Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

Clone DB: an integrated NCBI resource for clone-associated data.

The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represents an expansion and replacement of the former NCBI Clone Registry and has records for genomic and cell-based libraries and clones representing more than 100 different eukaryotic taxa. Records provide details of library construction, associated sequences, map positions and information about resource distribution. Clone DB is indexed in the NCBI Entrez system and can be queried by fields that include organism, clone name, gene name and sequence identifier. Whenever possible, genomic clones are mapped to reference assemblies and their map positions provided in clone records. Clones mapping to specific genomic regions can also be searched for using the NCBI Clone Finder tool, which accepts queries based on sequence coordinates or features such as gene or transcript names. Clone DB makes reports of library, clone and placement data on its FTP site available for download. With Clone DB, users now have available to them a centralized resource that provides them with the tools they will need to make use of these important research reagents.

Development of a rapid and sensitive LC-MS/MS assay for the quantification of commonly abused drugs in Asia in a micro-segment of a single hair using microwave-assisted extraction and dansyl chloride derivatization.

A high-throughput method using microwave-assisted extraction, chemical derivatization and liquid chromatography-electrospray tandem mass spectrometry (LC-ESI-MS/MS) was developed for the simultaneous analysis of illicit drugs and their metabolites, including amphetamine (AMP), methamphetamine (MA), methylenedioxy- amphetamine (MDA), methylenedioxy-methamphetamine (MDMA), morphine (MOR), 6-acetylmorphine (6-AM), ketamine (K), and norketamine (NK) in a micro-segment of a single hair (0.4 mm). In order to elevate the throughput and sensitivities of selected compounds, 3 min microwave-assisted extraction and 10 min derivatization with dansyl chloride (DC) were employed. After derivatization, all compounds except ketamine and norketamine were derivatized and enhanced the sensitivities significantly. Derivatives showed intense fragment ions and low background noise on DC-MOR, DC-6-AM, and four DC-amphetamine-type stimulants. The total sample preparation and analysis time was 50 min. The calibration range was from LOQ to 5000 pg/mg, the coefficient of determination was better than 0.997. Intra-assay precision and accuracy were generally less than 15%. Limits of detection ranged from 15 to 50 pg/mg, limits of quantitation ranged between 45 and 125 pg/mg. The matrix effect was better than 90%. The method was successfully applied to the analysis of actual hair samples collected from multi-drug abusers. This advanced method showed practicality in hair analysis and was suitable for the extremely insufficient sample.

Validation of a high-throughput method for simultaneous determination of areca nut and tobacco biomarkers in hair using microwave-assisted extraction and isotope dilution liquid chromatography tandem mass spectrometry.

For people with habits of chewing betel nuts and smoking, the probability of suffering from oral cancer is ten to a hundred times higher than others. Due to the serious health consequences of areca nut and tobacco, a reliable cessation program is needed. Hair is the best option to document long-term exposure. Unfortunately, the research on betel nut in hair did not attract much attention. In this study, a high-throughput method based on microwave-assisted extraction (MAE) and isotope dilution liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed to measure the four biomarkers of betel nuts and cigarettes, including areca alkaloids (arecoline), tobacco alkaloids (nicotine), and their metabolites (arecaidine and cotinine). The hair sample was washed, cut, weighed, and incubated for 3 min MAE with methanol/trifluoroacetic acid, then evaporated and reconstituted for LC-MS/MS analysis. The total experiment time was 50 min. The lower limits of quantification (LOQ) were 5-10 pg/mg. The intra-day and inter-day precision were 2.2-7.6%. Intra-day and inter-day accuracy were - 6.1-8.2%. The method showed good linearity (r2 > 0.995) over LOQ - 1000 pg/mg concentration ranges. It was successfully applied to analyze 11 subjects of regular areca nut chewers, also smokers. Eight samples were black hair; three samples were naturally black hair with partially gray hair. Measured concentrations in black hair were in the range 56.9 pg/mg to 3.2 ng/mg for arecoline, 12.8 pg/mg to 222.2 pg/mg for arecaidine, 3.8 ng/mg to 33.4 ng/mg for nicotine and 1.1 ng/mg to 6.1 ng/mg for cotinine. The results showed lower levels in gray hair. This method was utilized successfully to analyze pg/mg levels of arecoline, arecaidine, nicotine, and cotinine, and good recoveries were obtained. The mean concentration of arecaidine and cotinine in hair was 15% and 20% of arecoline and nicotine, respectively. A good positive correlation was found between the concentrations of these compounds and self-report. This method improved extraction speed, concentration, and analysis of samples and is useful for monitoring betel nut and smoking cessation programs.

Facial cellulitis arising from dens evaginatus: a case report.

