A semi-automatic cell type annotation method for single-cell RNA sequencing dataset

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type–specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

A semi-automatic cell type annotation method for single-cell RNA sequencing dataset

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type–specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

Necessity of Surgical Site Closed Suction Drain for Pterional Craniotomy

OBJECTIVE: The aim of this study was to assess the benefit of using a prophylactic surgical site closed suction drain in pterional craniotomy. MATERIALS AND METHODS: A retrospective review was conducted on 607 consecutive patients who underwent a pterional craniotomy for treatment of intracranial anterior circulation aneurysms over a 5-year period. Between January 2000 and December 2004, 607 patients were divided into two groups, those who had a prophylactic suction drain during closure of the surgical site (drain group, DG) and those who did not (non-drain group, NDG). Head computed tomography (CT) was taken routinely on postoperative day (POD) 1, 7, and 14. Patients' demographics, incidence of surgical site complications, and courses of surgical site healing which were evaluated radiologically by the thickness of the surgical site myocutaneous layer, were analyzed between DG and NDG. RESULTS: Patients' demographics and characteristics did not differ significantly between the two groups. The head CT showed that the degree of changes in the postoperative surgical site thickness was 148% at POD 1, 209% at POD 7, and 198% at POD 14 in DG, and 118% at POD 1, 152% at POD 7, and 158% at POD 14 in NDG compared to the preoperative value. Postoperative surgical site hematoma was 7.9% (22/274) in DG and 2.4% (8/333) in NDG. CONCLUSION: Prophylactic use of an epidural and/or subgaleal closed suction drain does not appear to be necessary for prevention of postoperative surgical site hematoma as well as for promotion of surgical site healing in pterional craniotomy.

Necessity of Surgical Site Closed Suction Drain for Pterional Craniotomy

OBJECTIVE: The aim of this study was to assess the benefit of using a prophylactic surgical site closed suction drain in pterional craniotomy. MATERIALS AND METHODS: A retrospective review was conducted on 607 consecutive patients who underwent a pterional craniotomy for treatment of intracranial anterior circulation aneurysms over a 5-year period. Between January 2000 and December 2004, 607 patients were divided into two groups, those who had a prophylactic suction drain during closure of the surgical site (drain group, DG) and those who did not (non-drain group, NDG). Head computed tomography (CT) was taken routinely on postoperative day (POD) 1, 7, and 14. Patients' demographics, incidence of surgical site complications, and courses of surgical site healing which were evaluated radiologically by the thickness of the surgical site myocutaneous layer, were analyzed between DG and NDG. RESULTS: Patients' demographics and characteristics did not differ significantly between the two groups. The head CT showed that the degree of changes in the postoperative surgical site thickness was 148% at POD 1, 209% at POD 7, and 198% at POD 14 in DG, and 118% at POD 1, 152% at POD 7, and 158% at POD 14 in NDG compared to the preoperative value. Postoperative surgical site hematoma was 7.9% (22/274) in DG and 2.4% (8/333) in NDG. CONCLUSION: Prophylactic use of an epidural and/or subgaleal closed suction drain does not appear to be necessary for prevention of postoperative surgical site hematoma as well as for promotion of surgical site healing in pterional craniotomy.

Application of Advance Directives for Patients with End Stage Renal Disease / 대한신장학회지

PURPOSE: In other countries, government guidelines related to chronic illness are being used to enhance supportive care of renal patients. In Korea, the number of old ages and hemodialysis patients with many complications has been increased. But we don't have any guidelines for palliative care of end stage renal disease. This paper reports a study exploring decisions about end-of-life treatment (e.g. cardiopulmonary resuscitation, renal replacement therapy) via routine use of advance directives in people with end stage renal disease undergoing hemodialysis. METHODS: 1) We revised advance directives in Seoul Medical Center. 2) We recommended the routine use of advance directives to patients who were treated in hemodialysis room of Seoul Medical Center from Jan, 2007 to Jun, 2007. So 35 patients were enrolled. 3) They had been interviewed about end- of-life treatment plans and filled up advance directives. RESULTS: 23 males and 12 females in total were enrolled. The advance directives include 18 questions about patient preferences for treatment of end-of-life. The majority of hemodialysis patients replied "I will follow doctor's decisions including cardiopulmonary resuscitation and renal replacement therapy" 8 females (67%), 15 diabetes (53%) and 11 geriatric patients above 60yrs old (52%), however, were against cardiopulmonary resuscitation. CONCLUSION: Routine use of advance directives will provide basic sources for end-of-life decisions in the care of end stage renal patients. And they would like to keep the high quality of life with the help of prepared therapeutic plan of care and well-dying presented advance directives.

