An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment.Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created.GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously. Escherichia, Bacillus, Helicobacter, Mycobacterium, Streptococcus, Staphylococcus and Listeria are available. Genomic data too, is diverse, ranging from COG functional classification data [Current efforts in genome sequencing have led to a rapid increase in the number of microbial genome sequences. A total of 522 ongoing microbial genome projects are listed in the GOLD database  and whilion data ,4, expreMicrobial Genomes Viewer [GenoMap [GenomeAtlas [GenomePlot [BugView [Genome2D [Several genome visualization tools have been developed in the last few years. The s Viewer  offers a[GenoMap  can be uomeAtlas  providesnomePlot  also pro[BugView  is anothGenome2D  offers uGenome2D  and ACT Genome2D  are convGenomeViz has been programmed in ActiveTcl. ActiveTcl  is availGenomeViz uses the concept of "tags" which may be applied to groups of genes for classification-type data. A tag file is tab-delimited text file of three columns. It has the "tags", their colors, and their brief descriptions. A pre-prepared tag file for the COG functional categories is available for immediate use. The map file has all the information required to create the plot (gene name, strand, start and end in genome, annotation, and the tag for the gene). It is also a tab-delimited text file. Both file formats (tag and map) are easy to manipulate in a spreadsheet application like Microsoft Excel. However, care must be taken while manipulating data in such applications since errors may creep in the data as demonstrated by Zeeberg et al. . The mapIn order to minimize initial difficulty that users may encounter in creating their own map files, we provide pre-prepared map files for over a hundred genomes. Of these nearly seventy genomes are loaded with the COG classification scheme and may be used immediately. The program also performs checks on the input map file for possible formatting errors and attempts to indicate location of errors (if any) before creating the plot. Several types of plots may be created; on either single or double strands and color gradients and line-graphs are available for numerical data. Once the plots are done, mouse-over on any gene immediately displays associated information from the map file in a display area.Using GenomeViz, it is also possible to search, highlight and retrieve genes of interest. Each loaded genome may be queried separately. Regular expression searches are fully supported and results are highlighted in the genome. For instance, the simple expression ribosomal|ribosome will mark in color all ribosomal proteins in any genome and retrieve all the information for these genes from the map file. The "|" operator is the standard OR operator in Tcl expressions. Genes involved in iron metabolism/regulation which are usually annotated with keywords like ferrous, ferric or iron may be retrieved with the expression "ferric|ferrous|iron". The results can be saved as a text file. Users can also use their own annotations to visualize and query their genome of interest provided these annotations are available in the map file format. It is also possible to display, in different colors, the results of different queries on the same genome by changing the search color before performing a search. This will enable visualization of, for instance, the distribution of genes/operons involved in iron and zinc metabolism/regulation separately.A 'Select COGs' option enables one to retrieve all genes from a particular COG category, e.g. "Cell division and Chromosome partitioning" or "Transcription". Each loaded genome can thus be queried separately. Usually, this is more useful when using a special tag file  that colors all genes as "grey", so that a neutral background is available for highlighting the distribution of genes of a particular COG category over the entire genome. Categories of interest can be highlighted in different colors simply by changing the selection color before selecting the category. Results of each query are also displayed in a text box from where they may be saved as a text file. Thus, GenomeViz allows a rapid overview of the similarities in distribution of various functional categories in closely related genomes Figure . It is aSeveral options are available for printing the circular plot. The graphics can be directly sent to the printer or saved to a PostScript file and read by standard graphics programs. A number of page size options are available and extra large plots spanning many pages may also be printed. A detailed program manual is available with notes on installation, usage and examples.We describe a rapid and convenient application GenomeViz for simultaneous visualization and comparison of varied genomic data from several microbial genomes. Future updates for software and data will be available from the project home page.Project name: GenomeViz• Project home page: • Operating system(s): Linux, Solaris, Unix• Programming language: Tcl/Tk• Other requirements: ActiveTcl, PERL• License: Free for academic use• Any restrictions on use by non-academics: Contact corresponding author for a license.• COG: Clusters of Orthologous GroupsSIGI: Score-based Identification of Genomic IslandsRG conceived the program, wrote and tested it, prepared the manuals and the website. TC oversaw the entire development process. TH offered suggestions on program features. RG and TC prepared the manuscript. All authors read and approved of the final manuscript.


