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Background and purposeA proper stratification of intracranial aneurysms (IA) is critical in identifying rupture-destined aneurysms (RDA) and unruptured intracranial aneurysms (UIA). We aimed to determine the utility of geometric and hemodynamic indexes in differentiating RDA and UIA, and to examine the characteristics of natural evolutionary changes of UIA.MethodsRDA was defined as having subsequent subarachnoid hemorrhage (SAH), and UIA was examined using follow-up time-of-flight magnetic resonance angiography (TOF-MRA). In addition to geometric indexes such as aspect or size ratio, aneurysmal signal intensity gradient (SIG), anin-vivoapproximated wall shear stress (WSS) from TOF-MRA, was measured. The difference (delta) between the maximum and minimum values of SIG in an aneurysm compared to parent arterial values was designated as the delta-SIG ratio.ResultsThis study analyzed 20 RDA in 20 patients and 45 UIA in 41 patients with follow-up TOF-MRA. While geometric indexes did not show significant differences between the RDA and UIA, the delta-SIG ratio was significantly higher in the RDA than in the UIA (1.5±0.6 vs. 1.1±0.3, P=0.032). The delta-SIG ratio showed a significantly higher area under the receiver operating characteristics curve for SAH than the size ratio (0.72 [95% confidence interval (CI), 0.58–0.87] vs. 0.56 [95% CI, 0.41–0.72], P=0.033). The longitudinal re-examination of TOF-MRA in the UIA group showed evidence of aneurysmal growth with hemodynamic stability.ConclusionsThe delta-SIG ratio showed significantly higher discriminatory results between RDA and UIA compared to geometric indexes. Aneurysmal rupture risk should be assessed by considering both geometric and hemodynamic information.This study was registered onClinicalTrials.gov(NCT05450939).

BACKGROUND AND PURPOSE Reportedly 30-50% of patients being treated for chronic illnesses do not adhere to their medication regimen. We assessed the impact of a nurse-led education program for caregivers of Korean de novo Alzheimer's disease patients who had newly been prescribed donepezil. METHODS This multicenter study analyzed 93 participants in a caregiver education group and 92 participants in a caregiver no-education group. At every visit up to the end of the study (1 year), caregivers in the education group were given educational brochures regarding Alzheimer's disease and the efficacy and adverse events of donepezil treatment. The primary endpoint was the discontinuation rate of donepezil treatment during the 1-year observation period. The secondary endpoints included the effect of education on compliance with donepezil treatment assessed at each visit using a clinician rating scale (CRS) and visual analog scale (VAS), and changes from baseline in cognitive assessment tests. RESULTS The donepezil discontinuation rates at 1 year were 5.38% (5/93) and 6.52% (6/92) in the caregiver education and no-education groups, respectively (p=0.742). No significant between-group differences in donepezil compliance rates on the CRS and VAS were observed, but significant changes were observed in some cognitive tests from baseline to the end of the study. CONCLUSIONS Caregiver education had no significant effect on treatment discontinuation, but this may have been due to the low severity of cognitive impairment among the included population at baseline. In addition, the low discontinuation rates meant that no significant difference in treatment compliance was observed.

BACKGROUND AND PURPOSE The rate of donepezil discontinuation and the underlying reasons for discontinuation in Asian patients with Alzheimer's disease (AD) are currently unknown. We aimed to determine the treatment discontinuation rates in AD patients who had newly been prescribed donepezil in routine clinical practice in Asia. METHODS This 1-year observational study involved 38 institutions in seven Asian countries, and it evaluated 398 participants aged 50-90 years with a diagnosis of probable AD and on newly prescribed donepezil monotherapy. The primary endpoint was the rate of donepezil discontinuation over 1 year. Secondary endpoints included the reason for discontinuation, treatment duration, changes in cognitive function over the 1-year study period, and compliance as assessed using a clinician rating scale (CRS) and visual analog scale (VAS). RESULTS Donepezil was discontinued in 83 (20.9%) patients, most commonly due to an adverse event (43.4%). The mean treatment duration was 103.67 days in patients who discontinued. Among patients whose cognitive function was assessed at baseline and 1 year, there were no significant changes in scores on the Mini-Mental State Examination, Montreal Cognitive Assessment, and Trail-Making Test-Black and White scores, whereas the Clinical Dementia Rating score increased significantly (p

Background and Purpose— In unilateral moyamoya disease, altered endothelial shear stress on the intact-side terminal internal carotid artery might trigger the progression to bilateral disease. We analyzed the endothelial shear stress parameters of the normally appearing terminal internal carotid artery in unilateral moyamoya disease and its association with the progression to bilateral disease. Methods— This retrospective cohort study included patients diagnosed with unilateral moyamoya disease by cerebral angiography and followed-up with regular magnetic resonance imaging/magnetic resonance angiography evaluations for >1 year. Endothelial shear stress parameters acquired were mean and maximum signal intensity gradients (SIG) and SIG SD at the vessel boundary in time-of-flight sequences in initial brain magnetic resonance imaging/magnetic resonance angiography. Contralateral disease progression defined as the detection of newly developed vessel steno-occlusion with an magnetic resonance angiography steno-occlusive stage of ≥2, in the previously intact side of the brain on follow-up magnetic resonance imaging/magnetic resonance angiography evaluation. Results— Among 146 patients (66 males [45.2%] and 80 females [54.8%]; 76 pediatric [52.1%]), contralateral disease progression was detected in 43 patients (29.5%) after a mean follow-up of 4.3±2.4 years. Multivariate analysis showed that SIG SD was significantly associated with this progression (odds ratio, 13.001 [95% CI, 1.764−95.794], P =0.012). In receiver operating characteristic curve analysis, SIG SD predicted the contralateral progression with area under the curve values of 0.803 (95% CI, 0.726−0.880, P Conclusions— Increased spatial variability of the endothelial shear stress around the normally appearing terminal internal carotid artery, as measured by SIG SD in time-of-flight sequences, may predict the contralateral progression of unilateral moyamoya disease.