Multicenter Investigation on Clinical Characteristics, Cognitive Impairments, Behavioral and Psychological Symptoms of Demented Elderly in Busan-Gyeongnam Province

OBJECTIVES: The purpose of this study is to examine the state of demographic findings with clinical characteristics, cognitive impairment and behavioral psychological symptoms of demented elderly in Busan-Gyeongnam Province. METHODS: Patients with dementia who were registered at nine medical centers in Busan Metropolitan City and Gyeongnam Province were the major subjects of this study. Data was collected by face-to-face interview. The final sample consisted of 144 cases after eliminating several incomplete questionnaires. Based on the collected data, the authors evaluated demographic findings, clinical characteristics, and cognitive impairment and behavioral psychological symptoms of the patients with dementia using statistical analyses. All of the patients were taken the Korean version of Mini-Mental State Examination(K-MMSE), the Clinical Dementia Rating Scale(CDR) and the the Korean version of Neuropsychiatric Inventory(K-NPI). RESULTS: Approximately 61% of the patients with dementia in Busan-Gyeongnam Province were women, and their mean age was 72.9(SD=8.3) years old. Their average education level was 2.3(SD=1.3) years. Among the demented elderly, Alzheimer's disease accounted for 68% compared with vascular dementia(32%) and the proportion of mild stage of dementia was above 50%. The mean K-MMSE score was 16.7(SD=6.2), the mean CDR score was 1.3(SD=0.8), and the Barthel Index with K-IADL score were 16.7(SD=5.4) and 1.5(SD=0.9). The average score of K-NPI was 22.6(SD=22.5) and the number of manifested K-NPI was 4.9(SD=2.8). The K-NPI score has increased in demented elderly as the severity of dementia getting worse according to the CDR score. The number of manifested K-NPI was significantly more prevalent in patients with AD than that of patients with VD. CONCLUSION: This study is a meaningful approach to the state of demographic findings, clinical characteristics, cognitive impairment and behavioral psychological symptoms associated with the dementied elderly who were comprehensively examined in Busan-Gyeongnam Province. Based on this study, we found that the demographic information was comparable with other epidemiologic study in Korea and our study patients were relatively mild stage of demenitia according to the assessment of cognition and behavioral symptom scales.

The Differences of Behavioral and Psychological Symptoms in the Patients of Alzheimer's Disease and Vascular Dementia

BACKGROUND: Behavioral and psychological symptoms (BPSD) are common in dementia. These may be helpful for clinical differentiation between Alzheimer's disease (AD) and vascular dementia (VD). Most previous studies have reported the prevalence and severity of BPSD regardless of severity of progression. However, we evaluated the differences of BPSD by grading dementia progression and including severe cases only. METHODS: 141 dementia outpatients from clinics of Busan-Gyeongnam Dementia Association in Korea were analyzed. All patients were administered the Korean version of the Neuropsychiatric Inventory (K-NPI), the expanded version of Korean Clinical Dementia Rating Scale (CDR), and the Korean version of Mini-Mental State Examination (K-MMSE). RESULTS: There were 95 patients with AD and 46 patients with VD. AD patients revealed higher frequency of manifested BPSD symptoms and most of subscales showed higher composite scores also. But apathy was more severely and frequently manifested in VD. AD patients had more frequent night-time behavior and aberrant motor symptoms above 3 point in CDR 0.5 and VD patients had more frequent apathy symptom above 3 point in CDR 1. CONCLUSIONS: These results suggest that generally AD patients revealed more frequent and severe BPSDs than VD patients. Apathy was a more dominant symptom in VD. It seemed that some of the symptoms were valuable clues for the differential diagnosis even though a better designed study was required.