Coordination of [Ca2+]i events among astrocytes was indicated by the broad cross-correlograms. Increased neuronal discharge was associated with increased astrocytic [Ca2+]i activity in individual cells and a robust coordination of [Ca2+]i signals in neighboring astrocytes. These findings indicate potential neuron–glia communication in the intact brain.Large and long-lasting cytosolic calcium surges in astrocytes have been described in cultured cells and acute slice preparations. The mechanisms that give rise to these calcium events have been extensively studied in vitro. However, their existence and functions in the intact brain are unknown. We have topically applied Fluo-4 AM on the cerebral cortex of anesthetized rats, and imaged cytosolic calcium fluctuation in astrocyte populations of superficial cortical layers in vivo, using two-photon laser scanning microscopy. Spontaneous [Ca Two-photon laser scanning microscopy was used to image calcium concentration changes in astrocytes in the cerebral cortex of anesthetized rats Astrocytes are nonneuronal cells of the brain with some known and hypothesized functions  in the cytosol undergoes large changes spontaneously or in response to various physiological and pharmacological manipulations, such as mechanical stimulation, membrane potential depolarization, and activation of metabotropic glutamate receptors  and/or metabotropic glutamate receptors  ester in juvenile rats in vivo. We find that [Ca2+]i dynamics in astrocytes is rather quiescent during baseline anesthesia. However, increased population bursting, brought about by attenuating γ-aminobutyric acid (GABAA) receptor-mediated neurotransmission, leads to increased magnitude [Ca2+]i surges, and the [Ca2+]i changes become more strongly coordinated in neighboring astrocytes.We have used two-photon laser scanning microscopy (2-PLSM) to monitor cytosolic CaTo examine the depth of penetration of the Fluo-4 AM, coronal brain slices (300 μm thick) were acutely prepared after the residual dye was washed off from the craniotomy. A large number of cells below the craniotomy showed fluorescence labeling . On the 2+]i transients , cells with astrocytic appearance (n = 185) were selected for long-term (10–20 min) monitoring. For quantitative studies, three states of [Ca2+]i activity were distinguished: (a) quiescent state with very slow (less than 0.025 Hz) oscillations of baseline fluorescence level, (b) [Ca2+]i spikes , and (c) [Ca2+]i plateau potentials . [Ca2+]i spikes and [Ca2+]i plateau potentials were automatically detected. In the control (baseline) condition, 11% of astrocytes had at least one spike event, and 52% had at least one plateau event in 10 min. The mean frequency of [Ca2+]i spikes among the cells that had at least one [Ca2+]i spike was 0.121 ± 0.098 per minute  and the mean frequency of [Ca2+]i plateau was 0.118 ± 0.058 per minute (mean duration: 160.4 ± 114.9 s).In our initial experiments, we made a large number of line scans (sampling rate ∼200 Hz) of dye-loaded cells to examine whether some of them were neurons. We never observed short-lasting [Ca2+]i dynamics were affected by increasing neuronal activity, we induced regularly occurring population bursts by local application of bicuculline (n = 7 rats). Large amplitude (0.69 ± 0.26 mV) synchronous field events (approximately 100 ms) occurred at relatively regular frequency (0.15 ± 0.06 Hz), associated with multiple unit discharges. No significant difference was observed in average heartbeat frequency between the control sessions and bicuculline sessions .To investigate whether the baseline values of [Ca2+]i in astrocytes (n = 214 cells). First, the incidence of [Ca2+]i spikes and plateau events was counted in the absence and presence of bicuculline-induced population bursts. Under bicuculline condition significantly more astrocytes had [Ca2+]i spikes , whereas the probability (52% versus 54%) of plateau potentials did not differ significantly. The mean duration of plateau potentials, however, was significantly longer  after bicuculline treatment. Among the cells that exhibited at least one spike or plateau event, there was not a significant difference in frequency of the event occurrences . Thus, the major difference between control and bicuculline conditions was the higher proportion of active astrocytes under bicuculline.We used two methods to evaluate the effect of neuronal activity on [Ca2+]i changes in the frequency domain. The 0ΔF/F trace was considered as a continuous process, and the power spectrum estimate was calculated with a multi-taper method for each astrocyte and averaged across cells. There was a general increase of power at all frequencies in bicuculline-treated animal. The most consistent significant increase (p < 0.05) of power appeared in the frequency range of 0.10–0.24Hz, reflecting the increased incidence of [Ca2+]i spikes. Short-term cross-correlation of neuronal field bursts and [Ca2+]i signals (± 10 s) did not show a significant time-locked relationship  and distant cell pairs (greater than 50 μm). In control conditions, the temporal correlation of [Ca2+]i signals in neighboring pairs was somewhat larger than in distant pairs, but this difference was not significant (n = 374 neighbor pairs and n = 1,138 distant pairs). Nevertheless, [Ca2+]i signals in astrocytes were not completely random, since the cross-correlograms had wide central peaks at the 10–100 s scale  was similar to those in the control condition. However, synchrony between local pairs (n = 1,282) increased several-fold relative to both distant pairs under the same condition (t-test, p < 0.0001) and to local pairs in the baseline condition (t-test, p < 0.0001).In individual experiments, propagation of synchronous activity could be observed visually  but the  s scale B. In conuculline C. Correln = 1,512 cell pairs, r = 0.019, p = 0.46). In