Background Warfarin is evidence-based therapy for the prevention of cardioembolic stroke, but has not been studied for its effects on whole blood viscosity (WBV). This study investigated the effect of warfarin versus aspirin on WBV in patients presenting with non-valvular atrial fibrillation (NVAF) and acute cardioembolic stroke. Methods We enrolled patients with acute cerebral infarction, aged 56–90 years who had NVAF, CHADS2 score ≥ 2, presenting with mild-to-moderate stroke (National Institute of Health Stroke Scale (NIHSS) score

Background: Autosomal dominant polycystic kidney disease (ADPKD) is an autosomal dominant genetic disorder in which cysts of various sizes invade the renal parenchyma. Intracranial aneurysms occur in 8-12% of ADPKD patients, which is approximately 3-4 times the rate of the healthy population. However, research on factors related to aneurysm incidence and rupture in patients with ADPKD is insufficient. Objective: We analyzed the factors associated with risk of aneurysm incidence and phenotype in ADPKD patients. Methods: From the ADPKD registry in the tertiary hospital, we screened patients with cerebral angiography enrolled between January 2007 and May 2017. Then, 926 enrolled patients were classified into three groups according to the intracranial aneurysm incidence and phenotype (multiplicity, size, location): no intracranial aneurysm (Group 1); low-risk intracranial aneurysm (Group 2); high-risk intracranial aneurysm (Group 3). We analyzed the difference of patients’ demographic factors, cardiovascular risk factors, laboratory data, echocardiographic data, and imaging data between groups. Results: The prevalence [C1] of intracranial aneurysm in ADPKD patients was 16.0%. Aneury[C2] sm-positive group (Group 2 and 3, n=148) was significantly older (p Conclusion: Factors associated with a high-risk aneurysms were age, sex, dolichoectasia, dyslipidemia, and mitral inflow deceleration time in ADPKD patients. Identification of these factors would help detect high risk aneurysms and manage the aneurysms in ADPKD patients.

Background: The occurrence of intracranial aneurysms is higher in patients with autosomal dominant polycystic kidney disease (ADPKD) than in the healthy population. However, research concerning the factors related to the risk of intracranial aneurysm rupture in patients with ADPKD is still insufficient. Objectives: The aim of the study was to investigate the prevalence of intracranial aneurysms and aneurysmal subarachnoid hemorrhage (SAH) and to analyze the systemic factors associated with high-risk aneurysms in patients with ADPKD. Methods: We screened patients who underwent cerebral angiography between January 2007 and May 2017 in the ADPKD registry. Patients were examined for the presence of intracranial aneurysms and subsequently reclassified into 3 groups based on the risk of aneurysmal rupture: the aneurysm-negative (group 1), low-risk aneurysm (group 2), or high-risk aneurysm (group 3). Various systemic factors were compared, and independent factors associated with high-risk aneurysms were analyzed. Results: Among the 926 patients, 148 (16.0%) had intracranial aneurysms and 11 (1.2%) had previous aneurysmal SAH. Patients with intracranial aneurysms were further classified into group 2 (low-risk aneurysms, 15.5%) or group 3 (high-risk aneurysms, 84.5%). Age (odds ratio [OR] 1.03, 95% confidence interval [CI] 1.01–1.05, p = 0.004), female sex (OR 3.13, 95% CI 1.94–5.0 6, p < 0.001), dolichoectasia (OR 8.57, 95% CI 1.53–48.17, p = 0.015), and mitral inflow deceleration time (DT) (OR 1.01, 95% CI 1.00–1.01, p = 0.046) were independently associated with high-risk aneurysms, whereas hypercholesterolemia (OR 0.46, 95% CI 0.29–0.72, p = 0.001) was negatively associated. Conclusion: In the present study among patients with ADPKD, the prevalence of intracranial aneurysms and aneurysmal SAH was 16 and 1.2%, respectively. Age, female sex, dolichoectasia, and mitral inflow DT were positively associated with high-risk aneurysms, whereas hypercholesterolemia was negatively associated. A subsequent large-scaled longitudinal study is needed to define the plausibility of the clinical parameters.

