We reviewed articles using computational RF dosimetry to compare the Specific Anthropomorphic Mannequin (SAM) to anatomically correct models of the human head. Published conclusions based on such comparisons have varied widely. We looked for reasons that might cause apparently similar comparisons to produce dissimilar results. We also looked at the information needed to adequately compare the results of computational RF dosimetry studies. We concluded studies were not comparable because of differences in definitions, models, and methodology. Therefore we propose a protocol, developed by an IEEE standards group, as an initial step in alleviating this problem. The protocol calls for a benchmark validation study comparing the SAM phantom to two anatomically correct models of the human head. It also establishes common definitions and reporting requirements that will increase the comparability of all computational RF dosimetry studies of the human head. Cell phone safety remains a topic of broad public concern that attracts frequent media attention. This attention is focused on two areas of scientific controversy concerning cell phone safety. The first area is that of non-thermal biological effects. The existence of these effects is an important open question, but it is not the topic of this paper. However, if these effects exist, their manifestation will certainly be related to the amount of RF energy deposited in the tissue – RF dosimetry . The secThe phantom head that is now the world-wide standard for compliance testing is the Specific Anthropomorphic Mannequin (SAM). SAM was developed by members of IEEE Standards Coordinating Committee 34, SubCommittee 2, Working Group 1 (SCC34/SC2/WG1). This working group was created to develop recommended practices for determining SAR in the head via measurement techniques , and Fedth-percentile anthropometric data corresponding to the adult male head as tabulated by the US Army [SAM is a lossless plastic shell and ear spacer. Because current technology does not allow reliable measurement of SAR in small complex structures, like a simulated pinna, SCC34/SC2 chose to use a lossless ear spacer on SAM to maximize the energy reaching the head and minimize measurement uncertainty. SAM's dimensions were taken from the 90 US Army . The SAMA primary design goal for SAM was that, "SAM shall produce a conservative SAR for a significant majority of persons during normal use of wireless handsets" . To testThe groups headed by Gandhi and Kuster are not the only ones pursuing computational RF dosimetry using anatomically correct models of the human head -25. Not The first, and the most significant of these problems, is the treatment of the external ear (pinna). Specifically, the problem is determining whether the pinna may, or may not, be considered as part of the 1- or 10-gram SAR averaging volumes. When considering SAR averaging volumes the head and the pinna should be viewed as mutually exclusive, in-other-words the pinna is not part of the head but it is attached to the head. Some investigators have chosen to treat the pinna in accordance with IEEE Std C95.1-1999  and the Other investigators have treated the pinna in accordance with draft revision IEEE Std C95.1-200X. This draft standard expands the definition of extremity to include the pinna, which makes the pinna subject to a higher spatial peak SAR, see Table When comparing published results it is often difficult, or impossible, to determine whether head tissue SAR values are based on averaging volumes that include or exclude the pinna. In fact, some papers make no mention of how the pinna was treated. Although head tissue SAR is the major focus of attention, papers that consider the pinna as an extremity can not simply ignore its existence, the pinna must still meet the higher spatial peak SAR for extremities.Another part of the problem dealing with the treatment of the pinna is simply determining what tissue constitutes the pinna. The IEEE defines the pinna as, the largely cartilaginous projecting portion of the outer ear consisting of the helix, lobule, and anti-helix . UnfortuThe second problem area is the lack of common models. The only computer models that are common to all the computational RF dosimetry studies are the SAM and the Visible Human Male. The anatomic data for the Visible Human Male originated at the National Institutes of Health but many groups and individuals lent a hand in converting it into a computational model. While a few investigators have different models the only ones that can be compared across all the published results are SAM and the Visible Human. This also means that the only repeatable comparison that can be made is between the SAM and the Visible Human. It seems obvious that one can neither prove nor disprove that SAM produces a SAR greater than the maximum local SAR induced in humans for a significant majority of persons during normal use of wireless handsets, when there is only one anatomically correct model available for comparison.Although not a major problem, it is still true that dielectric properties and names of tissue types in anatomically correct models have varied between investigators.Of course the head model is only half of any computational RF dosimetry study, the model of the RF source is the other half. The only common source that has been used in several published studies is a dipole ,28-30. SThe third problem is that of inconsistent positioning of the model cell phone relative to the head model. Simulated SAR in near-field situations is mainly a function of the geometry of the RF current density distribution on the source model and its geometric separation from the lossy head tissue . When thUsual practice is to align a monopole cell phone antenna with the FDTD grid to avoid the stairstep effect. The head model is then rotated to the correct position relative to the cell phone. After rotation, the voxelized model must be remeshed to align the voxels with the FDTD grid. This is not a trivial task and algorithms to perform remeshing are constantly being improved.The authors have noted some unintended artifacts in voxelized models after remeshing. The first of these is grooving. Figure The jagged edges caused by grooving are not limited to surface features. Figure Grooving has not been observed with all FDTD software and even when it has been seen it has not occurred with all models. Researchers should routinely examine their models after rotation to insure grooving is not a problem.All FDTD programs must, of necessity, perform their calculations on voxelized models. However some programs use CAD models which are only converted to voxelized format after all rotation has been done. These programs avoid most coordinate transformation problem but they are not infallible. They must still convert smoothly undulating biological surfaces into rectilinear voxels. Figure Because the FDTD method calculates the electric fields at the voxel edges, the X, Y and Z-directed power components associated with a voxel are defined in different spatial locations. These components must be combined to calculate SAR in the voxel. There are three possible approaches to calculate the SAR: the 3-, 6-, and 12-field components approaches. The 12-field components approach is the most complicated but it is also the most accurate and the most appropriate from the mathematical point of view . The 12-After the SAR in every voxel is determined multiple voxels must be combined to compute the 1- or 10-gram SAR spatial averaging volumes. These normally cubic volumes become difficult to construct at the surface of a model or when the volume is constrained to a particular tissue type. The particular algorithm used to construct these volumes can influence the resultant 1- or 10-gram SAR values. However, the actual algorithm used to construct the spatial averaging volumes is usually not reported.net) are related byWhen the cell phone model is placed next to the SAM or anatomically correct model, it changes the cell phone's antenna feed-point impedance. The antenna feed-point impedance (Z), feed-point current (I) and net input power . This working group was created to develop recommended practices for determining SAR in the head via computational techniques . This stThe protocol has two parts; a benchmark validation study; and a set of common definitions, models, and reporting requirements. The benchmark validation study is underway with fifteen participants. All participants should finish the study by mid-2004 and the results should be published by early 2005. Hopefully the common definitions, models, and reporting requirements will be used in future investigations making comparison of results easier.The protocol asks all participants to report peak spatial SAR for averaging volumes that both include and exclude the pinna. The voxels comprising the pinna in the provided anatomic models are flagged so all participants will conform to one definition of the pinna. The pinna voxels are flagged by prefixing the standard tissue type with pinna-; such as pinna-skin, pinna-cartilage, and pinna-fat. The electrical properties of the flagged pinna voxels are unchanged. The IEEE Std 1528 definition for the pinna was followed and the choice of each flagged voxel was confirmed by an Ear-Nose-Throat surgeon.The Benchmark Validation Study calls for each participant to run twelve simulations: three head models, at two frequencies (835 and 1900 MHz), and in two cell phone positions (touch and tilted). The models are SAM, the Visible Human, and a seven year old Japanese male . Each moFor the two anatomically correct models, the tissue names and properties in the header file were made consistent with the definitions found on the Italian National Research Council, Institute for Applied Physics web site .Although they are not part of the benchmark validation study, SCC34/SC2/WG2 plans on releasing several new anatomically correct models in the next few months to expand the population of models available for study.A generic cell phone is described for use