The Differences of Clinical Features between Alzheimer's Disease and Vascular Dementia According to Progression

BACKGROUND: The differences in clinical features are important when differentiating between Alzheimer's disease (AD) and vascular dementia (VD). There have been many studies comparing the severity of progression in both diseases. They have assessed individual symptoms but have not explained the differences and global change of progression comprehensively. We have evaluated the cognitive and non-cognitive functions at the same time and evaluated the differences between AD and VD. METHODS: One hundred and thirty-eight dementia patients from Busan?Gyeongnam Dementia Association outpatient clinics were analyzed. All of the patients underwent the Korean version of the Mini-Mental State Examination (K-MMSE), the expanded version of the Korean Clinical Dementia Rating Scale (CDR), the Korean version of the Neuropsychiatric Inventory (K-NPI), the scales for activity of daily living, and the Short form of the Samsung Dementia Questionnaire (S-SDQ). RESULTS: There were 93 patients with AD and 45 with VD. VD patients revealed more severe Barthel Index of Activity of Daily Living (B-ADL) deficits. AD patients had more severe memory and orientation deficiency in CDR 1 and CDR 2. VD patients revealed much faster decline of K-MMSE score between CDR 2 and CDR 3. CONCLUSIONS: These results suggest that VD patients display more severe B-ADL difficulty, while AD patients display more severe memory difficulty and disorientation. B-ADL progresses in the earlier stages in VD and in the later stages in AD. Global cognitive dysfunction progression is the opposite: in the earlier stages in AD and in the later stages in VD.

The Difference of Caregiver Burden in Patients with Alzheimer's Disease and Vascular Dementia

BACKGROUND: The burden on caregivers of patients with dementia has an impact on medical, economic, and social areas. However, not enough attention is given to this burden in Korea. There are also very few reports comparing the burden experienced by caregivers of patients with Alzheimer's disease (AD) and vascular dementia (VD). METHODS: One hundred and forty four Alzheimer's and vascular dementia patients were recruited by nine medical centers in the metropolitan city of Busan and the Gyeongnam province. We evaluated the global dementia state of patients in terms of cognitive functions, behavioral and psychological symptoms of dementia, and the activity of daily living along with caregiver burden with the length of care time per day. The Burden Interview, Caregiver Burden Inventory (CBI), Life Satisfaction Index-Z, Beck Depression Inventory, and Beck Anxiety Inventory were conducted by face-to-face interviews with the caregivers. We compared the differences of caregiver burden related to the cause of dementia and according to dementia severity. RESULTS: There were 98 AD patients (68.1%) and 46 VD patients (31.9%). There were 89 females (61.8%) and 55 males (38.2%). Most of the global dementia states did not differ between AD and VD except for the Barthel index (p<0.05). Most of the caregiver burden tests were scored worse in VD. The differences of CBI-time dependent burden and CBI-developmental burden were statistically significant in all the patients (p<0.05). CONCLUSIONS: Our study suggests that VD patients have more caregiver burden than AD patients and that the physical activity of daily living influences caregiver burden.

Factors Affecting Depression and Life Satisfaction in Family Caregivers of Patients with Dementia

BACKGROUND: The purposes of this study were to examine the state of depression and life satisfaction of family caregivers and to find out which factors would be significant in determining depression and life satisfaction of caregivers for the elderly with dementia. METHODS: Caregivers of patients with dementia who were registered at nine medical centers in Busan Metropolitan City and Gyeongnam Province were the major subjects of this study. Data was collected by face-to-face interviews. The final sample consisted of 144 cases after eliminating several incomplete questionnaires. Based on the collected data, the authors evaluated demographic findings, general characteristics, and factors influencing depression and life satisfaction of the caregivers using statistical analyses. RESULTS: The severity of depression and the degree of life satisfaction in family caregivers were low. We found that caregiver's anxiety, monthly income, caregiver burden, non-relative network, self-confidence of caregiving, and the degree of the Barthel index of activity of daily living (B-ADL) were significant factors in determining depression of the caregivers (p<0.05). The following two variables were significant factors in determining the caregiver's level of life satisfaction: burden of caregiving costs and patient's Korean mini-mental state examination (K-MMSE) score (p<0.05). CONCLUSIONS: Our results showed that the level of anxiety, caregiver burden and social support, rather than the conditions of dementia patients, influenced depression and life satisfaction for the caregivers of patients with dementia. Therefore, in order to improve the quality of life for caregivers, we should consider psychosocial factors as well as patient's medical factors in influencing depression and life satisfaction.