Background: Common carotid artery (CCA) and internal carotid artery (ICA) are aligned linearly, but their hemodynamic role in ischemic stroke has not been studied in depth. Objectives: We aimed to investigate whether CCA and ICA endothelial shear stress (ESS) could be associated with the ischemic stroke of large artery atherosclerosis (LAA). Methods: We enrolled consecutive patients with unilateral ischemic stroke of LAA and healthy controls aged >60 years in the stroke center of Jeonbuk National University Hospital. All patients and controls were examined with carotid artery time-of-flight magnetic resonance angiography, and their endothelial signal intensity gradients (SIGs) were determined, as a measure of ESS. The effect of right or left unilateral stroke on the association between carotid artery endothelial SIG and ischemic stroke of LAA was assessed. Results: In total, the results from 132 patients with ischemic stroke of LAA and 121 controls were analyzed. ICA endothelial SIG showed significant and independent associations with the same-sided unilateral ischemic stroke of LAA, even after adjusting for the potential confounders including carotid stenosis, whereas CCA endothelial SIG showed a significant association with the presence of the ischemic stroke of LAA. Conclusion: Although CCA and ICA are located with continuity, the hemodynamics and their roles in large artery ischemic stroke should be considered separately. Further studies are needed to delineate the pathophysiologic roles of ESS in CCA and ICA for large artery ischemic stroke.

Fusion proteoforms are translation products derived from gene fusion. Although very rare, the fusion proteoforms play important roles in biomedical science. For example, fusion proteoforms influence the development of tumors by serving as cancer markers or cell cycle regulators. Although numerous studies have reported bioinformatics tools that can predict fusion transcripts, few proteogenomic tools are available that can predict and identify proteoforms. In this study, we develop a versatile proteogenomic tool "FusionPro," which facilitates the identification of fusion transcripts and their potential translatable peptides. FusionPro provides an independent gene fusion prediction module and can build sequence databases for annotated fusion proteoforms. FusionPro shows greater sensitivity than the available fusion finders when analyzing simulated or real RNA sequencing data sets. We use FusionPro to identify 18 fusion junction peptides and three potential fusion-derived peptides by MS/MS-based analysis of leukemia cell lines (Jurkat and K562) and ovarian cancer tissues from the Clinical Proteomic Tumor Analysis Consortium. Among the identified fusion proteins, we molecularly validate two fusion junction isoforms and a translation product of FAM133B:CDK6. Moreover, sequence analysis suggests that the fusion protein participates in the cell cycle progression. In addition, our prediction results indicate that fusion transcripts often have multiple fusion junctions and that these fusion junctions tend to be distributed in a nonrandom pattern at both the chromosome and gene levels. Thus, FusionPro allows users to detect various types of fusion translation products using a transcriptome-informed approach and to gain a comprehensive understanding of the formation and biological roles of fusion proteoforms.

Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .

Objectives We examined the associations between HbA1c levels and various atherosclerotic vascular parameters among adults without diabetes from the general population. Methods A total of 6500 community-dwelling adults, who were free of type 2 diabetes and ≥50 years of age, were included. High-resolution B-mode ultrasound was used to evaluate carotid artery structure, including intima-media thickness (IMT), plaque, and luminal diameter. Brachial-ankle pulse wave velocity (baPWV), which is a useful indicator of systemic arterial stiffness, was determined using an automatic waveform analysis device. Results No significant associations were observed between HbA1c, carotid IMT, plaque, or luminal diameter in a fully adjusted model. However, the odds ratio (95% confidence interval) for high baPWV (defined as the highest quartile) increased by 1.43 (1.19–1.71) per 1% HbA1c increase after adjusting for conventional risk factors in a multivariate logistic regression analysis. In addition, HbA1c was independently associated with baPWV in a multivariate linear regression analysis. Conclusions High-normal HbA1c level was independently associated with arterial stiffness, but not with carotid atherosclerotic parameters, in the general population without diabetes. Our results suggest that the functional atherosclerotic process may already be accelerated according to HbA1c level, even at a level below the diagnostic threshold for diabetes.

One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to map and characterize the functions of protein isoforms produced by alternative splicing of genes. However, identifying alternative splice variants (ASVs) via mass spectrometry remains a major challenge, because ASVs usually contain highly homologous peptide sequences. A routine protein sequence analysis suggests that more than half of the investigated proteins do not generate two or more uniquely mapping peptides that would enable their isoforms to be distinguished. Here, we develop a new proteogenomics method, named "ASV-ID" (alternative splicing variants identification), which enables identification of ASVs by using a cell type-specific protein sequence database that is supported by RNA-Seq data. Using this workflow, we identify 1935 distinct proteins under highly stringent conditions. In fact, transcript evidence on these 841 proteins helps us distinguish them from other isoforms, despite the fact that these proteins are not predicted to make 2 or more uniquely mapping peptides. We also demonstrate that ASV-ID enables detection of 19 differently expressed isoforms present in several cell lines. Thus, a new workflow using ASV-ID has the potential to map yet-to-be-identified difficult protein isoforms in a simple and robust way.

Blood flow simulations can identify arterial regions that are vulnerable to atherosclerotic or thrombotic evolution. To accurately define vulnerable arterial regions, hemodynamic parameters such as arterial geometry, blood flow velocity and blood viscosity (BV) must be measured individually. However, previous numerical studies have largely employed either a single representative value or simply used a nonspecific curve of non-Newtonian characteristics of BV. This study aimed to evaluate whether various BV models could produce similar arterial wall shear stress (WSS) results. We performed a blood flow simulation in carotid arteries obtained from time-of-flight magnetic resonance (TOF MR) angiography using the hemodynamic characteristics of subjects via carotid duplex ultrasonography. The BV models were categorized into the following five types: patient-specific non-Newtonian BV (model 1), representative non-Newtonian BV based on the Carreau model (BV model 2), Newtonian BV measured at a specific shear rate of 300[Formula: see text][Formula: see text] (BV model 3), Newtonian BV obtained from a hematocrit-based equation (BV model 4) and a representative Newtonian BV of 4[Formula: see text]cP (BV model 5). In total, 20 carotid arteries from 20 healthy volunteers (mean age [Formula: see text] SD of [Formula: see text] years; 50% women) were examined. Compared with the mean values of carotid WSS in BV model 1 as the reference model, the other four models showed significant differences in both genders for all carotid segments. To obtain reliable physiological WSS results, patient-specific non-Newtonian BV should be carefully employed.

Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ~15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, which contains the simulated spectra of 173 907 human tryptic peptides determined by MassAnalyzer (version 2.3.1). To prove the enhanced analytical performance of the combination of the human iRefSPL and simSPL methods for the identification of missing proteins, we attempted to reanalyze the placental tissue data set (PXD000754). The data from each experiment were analyzed using PeptideProphet, and the results were combined using iProphet. For the quality control, we applied the class-specific false-discovery rate filtering method. All of the results were filtered at a false-discovery rate of1% at the peptide and protein levels. The quality-controlled results were then cross-checked with the neXtProt DB (2014-09-19 release). The two spectral libraries, iRefSPL and simSPL, were designed to ensure no overlap of the proteome coverage. They were shown to be complementary to spectral library searching and significantly increased the number of matches. From this trial, 12 new missing proteins were identified that passed the following criterion: at least 2 peptides of 7 or more amino acids in length or one of 9 or more amino acids in length with one or more unique sequences. Thus, the iRefSPL and simSPL combination can be used to help identify peptides that have not been detected by conventional sequence database searches with improved sensitivity and a low error rate.

Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

Objective This study attempts to clarify the clinical characteristics of chronic dizziness and its relationships with specific vestibular, oculomotor, autonomic and psychiatric dysfunctions. Methods 73 Patients with idiopathic chronic dizziness were recruited and classified based on history taking and clinical examination into the following four clinical subgroups; vestibular migraine (VM), dysautonomia, psychogenic, and unspecified groups. They were also evaluated using oculomotor, otolithic and autonomic function tests, and psychologic investigation. Results Patients in the VM group showed a high proportion of abnormality on smooth pursuit and otolithic function testing compared to the other groups. The dysautonomia group revealed significant abnormalities in sympathetic and cardiovagal autonomic function, while the psychogenic group had a high frequency of abnormality in sympathetic autonomic testing and in Beck’s anxiety inventory scale. The unspecified group showed abnormalities on saccade, smooth pursuit and autonomic function testing. Conclusions Clinical classification of patients with chronic dizziness was relevant and they showed a correlation with disease-specific abnormal results in oculomotor, otolithic, autonomic function and psychology testing. Significance Appropriate diagnostic investigation based on precise clinical diagnosis of chronic dizziness reduces the need for extensive laboratory testing, neuroimaging, and other low-yield tests.

Aim Deep pontine lacunar infarction (DPLI) not involving the basal pial surface of the medial part of the pons, is known to be a small vessel disease in the territory of the basilar artery (BA). In the present study, we examined whether morphological features of the BA differ in individuals with an advanced age and may be associated with DPLI. Methods This study included 338 healthy subjects and 78 patients with DPLI treated at the stroke centers of three university hospitals in Korea. Time-Of-Flight magnetic resonance angiographic images were transported to a central lab and analyzed blind to obtain the clinical data. For the quantitative analysis, the BA was projected two-dimensionally in the anteroposterior and lateral views and perceived as triangles of the vertebrobasilar junction, angulation point and BA division. The angles and triangular areas were summated into angulation indexes and used to quantify the degree of BA tortuosity. Results The BA showed a more acute angle at the angulation point in the elderly patients than in the healthy subjects. Compared to the healthy subjects, the DPLI patients exhibited significantly larger angles at the vertebrobasilar junction, in addition to the acute angles noted at the angulation point. A unit increase in the BA angle indexes at the vertebrobasilar junction and angulation points for DPLI was found to have an odds ratio of 1.15 (95% confidence interval, 1.05-1.26) and 0.95 (95% CI, 0.91-0.99), respectively, even after adjusting for potential confounders. Conclusions The angulation point of the BA becomes more acute in elderly individuals. In this study, the vertebrobasilar junction showed a larger angle in the patients with DPLI than in the healthy controls.

Objectives: There is little evidence for an association between gamma-glutamyltransferase (GGT) and carotid atherosclerosis, an independent predictor of cardiovascular disease. We examined the association between serum GGT and carotid atherosclerotic parameters, including carotid intima-media thickness (IMT) and plaques, in a large general population. Methods: The study population consisted of community-dwelling adults who participated in the baseline survey of the Namwon Study. A total of 9120 subjects aged 45–74 years were included in the analyses. High-resolution B-mode ultrasound was used to measure carotid IMT and to evaluate the presence of carotid plaques. A mean carotid IMT of ≥1.0 mm was classified as ‘high carotid IMT’. Results: Serum GGT levels were classified into quartiles. In a fully adjusted model, we found no linear trend between GGT quartile and mean carotid IMT (P for trend = 0.167). Compared with the first quartile (the reference category), the odds ratios (ORs) and 95% confidence intervals (CIs) for high carotid IMT were 0.89 (0.68–1.16), 1.10 (0.84–1.43), and 0.97 (0.71–1.33) for the second, third, and fourth quartiles (P for trend = 0.754), respectively. The ORs (95% CIs) for carotid plaques were 0.89 (0.77–1.02), 0.95 (0.82–1.10), and 0.94 (0.79–1.11) for the second, third, and fourth quartiles, respectively, in the fully adjusted model (P for trend = 0.644). Conclusions: No significant association of GGT concentration with carotid IMT or plaques was found in this large cross-sectional study. Further longitudinal studies are needed to confirm our findings.