Dens evaginatus is a developmental anomaly that produces a tubercle on the occlusal surface of a tooth. It is found most frequently in the mandibular premolars. The occlusal tubercle easily causes occlusal interferences. Attrition or fracture of the tubercle can lead to pulpitis, pulp necrosis, periapical pathosis, and periapical infection. This case report illustrates the treatment of facial cellulitis arising from dens evaginatus with open apex. Calcium hydroxide was used for the apexification procedure. One year after canal obturation, radiography revealed no apical pathosis and the apical seal was evident.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Postpartum Taiwanese women: their postpartum depression, social support and health-promoting lifestyle profiles.

BACKGROUND: To reach the Millennium Development Goals, maternal health-promoting behaviours need to be encouraged after childbirth; little is known about the health-promoting behaviour among first-time mothers during their postpartum period. AIM: To examine levels of engagement in health-promoting behaviours and related factors among postpartum women in Taiwan. METHODS: This cross-sectional study was conducted through a convenience sample of 122 qualified women. Participants self-completed a questionnaire and mailed it back using a stamped, self-addressed envelope from July to September 2003. Instruments of this study included a demographic questionnaire as well as three Likert-type scales: the Health Promotion Lifestyle Profile scale, the Edinburgh Postnatal Depression scale and a self-developed social support scale. RESULTS: The average overall Health Promotion Lifestyle Profile score was low (mean, 2.83 SD 1.35), with exercise rated lowest among the six subscales. Postpartum women perceived that they had high levels of social support from their mothers-in-law, mothers and husbands. An astonishing 42.6% of women experienced postnatal depression. Based on results of multiple regressions, 25% of the variance in health-promoting lifestyle practices was explained by postpartum depression and social support. Social support was found to predict all subscales significantly except exercise. Postpartum depression can significantly predict self-actualization, interpersonal relationships, nutrition and stress management. All modifying factors were excluded from the regression model. CONCLUSIONS: This study validates the theoretical relationships among concepts in the Health Promotion Model. Nursing interventions are recommended which are tailored to enhance women's social support and decrease their depression to promote their pursuit of healthy lifestyles. RELEVANCE TO CLINICAL PRACTICE: This study highlights the implications of social support to nursing practice, especially in Chinese culture which has a strict ritual during a women's postpartum period. Findings of this study provide information and data for service planning and community care to support postpartum care in the communities.

Development and testing of a scale to measure caregiving load in caregivers of cancer patients in Taiwan, the care task scale-cancer.

The purpose of this study was to develop and test an instrument to measure care tasks for Taiwanese spouse caregivers of cancer patients. A 37-item Care Task Scale-Cancer (CTS-C) was developed using both quantitative and qualitative approaches. The reliability and validity of the CTS-C was tested on a convenience sample of 150 spouse caregivers caring for patients with breast cancer, head neck cancer, or esophageal cancer. Factor analysis showed that the CTS-C had 4 underlying factors (subscales): (1) accompany patient and monitor care (12 items), (2) substitutive care for social and general affairs (12 items), (3) communication and emotional care (9 items), and (4) mobility maintenance care (4 items). These 4 factors explained 52.3% of the total variance. Cronbach alpha coefficients for these 4 subscales ranged from .83 to .88. Test-retest coefficients (r) ranged from 0.92 to 0.94. The construct validity of this scale was supported by demonstrating a negative correlation between CTS-C scores (demand, difficulty, and caregiving load) and functional performance status, and positive correlations with caregiver burden and symptom distress. These results showed satisfactory validity and reliability for the CTS-C.

Impact of cancer patients' quality of life on that of spouse caregivers.

GOALS OF WORK: This study aimed to examine the correlation between quality of life (QOL) in cancer patients and that of their spouse caregivers and to identify factors that influence this correlation. PATIENTS AND METHODS: This cross-sectional study collected data from 121 cancer patient/spouse caregiver dyads. The Functional Assessment of Cancer Therapy Scale-General (FACT-G) was used to measure patients' QOL, and the Caregiver Quality of Life Index (CQLI) was used to measure spouse caregivers' QOL. Correlation coefficients between patients' and caregivers' QOL were computed for four dimensions of QOL, as well as a total score for QOL. Correlations between patients' and caregivers' total QOL scores were furthered analyzed by three groups of factors: disease-/treatment-related, caregiving-related, and relationship-related variables. MAIN RESULTS: Only the social/family and functional dimensions of patient QOL and total score for patient QOL were associated with each dimension of their caregivers' QOL and with the total score ( r=0.27-0.44). Physical and emotional dimensions of patients' QOL did not significantly influence spouse caregivers' QOL for any dimension nor for the total score. Factors influencing the association between patients' and caregivers' overall QOL included cancer diagnosis, length of hospitalization, caregiving intensity and duration, marital satisfaction, and caregiving self-esteem. CONCLUSIONS: Social and functional aspects of patients' QOL play a significant role in determining the QOL of their spouse caregivers. The strength of association between patients' and spouse caregivers' overall QOL can be moderated by some factors.