contrast, a significant negative correlation was found between the synchrony of [Ca2+]i signals in the bicuculline condition .Using a different approach, the magnitude of the zero-timelag correlation coefficient for each cell pair was plotted against distance between the cell pairs. Under control condition, no notable relationship was observed between these variables  and NMDA receptors  in close contact with small brain vessels . It has ompounds . Furtherompounds . These fMale and female rats, 12–16 d postnatal (P12– P16), of the Sprague–Dawley strain were used in these experiments. Animals were deeply anesthetized with 1.7 g/kg urethane. An outline of the craniotomy above the primary somatosensory (barrel) cortex was marked with a dental drill. A metal frame, similar to what has been described in 3, 1.1 mM NaH2PO4, 2 mM CaCl2, 1 mM MgSO4; pH adjusted to 7.4) and mixed for a further 15 min. A small volume (up to 12 μl) of the dye-containing solution was applied to the cortical surface by a micropipette. The solution was retained in place by a small piece gelfoam. The unbound dye was removed 45–60 min after the surface application of Fluo-4 AM by irrigating the exposed surface with ACSF for at least 10 min. The craniotomy was then covered with 1% agar dissolved in phosphate-buffered saline (pH 7.4), and a glass coverslip was placed on a metal frame. This arrangement allowed access for a glass recording electrode from the side. Juvenile rats (P13–P15) were used because we found in preliminary experiments that in adult animals, mostly vascular cells were loaded with the current protocol.Fluo-4 AM  was mixed with 2 μl of Pluronic (P-3000, Molecular Probes) and 5 μl of dymethyl sulfoxide  for 15 min. The solution was then diluted in 18 μl of artificial cerebrospinal fluid (ACSF) (125 mM NaCl, 3 mM KCl, 10 mM glucose, 26 mM NaHCODuring the recording session, a heating blanket was placed under the rat to maintain body temperature at approximately 37°C. The electrocardiogram (EKG) was monitored continuously. The R wave of EKG was used to monitor brain pulsation-derived movement of artifacts during imaging. Population bursts of cortical neurons  were excluded from the analysis. For display purposes, the signal was convolved with a Hanning window of order three to smooth the signal trace. Power spectra of fluorescent signals were computed using the multi-taper method (NW = 4). For the calcium event detection, 0ΔF/F signal was convolved with a Hanning window of order 15. “Spike” events were defined as transient increase of 0ΔF/F signal exceeding 20%, lasting 5–50 s. “Plateau” events were defined as sustained increase of 0ΔF/F (greater than 20%) signal longer than 50 s. Peak amplitudes of both spike and plateau events required an increase of at least 50% 0ΔF/F from the onset of events. Calcium events were automatically detected with the above detection. Cross-correlation between cell pairs was computed by normalizing the 0ΔF/F signals to unity (zero mean, unity standard deviation) so that the computed values represent the correlation coefficient between the two signals at a given timelag. All numbers are indicated as mean ± standard deviation, unless otherwise noted.Fluorescence signal was quantified by measuring the mean pixel value of a manually selected somatic area for each frame of the image stack using ImageJ software. The values were exported to MatLab and the fluorescence change 2PO4, 155.17 mM NaCl, 2.96 mM NaHPO4, pH approximately 7.4), the slices were treated with S100B antibody (made in rabbit, 1:50 dilution) in Triton X-PBS (0.5% Triton X in PBS) overnight. The sections were subsequently washed three times in PBS, followed by incubation with the secondary fluorescent antibody  in Triton X-PBS solution for 2 h. Simultaneous viewing of the two image stacks allowed a systematic comparison of the extent of overlap between Fluo-4 loading and S100B immunoreactivity  because this antibody stains the somatic region of astrocytes as well as its processes . Followiactivity .Video S1The primary somatosensory cortex (P15) was stained with Fluo-4 AM in vivo and subsequently imaged in vitro. Acute slices (approximately 300 μm thickness) were cut in cold ACSF after the cells were loaded in vivo. .(49 MB AVI).Click here for additional data file.Video S2Same slice as shown in (48 MB AVI).Click here for additional data file.Video S3Detailed imaging of in vivo-loaded acute slice preparation of the primary somatosensory cortex . Z step = 1 μm; scale bar = 20 μm.(39 MB AVI).Click here for additional data file.Video S4Empty circles in layers II/III, presumed unloaded neurons (note their absence in layer I). The loaded cells have typical glial morphological appearance. Z step = 1 μm; scale bar = 50 μm.(50 MB AVI).Click here for additional data file.Video S5Acute slices (300 μm thickness) were prepared from the in vivo Fluo-4 AM-loaded somatosensory cortex. The slices were subsequently incubated in EDAC containing saline followed by formalin fixation. The loaded astrocytes were identified by examination at various depths and numbered (left). Next, the slices were processed for immunocytochemistry with astrocyte marker S100B. Depth scans (1 μm between the frames) were taken again to determine immunoreactivity of cells with S100B (right movie). An overlapping set of the cells was identified to be S100B-immunoreactive, indicating that nearly all Fluo-4 AM-loaded cells were astrocytes.(5 MB AVI).Click here for additional data file.Video S6Movie taken from a P14 rat. Image was taken with 2 Hz sampling rate for 10 min and compressed to 36 s for display purposes. Note spatial- and light-emission-stability of the recorded cells. Note also that at frames approximately 9 s and 15 s, two of the astrocytes in the middle display transient increased fluorescence. Scale bar 50 micro μ.(55 MB AVI).Click here for additional data file.


