MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets.

MS-based immunopeptidomics is maturing into an automatized and high-throughput technology, producing small- to large-scale datasets of clinically relevant major histocompatibility complex (MHC) class I-associated and class II-associated peptides. Consequently, the development of quality control (QC) and quality assurance systems capable of detecting sample and/or measurement issues is important for instrument operators and scientists in charge of downstream data interpretation. Here, we created MhcVizPipe (MVP), a semiautomated QC software tool that enables rapid and simultaneous assessment of multiple MHC class I and II immunopeptidomic datasets generated by MS, including datasets generated from large sample cohorts. In essence, MVP provides a rapid and consolidated view of sample quality, composition, and MHC specificity to greatly accelerate the "pass-fail" QC decision-making process toward data interpretation. MVP parallelizes the use of well-established immunopeptidomic algorithms (NetMHCpan, NetMHCIIpan, and GibbsCluster) and rapidly generates organized and easy-to-understand reports in HTML format. The reports are fully portable and can be viewed on any computer with a modern web browser. MVP is intuitive to use and will find utility in any specialized immunopeptidomic laboratory and proteomics core facility that provides immunopeptidomic services to the community.

Inclusion of Health Disparities, Cultural Competence, and Health Literacy Content in US and Canadian Pharmacy Curriculums.

Objective. To determine how US and Canadian pharmacy schools include content related to health disparities and cultural competence and health literacy in curriculum as well as to review assessment practices.Methods. A cross-sectional survey was distributed to 143 accredited and candidate-status pharmacy programs in the United States and 10 in Canada in three phases. Statistical analysis was performed to assess inter-institutional variability and relationships between institutional characteristics and survey results.Results. After stratification by institutional characteristics, no significant differences were found between the 72 (50%) responding institutions in the United States and the eight (80%) in Canada. A core group of faculty typically taught health disparities and cultural competence content and/or health literacy. Health disparities and cultural competence was primarily taught in multiple courses across multiple years in the pre-APPE curriculum. While health literacy was primarily taught in multiple courses in one year in the pre-APPE curriculum in Canada (75.0%), delivery of health literacy was more varied in the United States, including in a single course (20.0%), multiple courses in one year (17.1%), and multiple courses in multiple years (48.6%). Health disparities and cultural competence and health literacy was mostly taught at the introduction or reinforcement level. Active-learning approaches were mostly used in the United States, whereas in Canada active learning was more frequently used in teaching health literacy (62.5%) than health disparities and cultural competence (37.5%). Few institutions reported providing professional preceptor development.Conclusion. The majority of responding pharmacy schools in the United States and Canada include content on health disparities and cultural competence content and health literacy to varying degrees; however, less is required and implemented within experiential programs and the co-curriculum. Opportunities remain to expand and apply information on health disparities and cultural competence content and health literacy content, particularly outside the didactic curriculum, as well as to identify barriers for integration.

Assessment of MRI-based anomalous diffusion changes in brain ischemic stroke with a fractional motion model.

The actual diffusion process in human brain has been shown to be anomalous comparing to that predicted with traditional diffusion MRI (dMRI) theory. Recently, dMRI based on fractional motion (FM) model has demonstrated the potential to accurately describe anomalous diffusion in vivo. In this work, we explored the potential value of FM model-based dMRI in quantificational identification of ischemic stroke and compared that with the traditional apparent diffusion coefficient (ADC). We included 23 acute stroke patients, 8 of whom finished a follow-up scan, and 22 matched healthy controls. The dMRI images were acquired by using a Stejskal-Tanner single-shot spin-echo echo-planar-imaging sequence (diffusion gradients were applied in three orthogonal directions with 25 non-zero b values ranging from 248 to 4474 s/mm2) at 3.0 T MRI. We calculated the coefficient of variation (CV) for FM-related parameters in stroke lesions, and compared the mean values for FM-related parameters and ADC by using two-sample t-tests. Correlation analysis was achieved using Pearson correlation coefficient test. In acute stroke lesions, CV for FM-related parameters showed significant increase compared with normal tissues (P < 0.01), while those of ADC didn't appear statistical difference. Mean values for FM-related parameters showed significant decrease in acute lesion (P < 0.01) and their changing pattern during follow-up was positively correlated with ADC (P < 0.005). Our results initially verified the utility of the FM-model in detecting ischemic stroke compared with traditional dMRI.

