Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Pedometer Assessed Physical Activity Levels of Adolescents in a Selected School in Manila

An active lifestyle among children and adolescents plays an important role in their normal growth and development. However, studies from different countries have shown a decreasing participation of children in physical activity. In the Philippines, very little is known of adolescent’s involvement in physical activity. Objective: To determine the physical activity (PA) levels using pedometers of the adolescents in Metromanila and factors associated with the level of physical activity. Method: This study is a cross sectional study assessing physical activity patterns using the Yamax Pedometer (SW-200) of adolescents in a selected school in Metromanila. Results: A total of 90 males (15.17 ±1.38; BMI =21.69 ± 4.6 kg/m2) and 78 females (14.85 ± 1.19; BMI = 21.89 ± 4.9 kg/m2) participated in the study. Males had a mean number of steps 10,933.18 ± 4189.5/day while females had a mean of 8307.47 ± 4767.45 steps/day, with males having a significantly higher mean count (p value =0.002). Being male and regular physical exercise were factors associated with a higher pedometer count with a ß (SE) of -171.8 ± 744.1 (95% CI: -2941.3, - 2.5) and ß (SE) 775.6 ± 289.8 (95% CI: 203.4, 1347.8), respectively. Conclusion: Males were generally more active than female adolescents with females having a lower step count compared to studies from other countries. Participation in regular physical activity should be encouraged to prevent the increasing prevalence of lifestyle related diseases

Inter-rater and intra-rater reliability of sonographic median nerve and wrist measurements

Background: Electrophysiologic studies have been considered the “gold standard” in diagnosing carpal tunnel syndrome (CTS); however, reports of false-negative results, as well as discomfort for the patient during the procedure has paved the use of ultrasound, being a painless and cost-efficient tool, as an alternative means for its diagnosis. Various ultrasound parameters assessing the median nerve and wrist dimensions have been described, but description of landmarks to assess these in a reliable manner has been lacking. Methodology: A systematic search of different databases yielded data regarding ultrasound parameters for CTS diagnosis, the landmarks used, and presence of reliability testing. Based on this, three sonologists discussed the external and sonographic landmarks that will be used in measuring the median nerve measurements, bowing of the flexor retinaculum and the carpal tunnel dimensions. A pilot test with two consecutive healthy participants using the discussed ultrasound parameters was carried out, and results were subjected to inter- and intra-rater reliability testing. Modifications were accordingly made on the acquisition of ultrasound image using external landmarks. The reliability testing proper was done with ten consecutive healthy participants. Results: Based on the systematic review and the pilot study, external landmarks were used to locate the median nerve in the forearm, carpal tunnel inlet and outlet. For the forearm measurement, it was taken 10 cm proximal from the distal palmar crease. The distal palmar crease was the external landmark used for the carpal tunnel inlet, while for the carpal tunnel outlet; it was measured 1 cm distal to the distal palmar crease. Instead of using the inner edge of the hook of hamate and trapezium, the apices of these bones were used as the landmarks in measuring the carpal tunnel outlet dimensions. There was excellent intra-rater reliability (mid-forearm, carpal tunnel inlet and outlet) except for the following: cross-sectional area (CSA) of the median nerve at the carpal tunnel inlet and outlet; and bowing of the flexor retinaculum. All the parameters had an excellent inter-rater reliability measured at the three levels (intraclass correlation [ICC]: Of 0.77–0.99) except for CSA of the median nerve at the levels of the forearm (fair-to-good with ICC of 0.71) and the carpal tunnel inlet (fair-to-good reliability of ICC: 0.43). Conclusion: There was an improved inter- and intra-rater reliability when external landmarks were used instead of sonographic landmarks

Protocol for audit of current Filipino practice in rehabilitation of stroke inpatients

Background: Stroke is one of the leading medical conditions in the Philippines. Over 500,000 Filipinos suffer from stroke annually. Provision of evidence-based medical and rehabilitation management for stroke patients has been a challenge due to existing environmental, social, and local health system issues. Thus, existing western guidelines on stroke rehabilitation were contextualized to draft recommendations relevant to the local Philippine setting. Prior to fully implementing the guidelines, an audit of current practice needs to be undertaken, thus the purpose of this audit protocol. Methods: A clinical audit of current practices in stroke rehabilitation in the Philippines will be undertaken. A consensus list of data items to be captured was identified by the audit team during a 2-day meeting in 2012. These items, including patient demographics, type of stroke, time to referral for rehabilitation management, length of hospital stay, and other relevant descriptors of stroke management were included as part of the audit. Hospitals in the Philippines will be recruited to take part in the audit activity. Recruitment will be via the registry of the Philippine Academy of Rehabilitation Medicine, where 90% of physiatrists (medical doctors specialized in rehabilitation medicine) are active members and are affiliated with various hospitals in the Philippines. Data collectors will be identified and trained in the audit process. A pilot audit will be conducted to test the feasibility of the audit protocol, and refinements to the protocol will be undertaken as necessary. The comprehensive audit process will take place for a period of 3 months. Data will be encoded using MS Excel®. Data will be reported as means and percentages as appropriate. Subgroup analysis will be undertaken to look into differences and variability of stroke patient descriptors and rehabilitation activities. Conclusion: This audit study is an ambitious project, but given the “need” to conduct the audit to identify “gaps” in current practice, and the value it can bring to serve as a platform for implementation of evidence-based stroke management in the Philippines to achieve best patient and health outcomes, the audit team is more than ready to take up the challenge

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field