Purpose Right-to-left shunt (RLS) through a patent foramen ovale (PFO) is likely associated with ischemic stroke. Many studies have attempted to demonstrate the association between RLS and ischemic stroke. However, information on the association between the degree of RLS and the subtypes of ischemic stroke categorized by the Trial of ORG 10172 in Acute Stroke Treatment (TOAST) classification is lacking. Method This was a retrospective study involving 508 patients with ischemic stroke who underwent a transcranial Doppler (TCD) microbubble test between 2013 and 2015. The degree of RLS was divided into 4 grades according to the microbubble signal (MBS) as follows: no MBS, grade 1; MBS 20, grade 3; curtain sign, grade 4. The degree of RLS and the type of ischemic stroke as classified by TOAST were analyzed and compared with other clinical information and laboratory findings. Results The higher RLS grade was associated with the cardioembolism (CE) and stroke of undetermined etiology (SUE), and the microbubble signals were inversely related with small vessel disease (SVD). An MBS higher than grade 3 showed a 2.95-fold higher association with SUE than large artery atherosclerosis (LAA), while grade 4 MBS revealed an approximately 8-fold higher association with SUE than LAA. Conclusion RLS identified by the TCD microbubble test was significantly and independently associated with cryptogenic ischemic stroke (negative evaluation). Subsequent studies are needed to determine the biologic relationship between RLS and ischemic stroke, particularly the cryptogenic subtype of ischemic stroke.

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to fill the knowledge gaps between human genomic information and the corresponding proteomic information. These gaps are due to “missing” proteins (MPs)—predicted proteins with insufficient evidence from mass spectrometry (MS), biochemical, structural, or antibody analyses—that currently account for 2579 of the 19587 predicted human proteins (neXtProt, 2017–01). We address some of the lessons learned from the inconsistent annotations of missing proteins in databases (DB) and demonstrate a systematic proteogenomic approach designed to explore a potential new function of a known protein. To illustrate a cautious and strategic approach for characterization of novel function in vitro and in vivo, we present the case of Na(+)/H(+) exchange regulatory cofactor 1 (NHERF1/SLC9A3R1, located at chromosome 17q25.1; hereafter NHERF1), which was mistakenly labeled as an MP in one DB (Global Proteome Machine Database; GPMDB, 2011–09 release) but was well known in another public DB and in the literature. As a first step, NHERF1 was determined by MS and immunoblotting for its molecular identity. We next investigated the potential new function of NHERF1 by carrying out the quantitative MS profiling of placental trophoblasts (PXD004723) and functional study of cytotrophoblast JEG-3 cells. We found that NHERF1 was associated with trophoblast differentiation and motility. To validate this newly found cellular function of NHERF1, we used the Caenorhabditis elegans mutant of nrfl-1 (a nematode ortholog of NHERF1), which exhibits a protruding vulva (Pvl) and egg-laying-defective phenotype, and performed genetic complementation work. The nrfl-1 mutant was almost fully rescued by the transfection of the recombinant transgenic construct that contained human NHERF1. These results suggest that NHERF1 could have a previously unknown function in pregnancy and in the development of human embryos. Our study outlines a stepwise experimental platform to explore new functions of ambiguously denoted candidate proteins and scrutinizes the mandated DB search for the selection of MPs to study in the future.

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

The aim of the study was to calculate the arterial wall signal intensity gradient (SIG) from time-of-flight MR angiography (TOF-MRA) and represent arterial wall shear stress. We developed a new algorithm that uses signal intensity (SI) of a TOF-MRA to directly calculate the signal intensity gradient (SIG). The results from our phantom study showed that the TOF-MRA SIG could be used to distinguish the magnitude of blood flow rate as high (mean SIG ± SD, 2.2 ± 0.4 SI/mm for 12.5 ± 2.3 L/min) and low (0.9 ± 0.3 SI/mm for 8.5 ± 2.6 L/min) in vessels (p<0.001). Additionally, we found that the TOF-MRA SIG values were highly correlated with various flow rates (β=0.96, p<0.001). Remarkably, the correlation coefficient between the WSS obtained from the computational fluid dynamics (CFD) analysis and the TOF-MRA SIG was greater than 0.8 in each section at the carotid artery (p<0.001 for all β values). This new technique using TOF-MRA could enable the rapid calculation of the TOF-MRA SIG and thereby the WSS. Thus, the TOF-MRA SIG can provide clinicians with an accurate and efficient screening method for making rapid decisions on the risk of vascular disease for a patient in clinical practice.