Risk Assessment of An Earthquake-Collapse-Landslide Disaster Chain by Bayesian Network and Newmark Models.

Severe natural disasters and related secondary disasters are a huge menace to society. Currently, it is difficult to identify risk formation mechanisms and quantitatively evaluate the risks associated with disaster chains; thus, there is a need to further develop relevant risk assessment methods. In this research, we propose an earthquake disaster chain risk evaluation method that couples Bayesian network and Newmark models that are based on natural hazard risk formation theory with the aim of identifying the influence of earthquake disaster chains. This new method effectively considers two risk elements: hazard and vulnerability, and hazard analysis, which includes chain probability analysis and hazard intensity analysis. The chain probability of adjacent disasters was obtained from the Bayesian network model, and the permanent displacement that was applied to represent the potential hazard intensity was calculated by the Newmark model. To validate the method, the Changbai Mountain volcano earthquake-collapse-landslide disaster chain was selected as a case study. The risk assessment results showed that the high-and medium-risk zones were predominantly located within a 10 km radius of Tianchi, and that other regions within the study area were mainly associated with very low-to low-risk values. The verified results of the reported method showed that the area of the receiver operating characteristic (ROC) curve was 0.817, which indicates that the method is very effective for earthquake disaster chain risk recognition and assessment.

Environmental Risk Assessment of Metals in the Volcanic Soil of Changbai Mountain.

Tianchi volcano is a dormant active volcano with a risk of re-eruption. Volcanic soil and volcanic ash samples were collected around the volcano and the concentrations of 21 metals (major and trace elements) were determined. The spatial distribution of the metals was obtained by inverse distance weight (IDW) interpolation. The metals' sources were identified and their pollution levels were assessed to determine their potential ecological and human health risks. The metal concentrations were higher around Tianchi and at the north to the west of the study area. According to the geo-accumulation index (Igeo), enrichment factor (EF) and contamination factor (CF) calculations, Zn pollution was high in the study area. Pearson's correlation analysis and principal component analysis showed that with the exception of Fe, Mn and As, the metals that were investigated (Al, K, Ca, Na, Mg, Ti, Cu, Pb, Zn, Cr, Ni, Ba, Ga, Li, Co, Cd, Sn, Sr) were mostly naturally derived. A small proportion of Li, Pb and Zn may have come from vehicle traffic. There is no potential ecological risk and non-carcinogenic risk because of the low concentrations of the metals; however, it is necessary to pay attention to the carcinogenic risk of Cr and As in children.

CHA2DS2-VASc score as a predictor of long-term cardiac outcomes in elderly patients with or without atrial fibrillation.

BACKGROUND: The CHA2DS2-VASc score is often used for stroke risk stratification in atrial fibrillation (AF) patients. However, its usefulness in patients ≥75 years of age with or without AF is unclear. OBJECTIVE: We aimed to investigate whether the CHA2DS2-VASc score can predict ischemic stroke (IS), transient ischemic attack, thromboembolism (TE), and mortality in elderly patients with and without AF. MATERIALS AND METHODS: During 2013-2014, 1,071 patients (36.3% with concomitant AF) at least 75 years old were enrolled, and the follow-up ended on July 15, 2017. Variables included sociodemographic characteristics, complications, drugs taken, laboratory results, and echocardiographic parameters. The primary end points were IS, transient ischemic attack, and TE, expressed as IS/TE. All-cause mortality was a secondary end point. Survival curves and mortality risks were assessed via Kaplan-Meier survival analysis and compared by log-rank tests. RESULTS: The average follow-up duration was 2.57±1.37 years. Overall, 167 patients (5.6%) died and 77 (7.2%) developed IS/TE. The CHA2DS2-VASc score was associated with IS/TE in patients 75 years or older with and without AF, and patients with a CHA2DS2-VASc score ≥5 had a higher risk of stroke. However, the CHA2DS2-VASc score was not related to all-cause mortality. CONCLUSION: The CHA2DS2-VASc score can predict IS/TE, but not mortality, in elderly patients (≥75 years) with or without AF.