in all benchmark validation studies, see Figure The reference points, necessary for positioning the cell phone relative to the anatomically correct model, are also contained in the header file for each model.To aid comparison of results from all the participants, a common coordinate system was defined with origin at the acoustic output of the cell phone, see Figure The FDTD technique is called for by the P1529 draft . FDTD waThe participants are asked to report the following FDTD data for all simulations: The boundary conditions used and the minimum distance between the model and the boundary of the computational space. The time step size and the number of time steps used. The grid (voxel) size and whether the grid was homogeneous or graded. To calculate the SAR in each voxel the protocol recommends the 12-field components approach. All 1- or 10-gram spatial averaging volumes are to be constructed in accordance with IEEE C95.3, Annex E.The participants are asked to report the following SAR data for all simulations: The peak spatial SAR, both 1 g and 10 g averages, for all tissue (head plus pinna), head only, and pinna only averaging volumes and the location of the averaging cubes. The peak point value SAR and its location. A color coded SAR distribution for both 1 g and 10 g averages, in the ZY plane.For a realistic study it would be ideal to simulate the real world situation. The question that remains is: "Does a real-world cell phone keep the power or the feed-point current constant when placed next to different human beings with different head shapes and head sizes"? Unfortunately there is not a definitive answer to this question. The behavior of a mobile phone depends on the system design and the power amplifier circuits. A detailed discussion for real-world mobile telephones has to be addressed by future projects with more realistic mobile phones models for numerical simulations.For now it is important to scale the calculated SAR values to net input power and feed-point current and to present both results. The behavior of a real-world mobile phone is within the SAR range of scaling to the net input power and scaling to the feed-point current. For human health and safety considerations a worst case approach is desirable. Until further knowledge on the behavior of a real-world cell phone is available, the scaling producing the worst case result  must be taken into account.The current version of IEEE Std C95.1  does notInvestigators should inspect all models after rotation to be sure they are free of artifacts caused by meshing along the new coordinate axes. If necessary, artifacts should be manually corrected before running the simulation. Blindly accepting the output of meshing algorithms can lead to errors. All relevant data and assumptions for the computational RF dosimetry study, as discussed in section 2 "Problem areas", must be reported in such detail that the reader is able to compare the results to other studies. The names and electrical properties for all anatomically correct models should comply with those shown on the Italian National Research Council, Institute for Applied Physics web site.To facilitate broad based comparisons, new anatomically correct models should be placed in the public domain or made available for a modest fee. The number of anatomically correct models suitable for electromagnetic modelling and widely available for comparison to the SAM is still low. Because the SAM is intended to represent a significant majority of persons during normal use of wireless handsets, comparison to a large variety of anatomically correct models is desirable. It is the hope of IEEE SCC34/SC2/WG2 that consistent results in the benchmark validation will show that, by adhering to some common definitions and procedures, FDTD studies from different investigators using different anatomically correct models are comparable.Protocol for the Computational Comparison of the SAM Phantom to Anatomically Correct Models of the Human Head and this manuscript. WK, present chairman of IEEE SCC34/SC2/WG2, wrote approximately 25% of the manuscript, developed and simulated the phone model and supplied several of the figures. Both authors read and approved the final manuscript.BB, past chairman of IEEE SCC34/SC2/WG2, drafted the


Regulatory regions that function in DNA replication and gene transcription contain specific sequences that bind proteins as well as less-specific sequences in which the double helix is often easy to unwind. Progress towards predicting and characterizing regulatory regions could be accelerated by computer programs that perform a combined analysis of specific sequences and DNA unwinding properties.in vivo. The predicted region of minimal helical stability overlapped both the protein binding site and the unwound DNA region identified experimentally.Here we present PATTERNFINDER, a web server that searches DNA sequences for matches to specific or flexible patterns, and analyzes DNA helical stability. A batch mode of the program generates a tabular map of matches to multiple, different patterns. Regions flanking pattern matches can be targeted for helical stability analysis to identify sequences with a minimum free energy for DNA unwinding. As an example application, we analyzed a regulatory region of the human c-myc proto-oncogene consisting of a single-strand-specific protein binding site within a DNA region that unwindsThe PATTERNFINDER web server permits localization of known functional elements or landmarks in DNA sequences as well as prediction of potential new elements. Batch analysis of multiple patterns facilitates the annotation of DNA regulatory regions. Identifying specific pattern matches linked to DNA with low helical stability is useful in characterizing regulatory regions for transcription, replication and other processes and may predict functional DNA unwinding elements.PATTERNFINDER can be accessed freely at:  Types of cis-acting DNA elements include unique sequences that bind specific proteins, spacer elements that provide a proper distance for interaction among protein binding sites, and structural elements that determine the flexibility of the DNA sequence. The structure of DNA is crucial to genetic regulation. The double helix needs to be locally unwound at start sites for DNA replication [Regulatory regions in DNA are comprised of multiple functional elements that act in lication . Additiolication .in vitro and whose functional importance has been determined by mutational analysis in vivo. Not as well characterized, but also important, are less-specific sequences that play roles in determining DNA structure and flexibility. DNA in certain regulatory sequences has a low helical stability as revealed by hypersensitivity to single-strand-specific nucleases and by stable DNA unwinding seen in plasmid topoisomers [Little is known about functional elements in most gene regulatory regions. Annotation of regulatory regions lags far behind the annotation of features of coding regions in DNA sequence databases. Best characterized are specific sequences that bind known proteins oisomers ,4. Helicoisomers . Mutatiooisomers -9. Some oisomers ,11. Low oisomers ,10,12-14Progress towards characterizing and predicting regulatory regions could be accelerated by the availability of computer programs that perform a combined analysis of DNA sequence patterns and DNA unwinding properties. Here we present PATTERNFINDER, an easy to use web server that combines the search for specific or flexible sequence patterns with an analysis of DNA helical stability. The output of a DNA pattern search can be linked to THERMOCALC, a new program which ranks the helical stabilities of pattern matches, and an enhanced version of WEB-THERMODYN , which pWeb servers offer advantages to the user including platform-independent software that requires no installation and a friendly browser interface for data entry and display. The PATTERNFINDER web server searches DNA sequences for matches to specific or flexible patterns, and analyzes DNA helical stability within or flanking the matches. Examples of specific patterns include sequences known to be recognized by particular proteins or enzymes, or sequences complementary to oligonucleotide primers. Flexible patterns include, for example, consensus sequences containing ambiguous nucleotides and unspecified nucleotides (N's), or multiple specific patterns separated by a variable number of N's, or simple sequences that are repeated a variable number of times. The DNA pattern used in the search can be comprised of A, G, C, T, ambiguous nucleotides (IUPAC-IUB nomenclature), and N's. Tables listing abbreviations of ambiguous nucleotides  and annotations for patterns using N's and sequence repeats are provided on the home page of the web server . MismatcUsers input the name of the DNA molecule, the shape (linear or circular) and the nucleotide sequence. The sequence can be uploaded from a computer file (≤40 kb) in a various user-selected formats . Alternatively, the sequence can be pasted (≤30 kb) or typed into the DNA Sequence Query window of the browser. Acceptable characters are A, G, C, and T. Integers used for sequence numbering are permitted. Under the "Analysis Parameters" the user can select to search the whole DNA molecule or a part of the molecule from one position to another. Both DNA strands are searched by default in order to find matches to asymmetric patterns. If desired, the search can be restricted to only the upper  or lower  strand by selecting the appropriate checkbox.The output displays the molecule name, size in bp, and size of the region analyzed, and the DNA sequence of the upper and lower strands. Note that all DNA sequences in the output are displayed 5'->3' regardless of strand. This is useful for creating sequence alignments. The total number of hits and the pattern query are displayed. Tabulated are the position, strand (+ or -) and sequence of all pattern matches. The data are also output to an ASCII text file for printing, archiving and for any further processing .A BATCH version of PATTERNFINDER is included to search simultaneously for multiple patterns in a DNA sequence. Entries are pasted or typed into the BATCH query window, one per line. Entries take the form of "Pattern name, Pattern expression, Maximum span". A table of pattern names and expressions that were entered is included in the output. The tabular output of hits is similar to that for PATTERNFINDER (above) except that it also includes the names of patterns that are hit as well as those that are not hit. The ASCII output provides a tabular map of the positions and strands of different pattern matches found in the DNA sequence. In addition to flexible sequence patterns, BATCH lists can include a variety of specific DNA elements and landmarks such as protein binding sequences, restriction sites and oligonucleotide primers.Low helical stability of DNA is often a property of regulatory sequences ,5,6. A uDefault values for temperature and salt concentration  are presPATTERNFINDER was designed to be fast and user friendly. No password restriction or registration is required. All entries are error checked before processing and, if errors exist, the user is prompted with specific suggestions to correct the entries. The output is returned directly to the browser in real time, as opposed to a return via e-mail at a later time. The home page of the web server provides a DEMO link  containicis to stimulate c-myc promoter activity and a 42 bp sequence becomes single-stranded in vivo (HeLa cells) when the gene is actively transcribed [Ava I restriction enzyme site. PATTERNFINDER was used to search for specific Ava I sites and any ("n") 36 bp sequences in a 42 bp segment  with THERMOCALC enabled to rank the DNA helical stabilities of the segments. The search was restricted to the regulatory region from positions 1 to 2500 . The output is shown in Fig. Ava I sites found and the helical stability ranks  of the 42 bp segments are displayed. The site with rank 1 has the lowest free energy and begins at position 789 on the + strand. As shown below, this predicted region of low helical stability contains the single-stranded DNA region identified experimentally in the FUSE.The 5' regulatory region of the c-myc gene resides in the first 2500 bp of an ~11 kb DNA sequence. The sequence contains multiple elements that regulate transcription and replication ,12, but nscribed . The sinAva I site, and sequences of the -10 regions at the P1 and P2 promoters for c-myc transcription [Ava I sites, providing an informative tabular map of functional elements and landmarks in the regulatory region.To map the locations of other DNA elements in the 5' regulatory region, the BATCH version of PATTERNFINDER was used to search simultaneously for multiple, specific sequences. The patterns included two separate sequences that interact with the FUSE binding protein (FBP) in domains 3 and 4 , the Avain vivo (FUSE ssDNA), reflecting a reduced helical stability intrinsic to DNA at FUSE. A separate WEB-THERMODYN analysis of the entire 2500 bp regulatory region identified the identical sequence as the ΔG Min, indicating that the low helical stability at FUSE is unique within the entire 5' regulatory region. The location of the ΔG Min sequence  to the FBP_3 site  and retrieves the 200 nt sequences 5' and 3' for the WEB-THERMODYN analysis . Fig. The PATTERNFINDER web server provides a convenient means to search DNA regulatory regions for specific or flexible sequence patterns and to identify flanking sequences that are easy to unwind. Specific sequence searches permit localization of known protein binding sites and sequence landmarks such as restriction sites and oligonucleotide primers. The capacity to perform BATCH analysis of multiple patterns and generate accurate tabular maps facilitates the annotation of DNA regulatory regions. The latter lags far behind the annotation of protein coding regions in public sequence databases, and individual laboratories must usually draw on their own annotation resources in order to design experiments. The utility of PATTERNFINDER in annotation of known DNA elements can facilitate the design of experiments to further characterize regulatory regions. New DNA elements with potential functions can be predicted using flexible patterns such as consensus sequences containing ambiguous nucleotides and N's as well as using multiple motifs with fixed or variable spacing. Sequences found are displayed 5'->3' regardless of the DNA strand which is useful for creating sequence alignments for position weight matrices and for identifying evolutionary conserved sequences. More sophisticated pattern match and discovery methods exist  and HyperText Markup Language (HTML) and uses the Common Gateway Interface (CGI) for input and output to a web browser. The DNA sequence of the human c-myc gene was obtained from GenBank (accession number: X00364). The average ΔG for all windows was determined by analysis of the WEB-THERMODYN output using spreadsheet software.YH wrote the program code for PATTERNFINDER and established a web site. DK served as scientific advisor and participated in the program design and development.


Questionnaires are, by far, the most common method of data collection in the world. There is hardly anyone who has not been asked to answer questions from one form of questionnaire or another. Familiarity with the method may, on the other hand, give the impression that they are easy to develop and that their findings are unproblematic. For those who construct questionnaires, this is a laborious, time-consuming, artful exercise which requires considerable skills and expertise. In quantitative research, the validity and reliability of the instruments are crucial to the credibility of the findings. The rigorous development and testing of questionnaires are, therefore, essential for producing valid and reliable findings. Yet, as the authors of this book point out, "most text books offer minimal, if any guidance about pretesting methods".Since the mid-1930's we have learnt a lot about how to make survey instruments, in particular questionnaires, more rigorous and user friendly. Much of this progress was achieved in the last two decades. This book represents this body of work. It reviews key research studies which have evaluated the various techniques and strategies used to enhance the validity and reliability of survey questionnaires.The idea of this 'monograph'  was conceived at the Spring 1999 Questionnaire Evaluation Standards International Work Group meeting in London. The chapters evolved out of selected abstracts submitted to the International Conference on Questionnaire Development, Evaluation and Testing Methods in 2002 in South Carolina. As such they represent the latest thinking of an international array of experts on this topic.The book is divided into the following seven parts: 'cognitive interviews', 'supplements to conventional pretests', 'experiments', 'statistical modelling', 'mode of administration', 'special populations' and 'multimethod applications'. The twenty five chapters go well beyond conventional testing methods and reviews the different ways which can be used to evaluate survey questionnaires. Additionally the book sets the agenda for future research on this topic. It makes a significant contribution to the development and testing of questionnaires.The book is well sign-posted and the style is clear. I found it both very informative and interesting. It should appeal to those who construct questionnaires for the first time as well as to more experienced researchers. It is likely to become a reference text which research students, at any level, would find it hard to do without.


Some of us, when awake in the middle of the night, feel an urge to visit the kitchen. This could explain results of previous studies that have shown a link between short sleep duration and high body mass index (BMI). But a study by Emmanuel Mignot and colleagues suggests that it's not just the additional snacking opportunities that make short sleepers more likely to be overweight.Intrigued by the connection between sleep and BMI, and by recent studies showing that sleep deprivation in laboratory settings can cause a decrease in serum levels of leptin, a hormone known to control appetite, Emmanuel Mignot and colleagues set out to study the levels of various hormones known to regulate appetite and energy expenditure under “real life” conditions.They took advantage of the Wisconsin Sleep Cohort Study, an ongoing longitudinal study of sleep habits and disorders in the general population. The study began in 1989, when researchers mailed state employees aged 30–60 years a survey on sleep habits, health, and demographics. Mail surveys were repeated at 5-year intervals, and some of the respondents were recruited to sleep a night in the laboratory and undergo various tests. A number of participants were also asked to keep a sleep diary for 6 days. The study has already shown connections between sleep apnea and hypertension, and between menopause and sleep-disordered breathing.For their study, Mignot and colleagues measured sleep duration , BMI, and pre-breakfast blood hormone levels in 1,024 participants. Consistent with previous studies, they found that in individuals who sleep less than 8 hours , BMI was inversely proportional to sleep duration. In addition, short sleep was associated with low leptin and high ghrelin levels (ghrelin is a hormone thought to stimulate food intake).These hormonal differences are likely to increase appetite, which could be responsible for the increased BMI in short sleepers.These findings could explain, at least in part, why societies in which excess calories are much easier to come by than a good night's sleep are more prone to obesity. Mignot and colleagues plan to test this in intervention studies where they make people sleep more and measure the effects on body mass. “Good sleep, healthy eating habits, and regular exercise each may have important roles in fighting obesity in modern society,” suggests Mignot.