The Change of Cognitive Function and Prognostic Factor in Alzheimer's Disease: 1-Year Follow-up Study

BACKGROUND: The rate of cognitive change and prognostic factor in Alzheimer's disease are important for clinical management, but little is known in Korea. We report a one year follow-up study of comprehensive evaluation including cognitive functions, behavioral and psychological symptoms of dementia (BPSD) and activity of daily living (ADL). METHODS: 43 patients with Alzheimer's disease were enrolled. All subjects received the Korean version of Mini-Mental State Examination (K-MMSE), the Severe Dementia Scale (SDS), the extended version of Korean Clinical Dementia Rating Scale (CDR) and Sum of Box (CDR-SB), the Barthel index of Activity of Daily Living (B-ADL), the Korean Instrumental Activity of Daily Living (K-IADL) and the Korean version of the Neuropsychiatric Inventory (K-NPI). We retested each scale after 1 year and evaluated the changes. RESULTS: The mean change rates of K-MMSE, SDS, CDR, CDR-SB and B-ADL scores were 2.0 +/- 3.2 (-7~8) mean +/- SD (range), 3.5 +/- 4.9 (-7~14), -0.4 +/- 0.7 (-2~1), -0.8 +/- 4.4 (-10~9) and 1.5 +/- 3.7 (-7~9). The change of K-MMSE and B-ADLscore according to CDR were significantly different. The annual rates of changes of scores on K-MMSE, B-ADL and CDR were largest in CDR 1 group (K-MMSE: 4.0 +/- 2.7, B-ADL: 3.4 +/- 2.8, CDR: -1 +/- 0.7). The change rate of SDS was largest in CDR 4 (7.2 +/- 4.3). There were not any significant factors that affected the change of K-MMSE, SDS, B-ADL or CDR. CONCLUSIONS: These results suggest that K-MMSE is sensitive to the early stage and SDS is sensitive to the later stage. The deterioration rate of cognitive function in Alzheimer's disease is large at middle stage.

Two Cases of Holmes-Adie Syndrome

BACKGROUND: Adie's tonic pupil consists of mydriasis, accommodation defect, decreased light reflex, and tonic near reflex. When tonic pupil is combined with hypo- or areflexia, it is called Holmes-Adie syndrome. CASE: Fifty-two-year-old and 37-year-old female patients showed unilateral dilated irregular pupil, decreased light reflex, and decreased or absent DTR. When 0.125% pilocarpine was dropped on the dilated pupil, the pupil was constricted after pilocarpine application. Somatosensory evoked potentials were within normal ranges, and H-reflex responses were absent or delayed.

A Case of Rhino-orbital Mucormycoses with Orbital Apex Syndrome in Diabetic Patient / 대한내분비학회지

Rhino-orbital mucormycosis is a rare fungal infection that involves paranasal sinus and orbits and usually presented as acute invasive fungal sinusitis or orbital apex syndrome. It often occurs in patients with poorly controlled diabetes mellitus especially during or following episode of diabetic ketoacidosis. If the condition is not treated, the fungal infection may disseminated into the brain and death usually occurs in a day to week. Exenteration is often needed as a therapy. We have experienced a case of rhino-orbital mucormycosis that presented as a orbital apex syndrome and confirmed by maxillary and periorbital soft tissue biopsy. A 56-year-old female suffered from diabetes mellitus for 3 years was admitted with rapidly progressive visual acuity loss and left hemi-facial numbness. She was treated with daily intravenous amphotericin B and intraconal amphotericin B irrigation and packing. Exenteration was not neccisated.

Occipital lobe seizure due to hypertensive encephalopathy in youth

BACKGROUND & OBJECTIVES: Hypertensive encephalopathy is an acute neurologic syndrome characterized by abrupt and marked elevation of blood pressure, headache, vomiting, seizure, visual disturbance, and altered mental status. This syndrome may occur as a complication of toxemia, renal artery stenosis and acute glomerulonephritis. We report 4 young patients with occipital lobe seizure, as a presenting sign of hypertensive encephatopathy, whose brain MRI and perfusion scans showed lesions on bilateral occipital lobes. Case : Four young patients experienced moderate to severe headache, visual illusion, generalized seizure, and loss of sight for a few days. Their systolic blood pressure was 150-170mmHg and diastolic blood pressure 100-120mmHg. Three patients had proteinuria and hematuria as the results of acute glomerulonephritis. CSF findings were within normal limits. EEG showed intermittent generali,ed or bilateral temporoparietooccipital slowings in all patients and continuous parietooccipital slowings in one patient. Brain MRI man showed hyperintensity signal in T2WI and hypointensity signal in TlWl on bilateral occipital lobes and SPECT scan showed normal perfusion three patients and increased perfusion on occipital areas in one patient. They were treated with antihypertemsive agents and anticonvulsants (phenobarbital or valporic acid) for 2-10 months. Seizure was well controlled and didn't recur though discontinuing anticonvulsant. CONCLUSION: In young age, acute hypertension may cause clinically occipital lobe seizure and radiologically bilateral occipital lobe lesions.

