trial-by-trial analysis suggested that this improvement was due to increased error-sensitivity in the gradual protocol. Therefore, cerebellar patients exhibited an improved ability to learn from error if they experienced those errors gradually. This improvement coincided with increased error-sensitivity and was present in both groups of subjects, suggesting that control of error-sensitivity may be spared despite cerebellar damage.

Advanced scheduling for zygote intrafallopian transfer is possible via the use of a hormone replacement cycle for patients who have experienced repeated implantation failures.

PURPOSE: Zygote intrafallopian transfer (ZIFT) is an effective option for patients who have experienced repeated implantation failures (RIF) in assisted reproductive technology (ART) treatment. However, advance planning for the day of the operation can be problematic. Using a hormone replacement cycle (HRC) makes it possible to plan for the day of ZIFT. In the present study, we evaluated whether HRC-ZIFT is useful for RIF patients who have experienced difficulties obtaining morphologically good embryos in vitro. METHODS: A total of 55 patients with a history of five or more unsuccessful transfers received HRC-ZIFT between June 2008 and June 2013. The oocyte pick-ups were performed and the oocytes showing two pronuclei (2PN) were cryopreserved. After receiving more than five 2PN oocytes, the operation day was scheduled in advance, and as a consequence, a HRC was started and ZIFT was performed. The clinical outcomes were evaluated. RESULTS: The average age of the patients was 39.3 years, and the previous OPU and ET attempts numbered 7.5 and 6.9, respectively. The number of previously transferred embryos was 11.8, and the number of morphologically good embryos (MGEs) was only 1.2. The number of transferred 2PN oocytes was 6.7, and the subsequent pregnancy rate was 23.6 %. No ectopic or multiple pregnancies were observed, but there were 6 cases of miscarriage. CONCLUSION: Among RIF patients, in particular those who have difficulty obtaining MGEs in vitro, ZIFT might be a useful option. The HRC allows patients and medical staff to plan for the operation day in advance.

The Visualization of Intraneural Venous Compression in Trigeminal Neuralgia by Using Advanced Three-Dimensional Computer Graphics: An Illustrative Case Report.

Trigeminal neuralgia (TN) caused by venous compression presents challenges in surgical management, unlike the arterial type. Preoperative diagnostic certainty regarding venous etiology and anatomical relationships is crucial for surgical success. We discuss a case of TN caused by a vein passing through the nerve that was challenging to visualize on conventional MRI and was treated successfully by leveraging information from modern surgical simulation technology with 3D computer graphics. We recognized a potentially troublesome anatomical feature in advance and mitigated the risk by identifying a collateral drainage route for the causative vein, making it feasible to be sacrificed while ensuring treatment efficacy.

DMRT1 regulates human germline commitment.

Germline commitment following primordial germ cell (PGC) specification during early human development establishes an epigenetic programme and competence for gametogenesis. Here we follow the progression of nascent PGC-like cells derived from human embryonic stem cells in vitro. We show that switching from BMP signalling for PGC specification to Activin A and retinoic acid resulted in DMRT1 and CDH5 expression, the indicators of migratory PGCs in vivo. Moreover, the induction of DMRT1 and SOX17 in PGC-like cells promoted epigenetic resetting with striking global enrichment of 5-hydroxymethylcytosine and locus-specific loss of 5-methylcytosine at DMRT1 binding sites and the expression of DAZL representing DNA methylation-sensitive genes, a hallmark of the germline commitment programme. We provide insight into the unique role of DMRT1 in germline development for advances in human germ cell biology and in vitro gametogenesis.