Atmospheric deposition exposes Qinling pandas to toxic pollutants.

The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas, especially those of the Qinling subspecies, were exposed to toxicants in their diet of bamboo; the ultimate origin of these toxicants is unknown. Here we show that atmospheric deposition is the most likely origin of heavy metals and persistent organic pollutants (POPs) in the diets of captive and wild Qinling pandas. Average atmospheric deposition was 199, 115, and 49 g·m-2 ·yr-1 in the center of Xi'an City, at China's Shaanxi Wild Animal Research Center (SWARC), and at Foping National Nature Reserve (FNNR), respectively. Atmospheric deposition of heavy metals (As, Cd, Cr, Pb, Hg, Co, Cu, Zn, Mn, and Ni) and POPs was highest at Xi'an City, intermediate at SWARC, and lowest at FNNR. Soil concentrations of the aforementioned heavy metals other than As and Zn also were significantly higher at SWARC than at FNNR. Efforts to conserve Qinling pandas may be compromised by air pollution attendant to China's economic development. Improvement of air quality and reductions of toxic emissions are urgently required to protect China's iconic species.

Characteristics of hand involvement in a comparative study of two early RA cohorts from the UK and China.

AIM: To compare the characteristics of early hand involvement in rheumatoid arthritis (RA) using two matched populations, from the UK and China. METHODS: A cohort comparison study was conducted. Sixty Chinese patients recruited from Shanghai, China were matched on gender and age with 60 patients from a prospective early RA cohort from the UK (SARAH trial). The procedures of data collection in China followed the standard operating procedures employed in the SARAH trial. Outcome measures including Michigan Hand Outcomes Questionnaire (MHQ), medication history and physical assessments were used to assess functional ability and hand impairment. RESULTS: UK patients reported significantly more hand pain (P = 0.015), less satisfaction with dominant hand performance (P  = 0.040), more swollen and tender joints (P = 0.016 and P = 0.001) and greater dexterity of both dominant and non-dominant hands (P < 0.001 and P < 0.001), while Chinese patients had higher disease activity indicated by erythrocyte sedimentation rate and C-reactive protein, more rheumatoid factor, less satisfaction in both dominant and non-dominant hand appearances (P < 0.001 and P < 0.001, respectively) and greater dominant hand deformity (P  = 0.003). No statistically significant differences were seen in range of movement and overall hand function as reported by the MHQ. CONCLUSION: The severity of RA is not milder in China than in the UK and the characteristics of hand involvement tend to be different. Clinicians should consider country-specific differences in managing pain and delivering treatment. It would be helpful for a future study to investigate the RA impact characteristics on a wider range of patients both from within China and from other populations.

Follow-Up Renal Assessment of Injury Long-Term After Acute Kidney Injury (FRAIL-AKI).

BACKGROUND AND OBJECTIVES: Novel urinary kidney damage biomarkers detect AKI after cardiac surgery using cardiopulmonary bypass (CPB-AKI). Although there is growing focus on whether AKI leads to CKD, no studies have assessed whether novel urinary biomarkers remain elevated long term after CPB-AKI. We assessed whether there was clinical or biomarker evidence of long-term kidney injury in patients with CPB-AKI. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We performed a cross-sectional evaluation for signs of chronic kidney injury using both traditional measures and novel urinary biomarkers in a population of 372 potentially eligible children (119 AKI positive and 253 AKI negative) who underwent surgery using cardiopulmonary bypass for congenital heart disease at Cincinnati Children's Hospital Medical Center between 2004 and 2007. A total of 51 patients (33 AKI positive and 18 AKI negative) agreed to long-term assessment. We also compared the urinary biomarker levels in these 51 patients with those in healthy controls of similar age. RESULTS: At long-term follow-up (mean duration±SD, 7±0.98 years), AKI-positive and AKI-negative patients had similarly normal assessments of kidney function by eGFR, proteinuria, and BP measurement. However, AKI-positive patients had higher urine concentrations of IL-18 (48.5 pg/ml versus 20.3 pg/ml [P=0.01] and 20.5 pg/ml [P<0.001]) and liver-type fatty acid-binding protein (L-FABP) (5.9 ng/ml versus 3.9 ng/ml [P=0.001] and 3.2 ng/ml [P<0.001]) than did AKI-negative patients and healthy controls. CONCLUSIONS: Novel urinary biomarkers remain elevated 7 years after an episode of CPB-AKI in children. However, there is no conventional evidence of CKD in these children. These biomarkers may be a more sensitive marker of chronic kidney injury after CPB-AKI. Future studies are needed to understand the clinical relevance of persistent elevations in IL-18, kidney injury molecule-1, and L-FABP in assessments for potential long-term kidney consequences of CPB-AKI.