The Faculty of Medical Sciences, University of the West Indies first implemented the Objective Structured Clinical Examination (OSCE) in the final MB Examination in Medicine and Therapeutics during the 2000–2001 academic year. Simultaneously, the Child Health Department initiated faculty and student training, and instituted the OSCE as an assessment instrument during the Child Health (Paediatric) clerkship in year 5. The study set out to explore student acceptance of the OSCE as part of an evaluation of the Child Health clerkship.A self-administered questionnaire was completed by successive groups of students immediately after the OSCE at the end of each clerkship rotation. Main outcome measures were student perception of examination attributes, which included the quality of instructions and organisation, the quality of performance, authenticity and transparency of the process, and usefulness of the OSCE as an assessment instrument compared to other formats.There was overwhelming acceptance of the OSCE in Child Health with respect to the comprehensiveness (90%), transparency (87%), fairness (70%) and authenticity of the required tasks (58–78%). However, students felt that it was a strong anxiety-producing experience. And concerns were expressed regarding the ambiguity of some questions and inadequacy of time for expected tasks.Student feedback was invaluable in influencing faculty teaching, curriculum direction and appreciation of student opinion. Further psychometric evaluation will strengthen the development of the OSCE. The assessment of student's clinical competence is of paramount importance, and there are several means of evaluating student performance in medical examinations ,2. The OThe University of the West Indies was established in 1948 as a medical college of the University of London, which granted external degrees to those who successfully completed the course [th year, during the 1999–2000 academic year. It was felt timely in order to (a) direct and motivate student learning in areas not previously assessed in the 'traditional' curriculum, (b) verify students' competence in fundamental paediatric clinical skills, and (c) provide a forum for feedback to students on their strengths and weaknesses in clinical skills. It was thought that it would enhance faculty and student acceptance of this new assessment tool and promote faculty training for the newly introduced final OSCE examination.The Section of Child Health, Mona, Jamaica, implemented the OSCE examination as an end-of clerkship assessment for students in their 5In the absence of any previous information from this institution, the study was designed to evaluate student overall perception of the end-of-clerkship OSCE, determine student acceptability of the process and provide feedback to enhance further development of the assessment.The OSCE comprised a circuit of thirteen stations, which involved completion of a number of tasks such as examination of a system, eliciting a focussed history, counselling or communicating a problem, performing a procedure and problem-solving oriented around patient and laboratory data, and photographic material Figure . The areA standardised technique of marking was used and student performance was assessed by criterion reference for each station. Criterion-based scoring was used, with each checklist item scored as 0 , or 1–2 (correct or adequate).Face and content validity of each checklist was established by review and consensus by a core group of senior paediatricians. Stations were first selected to represent the curricular goals and objectives and to reflect authentic clinical situations. Checklists were designed to include the features thought to be most important by the development committee. Through discussions, consensus was achieved on the checklist items and structure.The study was conducted during the period July 2001 to December 2002. Five groups of students participated in the process, during their respective clerkship rotations. Student groups had at least two briefing sessions before the OSCE, and included an orientation about the examination process  and a review of commonly assessed competences. They were also apprised of the valuable contribution they could make towards improving the assessment and encouraged to participate in the evaluation.A cross-sectional survey using a 32-item self-administered questionnaire was completed at the end of each OSCE . StudentParticipation was on a voluntary basis and students were assured that those who declined involvement in the survey would not be penalised. The Curricular Affairs Section handled the administration and analysis of the questionnaires. Ethical approval was received from the University Hospital of the West Indies/University of the West Indies Faculty of Medical Sciences Ethics Committee. Following completion of the questionnaire, an OSCE review session was conducted with the students for feedback and teaching purposes, at the end of the clerkship. Students were given the opportunity to review their individual performances at the respective stations. Examiner evaluations were also used in the feedback process.Data were collated and descriptive and non-parametric tests applied using Stata version7 . Basic sEighty-one students responded to the questionnaire, representing 92 % (81/88) of those who completed the Clerkship.The majority of students agreed that the OSCE was comprehensive and covered a wide range of knowledge (95%) and clinical competencies (86%) in Child Health. Three quarters (78%) also agreed that the assessment process helped to identify weaknesses and gaps in their competencies Table .Most (73–82%) felt that the exam was well administered, and that the stations were arranged in an organised and well-sequenced order.Students believed that the assessment was fair (68%). Fifty-three percent were aware of the level of information required at each station, yet 28% felt that the examination process minimized their chances of failing.Students found the OSCE to be intimidating (48%) and more stressful (35%) than other assessment formats to which they were previously exposed. And most (70%) felt that they needed more time to complete the stations.The majority of students felt they were well oriented about the exam and that the required tasks were consistent with the actual curriculum that they were taught. They also felt that the process was fair but were not as satisfied with the time allocation for each station Table .Most saw the OSCE as a useful learning experience and that the content reflected real life situations in Child Health. More than half of the students were satisfied with the conduct, organisation and administration of the OSCE.Although half of the students believed that the scores were standardised, they were unsure whether their scores were an actual reflection of their paediatric clinical skills Table . StudentStudents were asked to rate the following assessment instruments to which they had been exposed . A likert scale was used to assess each according to the evaluative labels Table .Thirty-two percent of students felt that the clerkship rating was the easiest, while 48% rated MCQ as a more difficult form of assessment. The OSCE was overwhelmingly considered the fairest assessment format (80%), and essays (68%) to a lesser extent. OSCE (60%) and clerkship ratings (62%) were considered the most useful learning experiences. Compared to the other assessment formats, 52% considered that the OSCE should be used most in the clinical years.Students were asked follow-up questions related to positive and negative aspects of the OSCE and suggestions for improvement. The open-ended responses were grouped by thematic content.Among the positive attributes of the OSCE, students re-affirmed that the assessment was comprehensive (44 comments) and that it was an objective and fair process (43 comments). Some indicated that the opportunity for feedback helped to motivate them and drive the learning process (21 comments).Students felt that the time allocated to perform expected tasks was insufficient (36 comments), and that the procedure was stressful (18 comments) and tiring (13 comments). Technical problems (28 comments) included unclear instructions, inadequate time provision and instructions between stations and detention of some candidates at stations by examiners.Suggestions for improvement included increasing the duration of stations (29 comments), ensuring clear instructions (8 comments) and having more realistic expectations of students for the expected tasks. A few students wished to have more training with the OSCE and suggested that the examination should be videotaped to increase objectivity and permit review.Students overwhelmingly perceived that the OSCE in Child Health had good construct validity. This was demonstrated by the favourable responses concerning transparency and fairness of the examination process, and the authenticity of the required tasks per station. Excellent levels of acceptance of the OSCE by students have been previously described in the literature -14. TheySeveral felt that the examination was stressful and intimidating, yet paradoxically some students perceived it as an enjoyable, practical experience. Studies surveying student attitudes during the OSCE have documented that the OSCE can be a strong anxiety-producing experience, and that the level of anxiety changes little as students progress through the examination .It is well recognised that assessment is a catalyst for both curriculum change and student learning. The students recognised the value of the instrument for formative evaluation. In addition, as many medical schools have adopted a student-centred approach to medical education, greater student participation in quality assurance exercises must be encouraged. Students perceived the OSCE to be fairer than any other assessment format to which they were exposed. The findings were somewhat similar to the views of students at Newcastle medical school . AlthougThey offered constructive criticism of the structure and organisation of the process. At some stations they felt that the instructions were ambiguous and that the time allocation was inadequate for the expected tasks. The feedback was invaluable and facilitated a critical review and modification of the station content and conduct of the examination over time. Faculty perceived that the concerns about time allocation per station and the degree of stress expressed by the students were due to inadequate preparation for the examination, particularly in competences not previously assessed in the 'traditional' examination.The high student response rate has helped to ensure that the findings presented are a valid representation of student opinion. Students have traditionally viewed the end-of-clerkship assessment as a 'high-stake' examination and also perceive it as predictive of their performance at their final MB examination. Student perception of the OSCE however, may have been influenced by anxiety and lack of confidence associated with a new assessment. The responses may also have been affected by the timing of the inquiry (immediately after the examination); hence student stress and fatigue should be taken into consideration. Whereas the high response rate ensured that the views were reasonable representative of the students, differences in assessors could have influenced the interpretation of the results of open-ended responses.Implementing the OSCE in Child Health at the University of the West Indies, Jamaica has been challenging, however student participation in the evaluation and their overall acceptance of the instrument have been encouraging. Feedback from students and faculty has been useful in effecting improvements to the process and greater emphasis has been placed on the teaching and evaluation of history taking, communication and technical competencies. It is also sending a clear message to students that the achievement of overall competence is imperative to clinical practice in the current environment. Ultimately, these provide the loop necessary to drive the continuum of curriculum development. This has been timely considering that the Faculty of Medical Sciences, Jamaica is undergoing significant reform . FurtherIn summary, the findings highlight the need for student participation in the development of new assessment tools in medical curricula. Student acceptance will be more favourable for assessment formats that they perceive to be transparent, authentic and valid. 