Adenoid cystic carcinoma is a rare malignant parotid tumor. Metastasis can occur even a decade or more after initial treatment of the primary.We report a 60 year old female patient who presented with adenoid cystic carcinoma of the parotid gland. She underwent a total conservative parotidectomy followed by adjuvant radiotherapy. While on follow up, patient developed multiple liver metastases which manifested three years later. Patient lived for another two years before she died of her disease.Although distant metastases of adenoid cystic carcinoma develop frequently, isolated metastasis to liver is unusual. Even after manifestation of distant metastasis, patients can be expected to live for a number of years. Palliative chemotherapy can be considered in symptomatic cases while the usefulness of metastatectomy is controversial. Adenoid cystic carcinoma (ACC) is a rare malignant neoplasm of the salivary gland. Salivary gland neoplasms constitute 3% of cancers of all sites, of which, 10–15% are malignant . Though A 60 year old woman presented with a small swelling beneath the right ear lobe of 4 months duration. The swelling measured 2 × 1 cm placed in the superficial part of the parotid and was not fixed. There was no facial nerve palsy or palpable cervical nodes. A fine needle aspiration cytology (FNAC) was carried out which showed the lesion to be ACC [Although ACC is the second most common malignant salivary gland neoplasm and constitutes approximately one third of all salivary gland malignancies it constitutes only 2% of parotid neoplasms . As ACC Radiotherapy has been used as a primary modality for patients with surgical contraindications and in those with unresectable neoplasms. Though no improvement in survival is reported, the use of adjuvant radiation improves locoregional control and disease free survival. This patient received adjuvant radiation and did not have any locoregional recurrence.Regional metastasis is less common occurring in about 17% while systemic failure occurs in 33 to 50% of the patients ,8. ThougACC is a rare malignant tumor of parotid gland. Metastasis can manifest very late and hence a long term follow-up and a high index of suspicion is necessary to diagnose them early. An annual ultrasound study of abdomen would be desirable on follow-up. Unlike metastasis from other malignancies, these grow indolently and long term survival can be expected even with multiple metastases as also evidenced in the present case. Chemotherapy could be considered in selected patients as a therapeutic option in metastatic disease.ACC: Adenoid cystic carcinomaFNAC: Fine needle aspiration cytologyGy: GrayNone declaredKH was the principal clinician who planned the evaluation and procedure, in addition to conceptualizing and drafting the article.SRMG was the pathologist.Both the authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


The aim of this study was to explore the ethical challenges in surgery from the surgeons' point of view and their experience of being in ethically difficult situations.Five male and five female surgeons at a university hospital in Norway were interviewed as part of a comprehensive investigation into the narratives of nurses and physicians about being in such situations. The transcribed interview texts were subjected to a phenomenological-hermeneutic interpretation.No differences in ethical reasoning between male and female surgeons were found. They reasoned in both action and relational ethical perspectives. Surgeons focused on their relationships with patients and colleagues and their moral self in descriptions of the ethical challenges in their work. Dialogue and personal involvement were important in their relationships with patients. The surgeons emphasized the importance of open dialogue, professional recognition, and an inclusive and accepting environment between colleagues.The surgeons are personally challenged by the existential realities of human life in their relationships with patients. They realized that ethical challenges are an inherent part of performing surgery and of life itself, and say that they have to learn to "live with" these challenges in a way that is confirmed both socially and by their inner moral self. This means accepting their personal and professional limitations, being uncertain, being fallible, and being humble. Living with the ethical challenges of surgery seems to contribute to the surgeons' confidence and vulnerability in their professional identity. It is important for surgeons to be and to act in a right and good way towards patients, relatives, and colleagues. Studies have shown, however, that physicians often are in doubt about the best and correct actions to take for the patients in specific situations -3. This A relational ethical perspective means reflecting on the challenges we encounter in our relationships with others and how to fulfil our social roles and obligations in a good way – as a human being, a surgeon, and a colleague. It tries to answer questions such as "How can I adequately meet the challenges that confront me in the relationships in which I am involved in this situation?" . The quaAction and relational ethical perspectives are not interchangeable as surgeons have a dual responsibility for their actions in specific situations as well as their way of being in their relationships ,7. BeingMany authors argue that the respect and trust in the physician-patient relationship have eroded in recent years in spite of the physicians' increased therapeutic capabilities ,12. ShorMedical problems are always existential problems too because suffering, anxiety, life, death, and cure involve the core of human existence. Physicians are working with emotionally intense issues and have to accept the possibility of failures, continuing suffering, and death on the part of their patients . MeetingAlthough most clinicians are aware of the uncertainty and the limitations of medicine and their responsibility to try to reduce the likelihood of error, ,20 the