Objective: We aimed to determine the topology of anatomical pathways for verticality perception in the brainstem. Methods: We measured the subjective visual vertical (SVV) in 82 patients with acute unilateral infarction of the brainstem alone. The topology of the brainstem lesions responsible for pathologic SVV tilt were determined using MRI-based voxel-wise lesion-behavior mapping, from which probabilistic lesion maps were constructed. Results: Fifty percent of patients (41/82) with acute unilateral brainstem infarcts had abnormal SVV tilt, of which 76% (31/41) had ipsiversive tilt and 24% (10/41) had contraversive tilt. Patients with contraversive SVV tilt exhibited overlapping lesions of the rostral medial vestibular nucleus, medial longitudinal fasciculus, rostral interstitial medial longitudinal fasciculus, and interstitial nucleus of Cajal. In contrast, patients with ipsiversive SVV tilt and oculomotor disturbances exhibited lesions of the medial and inferior vestibular nuclei in the caudal medulla, while those with isolated vertical perceptual changes had injury to the medial side of the medial lemniscus. Conclusions: Our findings provide evidence of a pathway transmitting ipsiversive otolithic signals that bypass the oculomotor system at the medial side of the medial lemniscus, called the ipsilateral vestibulothalamic tract.

The reference interval for plasma total homocysteine (tHcy) and serum folate concentrations were estimated. Total of 3,154 reference individuals (1,029 men and 2,125 women) were selected based on stringent exclusion criteria. For plasma tHcy concentration (µM/L), reference values (median [5-95 percentile]) were 7.72 (5.03 to 13.80) and 6.09 (3.95-10.19) in men and women, respectively. For serum folate concentration (nM/L), reference values were 23.71 (11.73-38.44) and 28.95 (15.23-40.44) in men and women, respectively. The tHcy levels of both genders in the present study were lower than those in previous reports from other countries and Korea. Graphical Abstract

Background and PurposezzVascular shear stress is essential for maintaining the morphology and function of endothelial cells. We hypothesized that shear stress in the internal carotid artery (ICA) may differ between patients with ischemic stroke and healthy control subjects. MethodszzICA shear stress was calculated in 143 controls and 122 patients with ischemic stroke who had a normal ICA or an ICA with

We evaluated the association between APOE polymorphism and carotid atherosclerosis in two large independent cohorts from South Korea.The datasets were from the Dong-gu Study (N = 9056) and the Namwon Study (N = 10,158). Carotid ultrasonography was performed to measure carotid intima-media thickness (IMT) and the presence of carotid plaques. The APOE polymorphism was determined by PCR-RFLP. We performed combined and separate analyses for the two datasets.In the combined analysis, individuals with E2E2 or E2E3 genotype had a lower common carotid IMT compared with individuals with E3E3 genotype (0.684 mm vs. 0.736 mm, p = 0.007; 0.718 mm vs. 0.736 mm, p0.001, respectively). This association was very slightly attenuated but remained statistically significant after adjustment for blood lipids (0.690 mm vs. 0.736 mm, p = 0.033; 0.725 mm vs. 0.736 mm, p = 0.005, respectively). Compared with individuals with E3E3 genotype, individuals with E2E3 genotype had lower risk for carotid plaque (odds ratio (OR) = 0.83, 95% confidence interval (CI) = 0.75-0.93), while individuals with E3E4 genotype had a higher risk for carotid plaque (OR = 1.09, 95% CI = 1.00-1.20). After adjustment for blood lipids, ORs of E2E3 genotype for carotid plaque was slightly attenuated but remained significant (OR = 0.87 95% CI = 0.78-0.97), while OR of E3E4 genotype were slightly attenuated and not significant (OR = 1.08, 95% CI, 0.99-1.18).We found that APOE polymorphism is associated with carotid atherosclerosis and this association was partly mediated through blood lipid. Our results suggest that APOE polymorphism may influence atherosclerosis through non-lipid pathways.

Vitamin D plays an important role in bone metabolism and maintaining bone health. Recently, new evidence has revealed that vitamin D affects chronic diseases such as autoimmune diseases, cardiovascular diseases and certain cancers. The aim of this study was to evaluate the vitamin D status and the prevalence of vitamin D deficiency in an urban Korean population. This study included 8,976 participants (3,587 men and 5,389 women) aged 50 yr and older. Serum 25(OH)D level was measured by chemiluminescent microparticle immunoassay. The prevalence of vitamin D deficiency [25(OH)D < 20 ng/mL] was 59.7% and 86.5% in men and women, respectively. The prevalence of vitamin D deficiency increased significantly with age in men, but not in women and it decreased from April to July, more prominently in men than in women. These results suggest that sun exposure, intake of vitamin D supplement, and regular physical activities is recommended in an urban Koreans, especially in women.

It remains controversial whether APOE E4 polymorphism is related to cognitive function in general population. We aimed to evaluate an association between the APOE E4 genotype and cognitive function, and whether this association may differ by age. Cognitive function was assessed using the Korean version of modified Mini-Mental State Examination (K-mMMSE) in 10,371 Koreans aged 45-74 years in Namwon City. According to the APOE E4 status, all participants were classified as non-carriers, heterozygotes, or homozygotes. Multiple linear and logistic regression models were used to evaluate the association between APOE genotypes and cognition. The frequency of APOE genotypes in the study population was 0.4, 10.1, 1.1, 72.9, 14.7 and 0.8 % for E2E2, E2E3, E2E4, E3E3, E3E4, and E4E4, respectively. Compared to the APOE E4 non-carriers, the heterozygotes and homozygotes showed 1.3 and 7.3 % lower K-mMMSE scores at 65-74 years and 0.8 and 4.6 % higher scores at 45-55 years, respectively. Educational attainment modified the effect of APOE E4 on cognitive function in the 45-54 age group (p for interaction =0.003), showing that the E4 carriers with no-formal education showed significantly higher cognitive function than those with formal education. The present study demonstrates that the effect of APOE E4 on cognitive function depends on age and education.