'Traditional' medical curricula must be responsive to global paradigm shifts in undergraduate medical education.The authors declare that they have no competing interests.RP conceptualised the study; developed the proposal, coordinated the conduct of the project, completed initial data entry and analysis, and wrote the report. AW participated in the design of the study, coordinated the conduct of the project, performed the statistical analysis, and assisted in writing the report. MB was the main organizer of the clerkship OSCE, and assisted in editing the final report. MBr and CC participated in overall supervision of project and revision of report. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Caenorhabditis elegans is widely used for the genetic analysis of neuronal cell biology, development, and behavior. Because traditional methods for evaluating behavioral phenotypes are qualitative and imprecise, there is a need for tools that allow quantitation and standardization of C. elegans behavioral assays.The nematode C. elegans morphology and behavior. Using this system, it is possible to record the behavior of individual nematodes over long time periods and quantify 144 specific phenotypic parameters.Here we describe a tracking and imaging system for the automated analysis of C. elegans phenotypic information.These tools for phenotypic analysis will provide reliable, comprehensive scoring of a wide range of behavioral abnormalities, and will make it possible to standardize assays such that behavioral data from different labs can readily be compared. In addition, this system will facilitate high-throughput collection of phenotypic data that can ultimately be used to generate a comprehensive database of wschafer@ucsd.edu.The hardware configuration and software for the system are available from  Caenorhabditis elegans is among the most widely studied genetically-tractable experimental organisms. C. elegans is a soil-dwelling animal with a relatively simple and extremely well characterized anatomy; an adult hermaphrodite, for example, contains exactly 959 somatic cells, each with an identified position, morphology and cell lineage. Because of its short generation time, amenability to germline transformation, and completely sequence genome, it is ideally suited for classical and molecular genetic analysis. In particular, since the C. elegans nervous system is simple and well-characterized (the identity and connectivity of each neuron is known), it has become a facile model for studying the molecular basis for nervous system function. Robust behavioral phenotypes have been described for many C. elegans behaviors, including locomotion, egg-laying, mating and feeding, and these phenotypes have proven extremely useful for the genetic dissection of key aspects of neuronal function such as synaptic release, sensory transduction, and neuromuscular signalling [The nematode gnalling .C. elegans has been the lack of quantitative methods for the evaluation of behavioral phenotypes. For example, the phenotypes of many behavioral mutants, even those defective in key aspects of neuronal signal transduction, appear subtle to a real-time human observer, and are difficult to assay without time and labor-intensive analysis of video recordings [C. elegans behavioral studies  generalC. elegans behavioral patterns. Using this system, it is possible to record the behavior of individual animals at high magnification over long time periods and to simultaneously quantify a large number of behaviorally-relevant features for subsequent analysis. This system has wide applications for the dissection of complex C. elegans behaviors, and will also make it possible to comprehensively classify the behavioral patterns of C. elegans mutants on a genome-wide scale. By making this system widely available to C. elegans neuroscientists, we intend to define a software architecture that can be continually optimized and upgraded to incorporate new parameters that are useful to worm researchers, as well as a hardware platform that can be expanded to provide additional mechanical capabilities for the research community.To address these problems, we have developed an automated tracking and image analysis system for the quantification of C. elegans are small (1 mm) animals which, in the laboratory, are normally cultured on agar plates covered with a lawn of the common laboratory bacterium Escherichia coli. Nematodes move using an approximately sinusoidal wave motion that is propagated along the anterior/posterior axis in the dorsal/ventral plane. On an agar plate, the animal will normally lie on either its left or right lateral surface, making the waveform associated with movement visible from above. When crawling at maximum speed, an adult nematode travels at a rate of approximately 500 μm/s; thus, under the relatively high magnification (40–50 X) required to measure detailed features of body posture the worm can quickly crawl outside the field of view. It is therefore necessary to incorporate into the imaging system a motorized stage that can automatically follow the animal's movements and keep it in the microscope's visual field.To effectively capture the locomotion behavior of a freely-moving worm, it is necessary to acquire a sequence of images from which the animal's position, speed and body posture at any given point in time can be derived. The tracking system described here consists of (i) a Nikon SMZ-800 microscope with a stereoscopic zoom, for visualizing the animals; (ii) a Daedal motorized stage controlled by a National Instruments 4-axis controller, for maintaining the animal in the visual field; (iii) a Cohu monochrome analog CCD camera, for image acquisition; (iv) a Windows computer (PC) with a National Instruments video acquisition board, for tracking and image analysis Figure . An optiBriefly, the software for the system consists of four basic modules. The first module, called the tracker, allows the system to follow the worm as it crawls around the plate by directing the movements of a motorized stage to maintain the animal in the center of the field of view. As the video acquisition board acquires digital images from the microscope field, the tracker program identifies the animal from each acquired image based on 1. size of the objective isolated from background and 2. the direction of the animal crawling in previous frame if more than two objectives are found Based on the coordinates of the animal's centroid within the field of view, the tracker directs the movements of the stage to recenter the animal in the visual field when animals approach the edge of the image frame. The program then saves an image (460 × 380) of the worm containing visual frame , the position of the animal within the field of view, the position of the stage, the time the image was captured, and other information crucial for behavioral analysis. These data are saved into the widely used .avi multimedia format, with a MPEG-4 filter to significantly compress the size of data. Null images are not saved into the .avi format, and the user is notified of the null frame. The highest frame rate with which the tracker can perform these operations with our current hardware setting is 30 frame/sec.Next, the system contains a module  that processes the raw images to simplify parameter estimation. First, the grayscale image is thresholded and converted to a binary image representing the worm outline. The image is further simplified by generating a morphological skeleton along the midline of each binary image and then distributing 30 skeleton points along this skeleton. A third module  then orders the backbone points from head to tail. To distinguish head and tail, minor user input is required to achieve 100% accuracy. In wild type, this user input (which involves identifying the head with a mouse click) is only required on 1% of the frames. Otherwise, all image processing is completely automated.Thus, for each raw acquired image, the system generates 4 representations of the animal Figure  of increTo obtain this information, the system has a fourth, parameter estimation module  that measures specific features based on grey/binary image, centroid, or skeleton point analysis that define important parameters related to locomotion or morphology. Broadly speaking, these include measurements of morphology, body posture, movement, and locomotion waveform. Morphological features include measurements of size, length, transparency, and elongation/eccentricity. Body posture features include measurements of body curvature as well as the occurrence of specific postures such as coils and omega turns. Movement features include centroid-based measurements of global speed and direction, skeleton point-based measures of local movement, and the occurrence of directional reversals and large turns. Waveform features include measurements of the frequency and amplitude of body bends, the flex of the animal's body during the locomotion wave, and the frequency and magnitude of foraging movements by the animal's nose. A total of 59 distinct features Table  are measC. elegans.The software is available in a PC version (compiled and benchmarked on a PC with 1 G Hz Pentium-III running Windows 2000 or XP). Software is written with C/C++, Labview 7.0 and Matlab (release 13), and complied with NI LabWindow 7.0. Installation disk and dataset samples are available upon request for non-profit academic usage with a license fee  can be identified with relatively high reliability using the system [We describe here a prototype for a standard, open-source system for automated phenotypic analysis of e system . In addie system . Other sC. elegans phenotypic database that could be used to explore the clustering and relative similarities of mutant phenotypes.With appropriate controls, a standardized phenotyping system also makes it possible to compare behavioral data collected by different researchers in different labs with greater precision than is possible using qualitative observer-driven approaches. In particular, a computerized system makes it possible to comprehensively assay multiple aspects of behavior simultaneously, yielding a complex phenotypic signature that can be used for bioinformatic studies . In the Hardware listClick here for fileAlgorithms for feature measurementsClick here for fileCodesClick here for fileFile listClick here for file


This motif is missing from the spike protein of the severe acute respiratory syndrome-coronavirus (SARS-CoV), resulting in high level of surface expression of the spike protein when it is expressed on its own in vitro and in vivo. The 3a protein, which contains a tyrosine-dependent sorting signal in its cytoplasmic domain, is expressed on the cell surface and can undergo internalization. In addition, 3a can bind to the spike protein and through this interaction, it may be able to cause the spike protein to become internalized, resulting in a decrease in its surface expression.It has been shown that the severe acute respiratory syndrome-coronavirus genome contains open reading frames that encode for proteins with no homologue in other coronaviruses. One of them is the 3a protein, which is expressed during infection The effects of 3a on the internalization of cell surface spike protein can be examined biochemically and the significance of the interplay between these two viral proteins during viral infection can be studied using reverse genetics methodology.If this hypothesis is proven, it will indicate that the severe acute respiratory syndrome-coronavirus modulates the surface expression of the spike protein via a different mechanism from other coronaviruses. The interaction between 3a and S, which are expressed from separate subgenomic RNA, would be important for controlling the trafficking properties of S. The cell surface expression of S in infected cells significantly impacts viral assembly, viral spread and viral pathogenesis. Modulation by this unique pathway could confer certain advantages during the replication of the severe acute respiratory syndrome-coronavirus. A novel coronavirus was identified as the aetiological agent of SARS [The recent severe acute respiratory syndrome (SARS) epidemic, which affected over 30 countries, resulted in more than 8000 cases of infection and more than 800 fatalities  declare that they have no competing interests.Yee-Joo Tan is responsible for the entire manuscript.