bSurgeons' relationships with their colleagues have become more important as surgery has changed from relying heavily on the performance of individual surgeons to relying on a team of providers ,25. SeveThe vulnerability of patients is emphasized in the literature of medical ethics. Less is written about the vulnerability of the physicians in their relationships with patients, relatives, and colleagues. Being involved may engender feelings of helplessness and vulnerability in the physician. MacLeod  argues tStudies show that physicians seem to experience uncertainty and fallibility in different ways. Less experienced female physicians in paediatric care put on an air of certainty while the more experienced gained a kind of security by allowing themselves to feel uncertain . Female Few empirical studies have been found that explore the ethical challenges of surgery from the surgeons' point of view and their experience of being in ethically difficult situations. The present study is part of a comprehensive investigation of ethical reasoning among male and female physicians and nurses within surgical units. The results of this interview study with male and female surgeons will be presented in two articles. The present study describes the surgeons' experiences of being in ethically difficult situations from a relational ethics perspective. The other paper describes the ethical dilemmas as experienced by the surgeons from an action ethical perspective. The results from the interviews with the registered nurses (RNs) working in surgical units are in progress and will be addressed in a third paper.The aim of this study is to explore the meaning of being in ethically difficult situations in surgery as narrated by male and female surgeons.th Regional Ethics Committee in Norway.Five male and five female surgeons working on surgical units at a university hospital in Norway participated in the study. All were experienced and had been working in health care from 9 to 31 years (median = 21.5), and in surgery between 5 to 21 years (median = 13). The surgeons worked full time and were on duty when the interviews were conducted. No individual characteristics will be disclosed in order to guarantee confidentiality. The surgeons gave their informed consent to participate in the study, which was also approved by the 5The interviews were conducted by the first author and lasted from 35 to 75 minutes (median = 55). They were tape recorded and subsequently transcribed verbatim. The interviewees were asked to tell about one or more ethically difficult care situations that they had experienced in their work as surgeons. What constituted an ethically difficult situation was not defined, allowing the interviewees to determine what they considered ethically difficult themselves. The aim of the interviews was to obtain as many rich narratives as possible without interrupting the surgeons' narrative flow and reflection. If the surgeons did not spontaneously reflect on the events they talked about, their reflections were sought. Questions were asked when the interviewer wanted the interviewees to elaborate on their stories or had difficulty understanding the narration. These questions referred to the interviewees' thoughts, feelings, and actions . Field nThe method of interpretation used was inspired by the French philosopher Paul Ricoeur's phenomenological hermeneutics , and devnaïve reading was made of all the transcribed interviews as a whole to gain a first impression of the surgeons' experiences of being in ethically difficult situations during their clinical work. The repeated naïve reading was made as open-minded as possible, without any deliberate analysis of the text. The naïve reading shows the direction the structural analysis may take. Second, a structural analysis was performed in order to validate or refute the initial understanding obtained from the naïve reading and to explain what the text was saying. The interviews were divided into meaningful parts and patterns, i.e. one sentence, parts of a sentence, or a whole paragraph with a related meaning content. The meaning units were condensed and discussed among all the authors, and themes and subthemes were identified, and presented in 'Results'. Third, a comprehensive understanding was developed, taking into account the authors' pre-understanding, the naïve reading, and the structural analysis (results). The text was read as a whole and interpreted in relation to relevant theories of ethics and results from previous investigations into the meaning of being in ethically difficult care situations [Each interview was regarded as a text. However, it was not what the texts said that was a subject matter to be investigated, but rather the focus was on the ethics expressed in them or the essential meaning of ethically good phenomena . First, tuations . The comThe analysis was conducted by all the authors and the interpretative agreement was considered satisfactory and to be the most useful understanding of the meaning of the surgeons' experiences of situations of ethical difficulty. The authors' interpretation was not shared or validated with the surgeons. In this study, the focus was on obtaining the meaning of the text, which cannot be validated by the interviewees. A kind of validation is accomplished by the structural analysis as the objective part of the interpretation process . AccordiSeveral readings of the interview texts revealed that the surgeons told about ethical challenges that confront them in their relationships with patients and colleagues and about their experiences of living with these challenges. They also reported their experiences of ethical dilemmas in surgical practice. No gender differences between the male and female surgeons were found in the analysis of the interviews. The results showed that each surgeon created many and detailed narratives. When the surgeons were asked to narrate their experiences, they did not differentiate between action and relational perspectives in their ethical reasoning. This