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.

Sexual and reproductive health service needs of university/college students: updates from a survey in Shanghai, China.

AIM: To promote the provision of reproductive health services to young people by exploring the attitudes and perceptions of university students in Shanghai, China, toward reproductive health. METHODS: From July 2004 to May 2006, 5 243 students from 14 universities in Shanghai took part in our survey. Topics covered the demands of reproductive health-care services, attitudes towards and experience with sex, exposure to pornographic material, and knowledge on sexual health and sexually transmitted infections (STIs)/AIDS. RESULTS: Of the 5 067 students who provided valid answer sheets, 50.05% were female and 49.95% were male, 14.86% were medical students, and 85.14% had non-medical backgrounds. A total of 38.4% of respondents had received reproductive health education previously. The majority of students supported school-based reproductive health education, and also acquired information about sex predominantly from books, schoolmates, and the Internet. Premarital sexual behavior was opposed by 17.7% of survey participants, and 37.5% could identify all the three types of STIs listed in the questionnaire. Although 83.7% knew how HIV is transmitted, only 55.7% knew when to use a condom and 57.8% knew that the use of condoms could reduce the risk of HIV infection. CONCLUSION: The reproductive health service is lagging behind current attitudes and demands of university students. Although students' attitudes towards sexual matters are liberal, their knowledge about reproductive health and STIs/AIDS is still limited. It is therefore necessary to provide effective and confidential reproductive health services to young people.

HIV pharmacotherapy issues, challenges, and priorities in sub-Saharan African countries.

The use of potent antiretroviral drugs has led to successful treatment of HIV infection in most high-income countries. However, therapy remains largely unaffordable to the resource-limited world, particularly to countries in sub-Saharan Africa. The disparity and subsequent disease burden are devastating to the poorly resourced countries, hence creating a greater demand for international collaboration. This review outlines key examples of emerging HIV pharmacotherapy issues, challenges, and priorities within resource-limited settings in order to lay groundwork for potential enchancement of international research collaboration efforts. The prevalence and distribution patterns of HIV infection and sociocultural factors found in sub-Saharan African settings are discussed. Challenges include drug financing, drug distribution infrastructure, and government commitment to responding to the HIV pandemic. Priorities include prevention of HIV transmission, management of pediatric patients, availability of affordable medicines, and addressing concerns over the quality of medicines. The potential for the effective international collaboration is enhanced when expertise and resources from the developed world are combined with an understanding of the unique priorities of resource-limited settings.

Relationship between urban eco-environment and competitiveness with the background of globalization: statistical explanation based on industry type newly classified with environment demand and environment pressure.

Within the global urban system, the statistical relationship between urban eco-environment (UE) and urban competitiveness (UC) (RUEC) is researched. Data showed that there is a statistically inverted-U relationship between UE and UC. Eco-environmental factor is put into the classification of industries, and gets six industrial types by two indexes viz. industries' eco-environmental demand and pressure. The statistical results showed that there is a strong relationship, for new industrial classification, between the changes of industrial structure and evolvement of UE. The drive mechanism of the evolvement of urban eco-environment, with human demand and global work division was analyzed. The conclusion is that the development stratege, industrial policies of cities, and environmental policies fo cities must be fit with their ranks among the global urban system. At the era of globalization, so far as the environmental policies, their rationality could not be assessed with the level of strictness, but it can enhance cities' competitiveness when they are fit with cities' capabilities to attract and control some sections of the industry's value-chain. None but these kinds of environmental policies can probably enhance the UC.