To clarify the changes of cervical (cVEMP) and ocular (oVEMP) vestibular evoked myogenic potentials induced by air-conducted sound (ACS) and bone-conducted vibration (BCV) in patients with vestibular neuritis (VN), patients with VN (n = 30) and normal controls (n = 45) underwent recording of cVEMP and oVEMP in response to ACS (1,000 Hz, 5 ms, tone bursts) and BCV (500 Hz, short tone burst). Patients with VN showed a high proportion of oVEMP abnormalities in response to both ACS (80.0 %) and BCV at the forehead (Fz, 73.3 %) or the mastoid (76.7 %). In contrast, cVEMPs were mostly normal with both ACS and BCV in the patients. The dissociations in the abnormalities of cVEMP and oVEMP induced by ACS and BCV at the mastoids and at the forehead in patients with VN suggest that oVEMP reflects functions of the superior vestibular nerve and most likely the utricular function. The results of our study suggest that oVEMP induced by either ACS or BCV appears to depend on integrity of the superior vestibular nerve, possibly due to the utricular afferents travelling in it. In contrast, cVEMP elicited by either ACS or BCV may reflect function of the saccular afferents running in the inferior vestibular nerve.

Background Controversial results have been reported on the relationship between alcohol intake and metabolic syndrome (MetS). We examined the association of average volume of alcohol consumed and drinking patterns with MetS and its components. Methods This study was conducted as a baseline survey for the Dong-gu Study of adults aged 50 years or older. Drinking patterns were assessed using a structured interview, and average volume of alcohol consumed was calculated. MetS was defined according to the updated version of the National Cholesterol Education Program. Results Compared with individuals who never drank, the adjusted odds ratio (OR) for the prevalence of MetS was significantly higher in men who consumed 2.1 to 4.0 drinks/day (OR, 1.53; 95% CI, 1.17–2.00) and greater than 4.0 drinks/day (OR, 1.63; 95% CI, 1.23–2.14), whereas no significant association was observed in women. Significant dose-response relationships between average volume of alcohol consumed and all metabolic components were observed in men. A usual quantity of 5 to 6 drinks/drinking day (OR, 1.57; 95% CI, 1.19–2.09), 7 or more drinks/drinking day (OR, 1.88; 95% CI, 1.45–2.44), and binge drinking on at least 1 occasion/week (OR, 1.33; 95% CI, 1.01–1.76) were associated with a significantly higher OR for prevalence of MetS in men; however, none of these drinking patterns were associated with MetS in women. Conclusions Unhealthy drinking patterns such as high usual quantity and binge drinking were significantly associated with MetS, suggesting that the effect of alcohol consumption on MetS should be considered in the context of drinking pattern, particularly in men.

As a starting point of the Chromosome-Centric Human Proteome Project (C-HPP), we established strategies of genome-wide proteomic analysis, including protein identification, quantitation of disease-specific proteins, and assessment of post-translational modifications, using paired human placental tissues from healthy and preeclampsia patients. This analysis resulted in identification of 4239 unique proteins with high confidence (two or more unique peptides with a false discovery rate less than 1%), covering 21% of approximately 20, 059 (Ensembl v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially expressed preeclampsia-specific proteins. When these proteins are assigned to all human chromosomes, the pattern of the newly identified placental protein population is proportional to that of the gene count distribution of each chromosome. We also identified 219 unique N-linked glycopeptides, 592 unique phosphopeptides, and 66 chromosome 13-specific proteins. In particular, protein evidence of 14 genes previously known to be specifically up-regulated in human placenta was verified by mass spectrometry. With respect to the functional implication of these proteins, 38 proteins were found to be involved in regulatory factor biosynthesis or the immune system in the placenta, but the molecular mechanism of these proteins during pregnancy warrants further investigation. As far as we know, this work produced the highest number of proteins identified in the placenta and will be useful for annotating and mapping all proteins encoded in the human genome.

Although alpha-fetoprotein (AFP) is currently the major serologic biomarker for hepatocellular carcinoma (HCC), it cannot efficiently distinguish this cancer from other forms of liver disease in early diagnosis due to its low sensitivity. The aim of this study is to compare sensitivity and specificity of human carboxylesterase 1 (hCE1) and AFP biomarker. Antibody-based assays for hCE1 and AFP were used to test both biomarkers with respect to diagnostic efficiency, Youden's index and the area under the curve (AUC) through receiver operating characteristic (ROC) analysis in plasma from 208 patients with HCC (n=57), liver cirrhosis (n=27), chronic hepatitis (n=37), cholangiocarcinoma (n=22), gastric cancer (n=31) and pancreatic cancer (n=34), along with 52 healthy donors (HDs). The levels of hCE1 were significantly higher in patients with HCC than HDs and the other diseases (p