is an analytical distinction made by the authors in order to structure the results. The authors therefore decided to separate the presentation of the results in two papers: one paper about the surgeons' experiences of being in ethically difficult situations from a relational ethics perspective and the other paper from an action ethical perspective according to the theory presented in the introduction . This paThe themes and the subthemes from the structural analysis are shown in Table The surgeons emphasized the importance of dialogue with patients and especially being open and honest about all aspects of their treatment and care. Talking to patients about difficult issues before or after the operation is experienced as an important part of the surgeons' responsibility. Openness and honesty is especially important when surgeons had to tell patients that they have cancer or a fatal disease, when something had gone wrong, or the operation did not turn out as successful as expected. Using frightening words such as "death" and "cancer" is also considered to be part of an open and honest dialogue. The surgeons also felt responsible for "not involving patients with bad news they were not ready to receive, and feeling one's way in what it's right to inform about". They said that if the patients are taken seriously and are talked to in a way that they understand, there is seldom difficulty reaching a mutual understanding about diagnostics and treatment.The patients are always told the truth about their disease, although it was experienced as an emotional burden for the surgeons to disclose bad news or present difficult decisions to the patients. "It's a burden to tell the patient that we will withdraw all active treatment. You feel a bit guilty; in a way you feel that it's your fault if the treatment does not succeed". They stressed that knowing the patient from previous meetings is important to them, as is having antennae for how the patients experience their life and the present situation. "If I do not manage to achieve what I am trying to do, I always tell [the patients] what the situation is. I never try to conceal anything. That will only torment them".Talking openly with patients is also important for the surgeons in situations when they are in doubt about the right thing to do. They experienced relief if the patient had an answer to their doubts. They said that patients who are seriously ill usually have thought about life and death issues and have a conception of their condition, and that the question of withholding or withdrawing treatment seldom comes as a surprise to them. Some patients say that they have lived a good life and do not want an operation. Others strongly want an operation even though their prognoses are poor. "We often reach an agreement about ending a treatment that either does not lead to a meaningful life afterwards or leads to a life that would be experienced as a heavy burden".The surgeons said that they become personally involved with their patients, focusing on patients as persons and their quality of life as much as on their medical treatment. Being involved and knowing the patients' background and what they really want in life makes difficult ethical decisions easier to handle. The surgeons explained that caring for the patient can be felt as a personal, emotional burden. "It's not easy when people you have established a relationship with die. The only way to run away from it is to relinquish your responsibility. But that means disassociating yourself from or rejecting the patient. So you have to care, to be involved and to be a human being".The surgeons are involved in many patients' lives and destinies and said that keeping a certain distance protects their feelings and is a way of caring for themselves. They said that keeping a certain distance is necessary in order to give the patient neutral advice and the most suitable medical treatment. The surgeons feel a responsibility to care in situations where they find it difficult, for instance when they dislike the patients' personality, behaviour, or values. They said they work hard to get involved and care for demanding and non-compliant patients.Ethical challenges are discussed in both formal and informal social arenas among the surgeons. All new patients are presented at the daily morning meeting between all the surgeons, including what had been done to them and why. Only questions and short objections to the patients' diagnostics and treatments are raised at these meetings or shortly after. The surgeons arrange separate meetings to discuss problematic cases. "We assemble the nurses, the anaesthesiologists, the surgeons, and even other specialists like the nephrologists when we have patients who reside a long time in the intensive care unit. In a way we create a meeting-place for the case and discuss whether we should withdraw a life-sustaining treatment or start additional treatment for a kidney failure for instance." The informal running dialogues during the day were equally important for the surgeons. "You have to make the decision yourself, but we always discuss the problem together before difficult decisions are made. The discussions do help and are experienced as mutual support". The surgeons expressed confidence in the consensus that usually is achieved in these discussions. "I know that I would be content to receive the treatment we agree upon myself".The surgeons emphasized the importance of having a caring relationship with their colleagues. They said that talking together and giving and receiving collegial support is necessary in order to live with the personal responsibility of being in ethically difficult situations and with the emotional burden of decision making. "People say that surgeons are a bit tough and do not talk about feelings, and that may be true. But in my experience we really care for each other. Perhaps we do not go all mushy about our feelings, but we understand when someone is in difficulty. I have experienced receiving good