A case of wilson's disease showing palialia as an initial symptom

Wilson's disease is an autosomal recessive disorder resulting from an excessive accumulation of copper in the liver, cornea, kidneys, and in the basal ganglia of the brain. The prominent speech disturbances of Wilson's disease include monopitch, monoloudness, slow rate, low pitch, delayed in initiating speech and rarely palilalia. A19-year-old woman developed palilalia which was characterized by compulsive repetition of a phrase with increasing rapidity and with a decrescendo of voice volume. Although she had been suffering from liver cirrhosis for the past 8 months, the palilalia was the only neurological sign at initial examination. She showed a low serum ceruloplasmin, low serum copper, increased urinary copper excretion, and Kayser-Fleischer rings. Brain magnetic resonance images showed high signals in the bilateral basal ganglia in T2-weighted images, and slight cortical atrophy.

Threr cases of Hypertensive Encephalopathy in a cute Post-streptococcal Glomerulonephritis: MRI Findings

Two cases of giant cell tumor of bone diagnosed by fine needle aspiration cytology are described. Case 1 was a 28-year-old male who had pain sense for one year at the right distal thigh. His radiologic finding revealed a destructive cortical lesion with soft tissue extension at medial side of epiphysis of the distal femur. Case 2 was a 21-year-old female complaining pain at left distal forearm for eight months and showed a well-demarcated expansile osteolytic lesion with multiseptation, and cortical destruction at epiphysis and metaphysis of the left distal radius on the X-ray. Fine needle aspiration of each lesion was performed. The aspirate of the case 1 revealed moderate cellularity, which was composed of scattered giant cells of osteoclastic type and small round to oval monotonous stromal cells in large areas. Giant cells were evenly distributed in single or small groups and had irregular but abundant cytoplasms with 10 to 20 nuclei in the center. The nuclei showed ovoid shape, fine granular chromatin, and a small but conspicuous nucleolus. Stromal cells were dispersed in isolated pattern or sometimes aggregated in clusters and showed the same nuclei as those of giant cells and scanty cytoplasms. Comparing to case 1, case 2 had a more translucent abundant cytoplasm in the giant cells and more spindled stromal cells. All two cases revealed neither nuclear atypism nor increased abnormal mitoses in both giant and stromal cells, suggesting no evidence of malignancy. Thereafter the lesions were treated with excision and curettage, and histologically confirmed as giant cell tumors of the bone.

One Case of Percutaneous Transluminal Angioplasty of Renal Artery Stenosis Caused by Takayasu's Arteritis

Takayasu's arteritis is one of the most important causes of the renovascular hypertension in orientals. Among the multiple treatment modalities, percutaneous transluminal renal angioplasty(PTRA) has become the treatment of the choice for major renal artery stenosis and is a safe, repeatable, effective procedure for the treatment of renovascular hypertension due to Takayasu's arteritis. We experienced a case of percutaneous transluminal balloon angioplasty of Takayasu's arteritis involving the proximal left renal artery. After PTRA, clinical and angiographical improvements were achieved.

Polymorphonuclear CSF Pleocytosis during the Treatment of Tuberculous Meningitis

Among 73 patients with possible and definite tuberculous meningitis, 14 cases showed a sudden unexpected polymorphonuclear (PMN) CSF pleocytosis during treatment. Patients with superimposed bacterial meningitis were excluded. Eleven patients(15. 1%) matched inclusion criteria. The intervals between the onset of the treatment and the onset of the PMN CSF pleocytosis were 7-54 days(mean 17.2+ 14.4 days). The mean duration of PMN CSF pleocytosis was 14.2+12.4 days. A PMN CSF pleocytosis may develop occasionally weeks or months after the start of the treatment for tuberculous meningitis. Though the cause is uncertain, we suggest that probably its cause is superimposed acute meningeal inflanunation by the release of Mycobacterium from tuberculomas or.delayed Jarisch-Herxheimer reaction.