The purpose of this study was to evaluate the individualized and standardized quality of life (QL) and psychological distress of patients participating in a Phase I trial of the novel therapeutic reovirus (Reolysin).16 patients with incurable metastatic cancer were interviewed prior to being accepted into the phase I trial with a semi-structured expectations interview, the Schedule for the Evaluation of Individual Quality of Life – Direct Weighting (SEIQoL-DW), the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30), the Brief Symptom Inventory (BSI), the Beck Depression Inventory (BDI), and the Spiritual Health Inventory (SHI).Patients were able to complete all measures. They felt hopeful and excited about the trial, with about two thirds hoping for disease regression and one third hoping for a cure. The most commonly spontaneously nominated areas of QL were family relationships, activities and friends, and the overall SEIQoL mean index score was 69. Health was nominated by only 38% of the sample. Scores on the SEIQoL were correlated with global QL on the EORTC QLQ C-30. Scores on the BDI and BSI were lower than reported for similar populations, and on the SHI scores were similar to other samples. Global QL on the EORTC QLQ C-30 and depression scores were associated with time to death in the nine patients who had died at the time of writing.Individualized QL is easy to assess in seriously ill cancer patients, provides useful information relative to each individual, and is related to standard QL measures. Repeated assessment of individualized QL of patients in Phase I trials would be a useful addition to the research. As health care professionals begin to understand the importance of quality of life (QL) and emotional and social well-being in the treatment and progression of cancer, it has become standard practice, and in fact has been described as a bioethical imperative, to include QL assessment in all oncology clinical trials -7. This We report here on the initial QL of patients enrolled in the Reolysin Phase I trial, the first clinical usage of the reovirus in humans with cancer. The reovirus as a possible treatment for cancer attracted a great deal of media attention when the journal Science, in 1998, published very encouraging results showing tumor regression in animal models . FurtherDue to the nature of the population under study, it seemed especially important to use instrumentation that was flexible enough to allow these very ill patients to identify what was important to each of them as individuals, as well as to collect data from standardized instruments that would allow direct comparisons with other patient populations. Thus, a battery of tests to measure both individualized and standardized QL, distress levels, and spirituality was selected. Important aspects of QL were measured, including physical, psychological, emotional, social, and spiritual functioning, with emphasis on mood states and psychopathology. Expectations and hopes regarding participation in the trial were also elicited during a semi-structured interview.The specific instruments used included an interview-based subjective measure of QL, the Schedule for the Evaluation of Individual Quality of Life – Direct Weighting (SEIQoL – DW). The SEIIn past studies, the most important areas of QL that patients on Phase I clinical trials identified were equally health and family . HoweverThe other QL questionnaire used in this study is the very widely used European Organization of Research and Treatment of Cancer (EORTC) Quality of life Questionnaire (QLQ C-30), a 30 item standardized self-administered questionnaire that taps into important domains of QL, including physical, psychological, emotional and social functioning. This was included to allow comparisons with a well-known and validated standardized quality of life questionnaire with set domains and subscale scores. Another study at our Centre directly compared the SEIQoL to the EORTC QLQ C-30 in a sample of early stage prostate cancer patients . The autThe area of spirituality was also of interest in this population of very ill people, as issues of death and dying are often accompanied by questioning in the realm of spirituality. The Spiritual Health Inventory  was usedPrevious work with patients in Phase I trials has found that patients' expectations going into trials are generally more optimistic than oncologists'. Patients with incurable malignancy in a Phase I trial estimated a greater potential for benefit from the experimental therapy than did oncologists . They alThe purpose of the current study was to investigate individualized QL in a group of patients with metastatic incurable cancer participating in a Phase I trial of a highly media lauded new therapeutic, and investigate their expectations regarding the trial. Areas of importance and SEIQoL Index scores for these patients will be compared with those of patients in other studies, and compared to their own scores on the standardized QL and psychological measures assessed. Relationships between the different measures will also be explored.2, and accessible and measurable for delivery of an intralesional injection. Patients were required to have a life expectancy of at least 12 weeks and a ECOG performance status of ≤ 3 and must not have received active cancer treatment for least 21 days prior to entrance onto the trial. Adequate organ reserve in terms of bone marrow, hepatic, renal and cardiac functions was required. Patients on immunosuppressive therapy or alternative/complimentary/unproven systemic or local therapies were ineligible.Patients were recruited as specified in the protocol: "A Phase I Clinical Trial to Evaluate Dose Limiting Toxicity and Maximum Tolerated Dose of Intralesional Administration of REOLYSIN for the Treatment of Histologically Confirmed Malignancies". All patients had histologically confirmed evaluable palpable tumors of any histological type that had failed to improve on existing standard therapy. The injectable lesion was required to be between 1 and 10 cmAfter patients had been referred to the above mentioned trial, but prior to being definitively accepted (pending complete assessment of inclusion/exclusion criteria), patients met with a psychologist (LC) for the assessment protocol. At that time they were interviewed concerning their expectations about their health, both without any further conventional treatment and with the potential experimental treatment. They then completed the interview-based individualized QL interview, followed by the quantitative questionnaires as detailed below. All 16 patients followed the same procedures.Demographic information including age, education, marital status, occupation and current employment status was obtained on a form created for this study. Medical history including type of illness, dates of first diagnosis and subsequent relapses and site of metastases were collected, and later verified from patient charts.Patients were asked three questions in a semi-structured interview: How do you feel about potentially being a part of this trial? How do you see your disease progressing without any further conventional treatment? Once on the trial, how do you see your disease progressing? Short answers to these questions were recorded verbatim at the time of the interview.This schedule takes the form of a semi-structured interview, in which the investigator first describes quality of life as an individually defined construct, then elicits from the patient their own five most important domains of QL, rather than asking them about pre-set areas. Patients are asked to think of what areas of life determine their own happiness, or quality of life. After patients identify their most important domains ("cues"), they rate the quality of each domain currently in their lives by drawing a bar graph on a 100 mm scale from worst possible to best possible. This is called the "level" of the cue. Finally, they rate how important each domain is overall in their lives using a direct weighting disk. This disk consists of five overlapping different colored laminated disks that can be rotated around a central point to form a pie chart. Each piece represents one of the five chosen domains. The patient manipulates the disk until the proportion of each piece making up the pie represents the relative importance of that domain in their lives ("weight"). The weight value of each cue is calculated by determining the percentage of the overall pie that each piece covers by reading off a larger backing disk that is labeled with a 0–100 scale around the pie. Then by multiplying the level of each domain by its weight and summing the product for all five items, a summary score representing overall subjective quality of life can be calculated. This is called the SEIQoL Index Score. More detailed descriptions of the procedures are available in other publications ,18,24.This 30-item questionnaire includes five functional domains of quality of life: physical function (5 items), emotional function (4 items), cognitive function (2 items), social function (2 items) and role function (2 items). There are also several symptom scales: fatigue (3 items), pain (2 items), nausea and vomiting (2 items), and one item each for dyspnea, sleep disturbance, appetite, constipation, diarrhea and financial difficulties. Finally, two items assess global quality of life. The questionnaire shows high internal consistency, and overall reliability and validity of the survey has been demonstrated in international clinical trials with cancer patients of heterogeneous diagnoses including lung cancer .This 21-item questionnaire gives a global score on depressive symptoms, and norms are available for many different populations, including cancer patients. Higher scores represent more depressive symptoms.A general mental health measure of 58 questions which provides scores on nine dimensions of psychopathology or psychological distress: somatization, obsessive-compulsive, interpersonal sensitivity, depression, anxiety, hostility, phobic anxiety, paranoid ideation, and psychoticism. Three global scores can be calculated: the Global Severity Index (GSI), the Positive Symptom Total (PST) and