support in such situations. Colleagues contact you and say: "Ok, listen, a couple of years back the same thing happened to me", or: "You must not take this too hard, it could have happened to anybody". That helps".Personal and emotional support is informally and silently shared among trusted colleagues and great value is attached to it. After having presented a difficult decision about withholding treatment at a morning meeting, one of the surgeons commented: "That same afternoon, four or five of the most experienced surgeons came to me independently, and told me that they thought that what I had done was great. They said that most surgeons were not able to do what I had done. I remember it well because I think it was so well said".The surgeons emphasized the importance of "playing with an open hand" and that openness and honesty in the relationships with colleagues presupposes a trusting atmosphere that allows everybody to feel free to voice their opinion and be listened to. They feel that it is important that everyone who is involved in the treatment and care of the patient should have an opportunity to express their opinion and to be heard before any final decision is made. Openness and honesty are particularly important when medical errors occur or when something has gone wrong during an operation. Talking about medical errors or mistakes is considered an opportunity for learning and for improving surgical routines. "You have to have an including and accepting environment that allows you to say that you could have chosen a different solution. If there is no room for you saying something like that, then there will be a tendency to conceal it. We all make mistakes and we all make wrong deliberations and sometimes choose bad solutions. We have to live with that. Therefore it's important that we try to learn from the cases where something [erratic] happens".The surgeons focused on the necessity of dialogue and cooperation with their colleagues. "We are used to working close together in a team and it makes these difficult situations easier to handle". They found it satisfactory to work in a hospital because "there is always someone you can ask for advice when in doubt". They said they find it easier to talk to patients about difficult treatment options when the question has been discussed with experienced colleagues or senior surgeons first. This is especially important for less experienced physicians. The surgeons also make a contrast between the importance of cooperation with colleagues and the burden of being alone and being responsible decision makers.The surgeons said that they experience ethically difficult situations as an important part of their everyday activities that cannot be separated from the rest. "These situations are a part of our profession that are not necessarily experienced as difficult, but are sometimes unpleasant to be in". They said they have to experience these situations personally and be involved in order to understand them and to learn to live with them.Some ethically difficult situations are experienced as dramatic and tragic, especially when the surgeons feel the personal responsibility for saving the lives of trauma patients after major accidents. "If you are not able to cope with being in this situation and be responsible, and be the leader of the trauma team trying to save peoples' lives after a serious accident, if you cannot do that but go on wondering if you have done something wrong, then I think you will find something else to do".The surgeons told about situations where they are alone on duty and responsible for rapid deliberations and decisions in acute and emergency situations as especially challenging. "There are no other times in this job when you feel as lonely as you do in those situations". The decision whether to continue or withdraw treatment from traumatized young patients and children is experienced as especially challenging to make alone. "It's not easy [being alone]. It's the kind of decisions you often ponder about for several days afterwards, also at home. It's the sort of decisions you really try to closely think through, and it often troubles you even after you have made a decision".The surgeons said they have to learn to live with the unpredictable consequences of their decisions. "The practice of surgery is very specific and you feel more responsible in a way than in other areas of medicine. You have the feeling of being the direct cause when things go wrong, e.g. that you operated at the wrong time, you operated incorrectly or that you should have found the right diagnosis earlier".The surgeons spoke about "living with" the inherent uncertainty of surgery and emphasized that they can never be completely sure of the right thing to do in ethically difficult situations. They have to live and work with the uncertainty of the course of the disease, the patients' chances of survival, the risk of serious and fatal complications and the uncertainty of the patients' quality of life after extensive operations. The surgeons said they have to learn to live with the uncertainty of their deliberations and operations as there can be no right answer to ethical challenges, and no criteria to guide them when they make their decisions.Living with uncertainty is experienced as both frightening and satisfying. The surgeons said that not knowing what to do in an uncertain situation, finding a way, and succeeding in their attempt to restore health or save life is a satisfying aspect of their work. They also commented that they have to live with their doubts and fears of being too active and the risk of knowingly imposing severe complications and a poor quality of life on their patients.The surgeons said that their aim is to make all patients better. Accepting the limitation of surgery and not being able to cure a particular patient or alleviate his or her suffering is not an easy task for surgeons. They commented that it feels difficult not to be able to or not to be allowed to help patients. Sometimes they