Background: Kidney dysfunction and albuminuria may be associated with BMD. However, little evidence has been reported on relationships between BMD and eGFR and albuminuria. Methods: A total of 8,992 subjects aged 50 years or older participated in a survey conducted. Participants had their lumbar spine and femoral neck BMD measured by a Lunar Prodigy bone densitometer (GE, Madison, WI). Kidney function was assessed using MDRD eGFR and diagnosis of albuminuria was based on albumin-creatinine ratio. Results: ACR was negatively associated with lumbar spine and femur neck BMD in females (lumbar spine: 1.001, 0.988, 0.974 and 0.979 g/cm2, p < 0.001; femur neck: 0.796, 0.790, 0.783 and 0.782 g/cm2, p = 0.002), but not in males, after adjusting for covariates. Additionally, eGFR was shown to be negatively associated with lumbar spine BMD after adjusting for covariates (male: 1.181, 1.166, 1.152 and 1.149 g/cm2, p = 0.001; female: 0.997, 0.980, 0.979 and 0.982 g/cm2, p = 0.005), but demonstrated no association with femur BMD. Conclusions: ACR in females was negatively associated with lumbar spine and femur neck BMD, but not in males. eGFR was negatively associated with lumbar spine BMD in both males and females.

We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 "missing" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of "missing" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.

In an effort to map the human proteome, the Chromosome-centric Human Proteome Project (C-HPP) was recently initiated. As a member of the international consortium working on this project, our laboratory developed a gene-centric proteomic database called GenomewidePDB, which integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. As an example case, we chose chromosome 13, which is the largest acrocentric human chromosome with the lowest gene density and contains 326 predicted proteins. All proteins stored in GenomewidePDB are linked to other resources, including neXtProt and Ensembl for protein and gene information, respectively. The Global Proteome Machine database (GPMdb) and the PeptideAtlas are also accessed for observed mass spectrometry (MS) information, while Human Protein Atlas is used for information regarding antibody availability and tissue expression, respectively. Gene ontology disease information is also included. As a pilot work, we constructed this GenomewidePDB with the identified 3615 proteins including 53 chromosome 13-origin proteins that are present in normal human placenta tissue. Thus, developing a comprehensive database containing actual experimental proteomics data will provide a valuable resource for cross chromosomal comparison in the C-HPP community.

The hemodynamics of the carotid artery was numerically investigated with an approach of fluid-structure interaction (FSI). To predict the blood flow and arterial deformation of carotid artery, a framework for the FSI analysis was developed by coupling computational fluid dynamics and structural analysis. Using this framework, the hemodynamics of the carotid artery was simulated with the patient- specific clinical data of the arterial geometry, pulsatile blood flow, blood rheology and arterial deformation. It is found that the hemody- namic characteristics of the carotid artery are significantly affected by its geometric factors and flow conditions, and relatively low values of the wall shear stress were observed in the post-plaque dilated region of the carotid bifurcated area, which is known to be responsible for the growth of an atherosclerotic plaque. Since the characteristics of the blood flow in a carotid artery are also affected by the hemody- namic factors, the effects of the cardiac output, distal vascular resistance and blood viscosity on hemodynamics were also numerically analyzed.

Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.

Low levels of vitamin D have been associated with increased cardiovascular disease risk. However, few studies have evaluated the association between vitamin D status and peripheral arterial disease (PAD). We therefore aimed to investigate whether low 25-hydroxyvitamin D (25(OH)D) levels were associated with increased risk of PAD in the Korean population. This cross-sectional study was conducted among 8,960 subjects aged 50 years or older without known myocardial infarction or stroke. PAD was defined by an ankle brachial blood pressure index

In type 2 diabetic patients, the relationships between 25-hydroxyvitamin D and parathyroid hormone levels, and glycemic control, remain unclear. We evaluated associations between 25-hydroxyvitamin D, parathyroid hormone, and hemoglobin A1c levels after adjusting for other covariates, including log transformed 25-hydroxyvitamin D levels and log transformed parathyroid hormone levels, in Korean patients with type 2 diabetes. In total, 1,175 patients with type 2 diabetes were selected from 8,857 individuals who completed the baseline survey of the Dong-gu study, conducted in Korea from 2007 to 2010. After adjusting for other covariates, we found that the mean hemoglobin A1c level was inversely associated with the 25-hydroxyvitamin D level (Q1: 7.47% [7.30-7.63], Q2: 7.25% [7.09-7.40], Q3: 7.17% [7.02-7.32], Q4: 7.19% [7.02-7.35]; p for trend = 0.021, p for between groups = 0.050) and the parathyroid hormone level (Q1: 7.35% [7.19-7.51], Q2: 7.34% [7.19-7.50], Q3: 7.28% [7.13-7.43], Q4: 7.09% [6.94-7.24]; p for trend = 0.022, p for between groups = 0.048). However, the mean fasting glucose level was not associated with either the 25-hydroxyvitamin D or parathyroid hormone level. In conclusion, inverse associations were evident between hemoglobin A1c, 25-hydroxyvitamin D and parathyroid hormone levels in Korean patients with type 2 diabetes. The associations remained significant after adjusting for other covariates, including the log transformed 25-hydroxyvitamin D levels and log transformed parathyroid hormone levels.