the Positive Symptom Distress Index (PSDI). The GSI was used as the global score in this study.This instruments defines spiritual health as the capacity to transcend oneself and meet three basic needs; the need for self-acceptance, the need for relationships with others and/or a supreme being, and the need for hope. These three factors accounted for 71% of the variance in validity studies. A single total score is calculated by summing all items. The possible range of scores is 31–155, with higher scores indicating higher levels of spiritual health. The 31-item questionnaire takes very little time to complete.Demographic characteristics and disease variables of participants are presented in Table Interviews were conducted with all of the 16 patients. To the question "How do you see your disease progressing without further conventional treatment?", nine of the patients indicated they felt it would get worse and they would eventually die of their disease. This was stated in different ways: Nothing else left...getting gradually worse...terminal – could be months, could be years...wouldn't go very well. The other seven patients offered more hopeful or neutral prognoses: don't think about it – stay positive...still hopeful and optimistic...other things available still...would still take chemo, hope it would work...wouldn't ever give up on hope...faith...not sure, unknown. When asked how they felt about being in the trial, most patients indicated feeling excited, fortunate, grateful and hopeful. One indicated that they felt scared as well as hopeful, not knowing what to expect, and one said they felt like a guinea pig. To the question "Once on the trial, how do you see your disease progressing?", ten of the patients mentioned hoping for the tumor to shrink, for a remission, or for some extension of life. Five patients mentioned hoping for a cure, to be cancer free. One patient just mentioned hoping to help others, and four others said that although they were hoping for personal benefit, if it didn't help them it might help others in the future. In general, patients were hopeful yet philosophical about the trial. The 54-year old woman with melanoma captured these sentiments with her comments: It feels hopeful. Maybe it won't help me – I won't be disappointed. It might help others down the road. It's on the frontier – exciting. If it works it's a bonus. I don't totally expect anything. It may extend life. Just day by day carry on.Quality of life scores on the EORTC QLQ C-30 are presented in Table Correlations between subscales are presented in Table 6 ; "I actively participate in decisions concerning my health care" (4.5); "I believe my nurses and doctors care about me" (4.3); "My life has a purpose" (4.2); "I feel accepted and forgiven despite some past actions" (4.0). The lowest scores were on the following items: "I wonder if God is angry with me" (1.1); "I feel angry with others" (1.3); "I feel a need to be forgiven for some of my thoughts and feelings" (1.7); "I worry about life after death" (1.9); "I feel angry with myself" (1.9); and "I feel out of touch with my own feelings and with others" (1.9).All 16 patients completed the SEIQoL. The average time taken was 13.5 minutes, range 5–30 minutes. Areas identified by patients as the most important in determining their overall quality of life are presented in Table 2 values ranged from .19–.76, median .47, mean .50. The highest R2 value was for the first cue generated, and the lowest value was associated with the fourth cue. This is much lower than in previous reports [The internal validity of each of the cues was assessed by performing regressions of the combination of each cue level and its weight onto the total index scores. The resulting R reports ,17 and mTwo examples of cues, cue levels and cue weights are illustrated in Figures Correlations between the SEIQoL index and scores on the other measures are presented in Table 6 , and the EORTC global QL score was positively correlated  with time to death. This indicates an association between higher levels of depression and lower global QL at the time of the interview, and fewer days to death.This study is the first to use the SEIQoL-DW instrument to assess individualized QL in a population of patients with advanced cancer participating in a Phase I clinical trial. Of note is that the instrument was easy to use in this population and acceptable even to those patients who were quite ill. Replication of the wide range of individual differences in the cues chosen and the weights associated with each cue was seen in this group. The areas of QL that were nominated by patients as the most important factors in the determination of their overall QL were primarily family relationships, the ability to participate in pleasurable activities, and friendships. Only 38% of this sample mentioned health or health-related domains such as mobility, fitness and energy as one of the five cues. This is in contrast to other samples of cancer patients where over 70% of patients nominated health as an important domain. For example, health was nominated by 73% of cancer patients in phase I trials (not necessarily advanced cancer) , 87% of In terms of the index scores for other illness populations, patients prior to hip arthroplasty scored 59, after the surgery scores increased to 69 , on par Another indication of the construct validity of the SEIQoL-DW is its high correlation to global QL scores on the EORTC QLQ C-30. This speaks to the validity of the self-generated items, as the sum of the products of their importance and current status was associated with the overall global assessment of QL on standardized domains. Predictably, our patients had a global QL on the EORTC of 57, much lower than the 77 reported in a large normative community sample . Scores Interestingly, lower global QL scores on the EORTC and higher depression scores on the BDI were associated with a shorter time to death in those patients who had already passed away, an association that has been reported in other studies -35. In fPatients who were in terminal care from a large sample from 12 oncology outpatients departments around the United States scored an average BSI Global severity index score of .93. Those who were under symptom control scored .80, whereas lower scores were seen for patients in active therapy (.59), adjuvant therapy (.60) or no current therapy (.65). Our samThe spirituality scores of this group average 118. This is very similar to a group of lung cancer patients who had a mean of 120 [In summary, these patients in a Phase I trial of a promising novel therapeutic were easily able to complete the SEIQoL-DW interview as well as a battery of other psychological questionnaires. They reported feeling excited and hopeful about the trial, with about two-thirds hoping for disease regression, and another third optimistically hoping for a cure. However, most acknowledged that although they hoped for the best they were realistic in their expectations. The individuality of QL as defined by each person was reinforced in this group, as many different cues were nominated as important and variable weights were assigned to the same cues. Consistent with reports from other seriously ill groups, health status received less focus than other aspects of life, primarily family relationships and activities. Overall QL on standardized measures and psychological status was generally better than other seriously ill patient groups, but comparable to cancer patients in general. QL and depression scores were related to time until death in those patients who had passed away.LC wrote the research proposal and ethics applications, conducted the interviews with the patients, designed the database, conducted the statistical analysis, and wrote the first draft of the paper. BB is the department head for Psychosocial Resources, and in conjunction with LC conceived of and designed the study. He also made the linkages with medical oncology to facilitate the study. DM is the oncologist and principal investigator of the Phase I Reovirus trial, and recruited all the patients. All authors reviewed and edited the final manuscript.Table 6: Correlations between scores on the SEIQoL, BDI, BSI, SHI and EORTC QLQ C-30Click here for file


Interval since most recent screening fecal occult blood test (FOBT): (0 = >1 year since last screening vs. 1 = screened within the past year), and screening sigmoidoscopy (SIG): (0 = > 5 years since last screening vs. 1 = within the past 5 years) were the outcomes.Results differed between men and women. After adjusting for age, health insurance, race, and smoking, we found that, compared to normal weight men, men in the overweight  and obesity class I  categories were more likely to have obtained a screening SIG within the previous 5 years, while women in the obesity class I  and II  categories were less likely to have obtained a screening SIG compared to normal weight women. BMI was not associated with FOBT.Weight may be a correlate of CRC screening behavior but in a different way between men and women. Colorectal cancer (CRC) is the third most common cancer in the United States with approximately 150,000 cases annually leading to about 57,000 annual deaths . AlthougHowever, studies suggest that overweight and obese women are more likely to delay cervical and breast cancer screenings than normal weight women ,5. In coThe Center for Disease Control and Prevention's BRFSS collects state-based data on preventive health practices and risk behaviors in the non-institutionalized civilian population aged ≥ 18 years . The ana2), calculated from self-reported weight and height, was the predictor.Body mass index , and sigmoidoscopy (SIG) in adults aged ≥ 50 years who reported ever having had the respective screening examination. BRFSS codes FOBT responses as: 'within past year', 'within past 2 years', 'within past 5 years', '5 or more years ago', 'don't know/not sure', or 'refused'. SIG is coded as: 'within past year', 'within past 2 years', 'within past 5 years', 'within past 10 years', '10 or more years ago', 'don't know/not sure', or 'refused'. Consistent with screening recommendations [We included age, education, race, income, self-reported general health status, smoking, employment, and health insurance as covariates.We grouped respondents into 5 BMI-defined categories . Respondents  with BMI's <18.5 ("underweight") were omitted from the analyses.We used multivariate logistic regression to estimate BMI-screening associations by entering the BMI-defined categories and potential confounders into the model as either continuous  or dichotomous variables . Using the guidelines proposed by Greenland , we retaTo evaluate whether sex moderated the BMI-screening association, we ran adjusted logistic models that also included BMI × sex interaction terms. Finally, because we observed a significant BMI × sex interaction, we then analyzed the data for men and women separately. Analyses were performed with SPSS 11.5.2(1) = 6.61, p = .010) reported obtaining a screening FOBT within the previous year, and 84.4% of men and 80.3% of women (χ2(1) = 98.4, p < 0.001) reported obtaining a screening SIG within the previous 5 years.The mean age of the respondents was 65 years (median = 63). The mean BMI was 30.2 (median = 31) and 93% reported having health insurance. Less than half reported ever having either a screening FOBT or SIG (Table BMI was not associated with obtaining a FOBT (OR's ranged from 0.90 to 0.98). Compared to normal weight adults, however, those in the overweight , obesity class I , II  and III  categories were more likely to have obtained a screening SIG within the previous 5 years (p's < 0.05).2(4) = 8.64, p=.071). However, the interaction effect between sex and BMI categories on SIG screening was significant, (χ2(4) = 114.03, p < .0001). BMI was not associated with obtaining a FOBT for either sex (OR's ranged from 0.87 to 1.05). However, compared to normal weight men, men in the overweight  and obesity class I (1.21 95%CI 1.03–1.75) categories were significantly more likely to have obtained a screening SIG. In contrast, obesity class I (0.86 95%CI 0.78–0.94) and II (0.88 95%CI 0.79–0.99) women were less likely to have obtained a screening SIG compared to normal weight women  declare that they have no competing interests.MH drafted the paper and assisted with the statistical analysis and interpretation. DB assisted with the writing of the manuscript and in the interpretation of the results. KF obtained and analyzed the data and assisted with the preparation of the manuscript.The pre-publication history for this paper can be accessed here:


Mycobacterium RD1 locus encodes a specialized secretion system that promotes mycobacterial virulence by an unknown mechanism. Using transparent zebrafish embryos to monitor the infection process in real time, we found that RD1-deficient bacteria fail to elicit efficient granuloma formation despite their ability to grow inside of infected macrophages. We showed that macrophages infected with virulent mycobacteria produce an RD1-dependent signal that directs macrophages to aggregate into granulomas. This Mycobacterium-induced macrophage aggregation in turn is tightly linked to intercellular bacterial dissemination and increased bacterial numbers. Thus, mycobacteria co-opt host granulomas for their virulence.Granulomas are organized host immune structures composed of tightly interposed macrophages and other cells that form in response to a variety of persistent stimuli, both infectious and noninfectious. The tuberculous granuloma is essential for host containment of mycobacterial infection, although it does not always eradicate it. Therefore, it is considered a host-beneficial, if incompletely efficacious, immune response. The  A zebrafish model of mycobacterium infection demonstrates that formation granulomas - immune structures composed of macrophages - requires a bacterial gene, indicating that mycobacteria exploit granuloma formation for infection Infection with pathogenic mycobacteria is thought to proceed through a series of defined steps. Mononuclear cells present at or recruited to sites of infection phagocytose bacteria and migrate deeper into tissues. Then additional macrophages and other immune cells are recruited to form complex, tightly aggregated structures called granulomas . GranuloMycobacterium virulence determinants (Mycobacterium infection in zebrafish. Zebrafish embryos and larvae (henceforth we will refer to both stages as embryos) are naturally susceptible to infection by Mycobacterium marinum, and we have previously shown that their optical transparency may be used to monitor the cellular dynamics of infection in real time  vaccine strains but present in virulent M. tuberculosis isolates (M. tuberculosis RD1 deletion mutant has a growth defect in the mouse model of tuberculosis (M. marinum infection model to elucidate the precise steps at which infection with wild-type (WT) and RD1 mutant bacteria differ. Our data suggest that the RD1 locus independently mediates macrophage aggregation and intercellular bacterial spread via host cell death within aggregates. These steps are associated with increased bacterial numbers and enhanced virulence, lending support to the idea that mycobacteria actually promote and exploit granuloma formation for the establishment of infection.In this study, we use the zebrafish infection model to probe the cellular mechanisms of virulence of the isolates . The RD1isolates . The M. rculosis , and sturculosis . In vitrrculosis . Others rculosis . It is uM. marinum RD1 region are homologous to those in M. tuberculosis  and the regions in the two organisms are syntenic  was attenuated for growth in mouse and human monocyte/macrophage cell lines , we infected embryos with red-fluorescent WT bacteria and allowed aggregates to form. These embryos were then superinfected with green-fluorescent ΔRD1 or WT bacteria . Both suIn a reciprocal experiment, embryos were first infected with green-fluorescent ΔRD1 bacteria, and after 4 d, when there were abundant individual infected macrophages (but no aggregates) in the tissues, the embryos were superinfected with either WT or ΔRD1 red-fluorescent bacteria. As expected, both superinfecting strains were rapidly phagocytosed by uninfected macrophages. ΔRD1 superinfection did not cause aggregate formation, and individual macrophages carrying both the original or superinfecting ΔRD1 were scattered throughout the tissues C. In conHaving demonstrated that ΔRD1 infection results in both reduced aggregation and lower bacterial numbers, we next pursued experiments to determine the relationship between these two phenotypes. In contrast to the notion that a primary reduction in bacterial numbers obviated the need for aggregation see E, we fouOne way that aggregation could impact bacterial numbers is by facilitating the spread of bacteria to uninfected macrophages that are recruited to the aggregates. If so, then aggregate formation should correlate with a dramatic increase in the number of infected macrophages and bacterial burdens. To test this hypothesis, we assessed the number of infected macrophages and bacterial numbers in relation to the time of aggregate formation . We enumIn the case of ΔRD1 infection, macrophage aggregation did not result in an increase in the number of infected macrophages A. This dM. tuberculosis RD1 locus is thought to promote intercellular bacterial spread in confluent cultured macrophage monolayers by promoting death of infected cells and subsequent phagocytosis of the released bacteria by surrounding cells . The TUNEL-positive cells were often M. marinum-infected  . These sM. marinum infection model to identify the steps at which the Mycobacterium RD1 virulence locus impacts the infection process. We found that two steps are independently affected: macrophage aggregation into granulomas and intercellular spread therein. Promotion of cell death within these aggregates appears to be at least one of the means by which RD1 affects intercellular spread. By comparing WT and ΔRD1 infection in real time, we have uncovered the promotion of granuloma formation as a mechanism of Mycobacterium virulence.We used the zebrafish-M. tuberculosis RD1-defective strain as a candidate vaccine for tuberculosis  and downstream  of the region to be deleted (see M. marinum as described ((dsRed2) or green-fluorescent protein (gfp) to a constitutive M. marinum promoter as described  equipped with 10×, 20×, and 40× magnifications, or a Nikon DIC 60× water “fluor” objective. Fluorescent as well as black and white images were collected with a Photometrics CoolSnap “cf” camera . Overlays of DIC and fluorescent images and video compilations were produced by using Metamorph software as described .Individual embryos were placed in microcentrifuge tubes containing 100 μl of embryo medium containing 20 μg/ml kanamycin for 1 h at room temperature. This medium was removed by aspiration and replaced with 150 μl of 0.25% Trypsin-EDTA. After incubation for 6–8 h at room temperature, Triton X-100 was added to a 0.1% final concentration, and the tubes were sonicated for 10 min in an ultrasonicator . The entire sample from each tube was plated onto individual 7H11 solid media plates containing 20 μg/ml kanamycin.5 d following infection, embryos were fixed in 4% paraformaldehyde in PBS overnight, dehydrated in methanol for a minimum of 24 h at 4 °C, rehydrated in PBS in a graded series of 5-min washes , and washed four or five times in PBST (0.5% Tween 20 in PBS). Embryos were permeabilized using 10 μg/ml proteinase K in PBST for 30 min at 37 °C, postfixed in 4% paraformaldehyde in PBS for 20 min, washed five times for 5 min each in PBST, and twice for 5 min each in TTase Buffer  plus 1 mM CoCl. Embryos were then incubated with TUNEL enzyme  and TUNEL label mix  according to the manufacturer's specifications. Primary antibody staining with sheep anti-fluorescein  was done in Western blocking solution  overnight at 4 °C. Secondary antibody staining with horseradish peroxidase-conjugated rabbit anti-sheep  was done for 2 h at RT. Detection was done with Tyramide Amplification Signal kit with AlexaFluor 555  according to the manufacturer's specifications.Fish were fixed in Dietrich's fixative  and sectioning and staining were performed by Histo-Tec .Statistics were calculated using GraphPad InStat version 3.05.