feel guilty if the treatment does not succeed, but said that they have to accept the possibility of making mistakes as an essential part of the profession. "You have to face the reality of how things are. What we are dealing with are human beings in marginal situations where things can go wrong. Everybody who is dealing with these things makes errors of deliberation and judgment. It's a part of the game that you have to live with when the margins are so tight. It would not be better if you quit. Your dearly purchased experience will be of use to nobody then".The surgeons said that they are focused on healing and curing and that they try to operate on the patients in most situations. "I believe that surgeons feel that it's good to do something, curing, and saving lives. That is what we have learned to do. We are in a profession that can do many useful things and that is the gratifying part of practicing surgery, – that you can identify a problem and do something about it".The clinical experience of deliberating and choosing and finding workable solutions in clinical and ethical difficult situations makes the surgeons confident. "Most surgeons are action-oriented. If not, it's almost impossible to practice surgery, because you have to makes decisions all the time and be accountable for your decisions". Receiving social confirmation from patients, relatives, and colleagues when they succeed contributed to the surgeons' experience of confidence in their own decisions and actions. The surgeons also said that having the courage of your convictions and a set of personal ethical values is equally important in order to do a "proper and conscientious job". This means acting according to the patients' best interests and the standards of their profession. Their conscience helps them to decide which action is morally wrong, to make controversial decisions, and to voice personal, professional, and moral opinions to colleagues and patients.The surgeons emphasized that although they deal with existential issues of life and death, they do not rule over these human conditions. "The essence is that we are not almighty. We do not save lives, we just postpone death. The only thing that is certain is that we are all going to die. You are just doing repairs and trying to help the patients to live a bit longer. " "Fortunately it's not we who rule over life and death. What we can do means less than you think and that is how it should be. I think it's important that we all acknowledge this and everyone else too".All the surgeons said they are against active euthanasia. They also commented that a humble attitude in their work helps them acknowledge their personal and professional limitations and to recognize what they cannot and ought not do. "There is a dimension in surgery of being right about having a good reason to operate and being considerate about the benefits of carrying out an operation".The surgeons in this study reasoned in a relational ethics perspective, focusing on dialogue, openness, and involvement in their relationships with patients and colleagues. While the surgeons in the interviews described their experience of being in ethically difficult situations, it seems at the same time that identity was central to their experience of ethics and their enactment of moral agency. The surgeons identified themselves by telling about their ethical experience, expressing the way they are living their identity. By narrating our lived experience, we give meaning to our experiences. We understand ourselves through the stories we tell and live, as well as those told about us and by interpreting them. Personal identity is said to be constructed through the stories we tell about our lives, stories which are in turn shaped by more general institutional, cultural, or national meta-narratives that live within the culture, of surgery, medicine, and society -42. ThusBeing open and honest about all aspects of patients' treatment and care is experienced as important for the surgeons. This is even true in situations when they have to disclose bad news and tell the patient that they are not able to or did not succeed in their efforts to restore health. Openness of speech is one of the spontaneous expressions of life, designated as "utterances of life" according to the writings of Løgstrup . That opHuman life means expressing oneself with the expectation of being met by others according to Løgstrup . OpennesAlthough disclosing bad news to the patient is experienced as an emotional challenge by the surgeons, concealing the truth does not seem to be an option they consider. Concealing the truth from the patient is experienced as difficult. It seems that surgeons need to share their experiences by speaking openly to patients so they can live with their demanding professional life in a satisfactory way. Therefore, honesty and openness are important because the relationships with patients are important for the surgeons' lives.The surgeons said that it is important not to hide their uncertainty and doubts from themselves or from their patients. They accepted that uncertainty is an inherent part of their profession and realized that they often have to decide in spite of lack of scientific knowledge. They also deal with problems that may have no desirable solutions. Previous studies of surgeons , female The surgeons said that they sometimes feel guilty when they have to disclose the bad news to patients that the treatment did not succeed. We feel guilty when we fail to do what is required of us in a situation according to Løgstrup , either Feeling guilty is our fundamental ethical condition as human beings according to Pahuus  because The surgeons said that they experience a relief when the patients give answers to their own uncertainty and doubts about the right or good thing to do. It seems as if the surgeons are relieved when patients want to decide for themselves and take responsibility for their lives, appreciating that they do not hand over this responsibility to the surgeons. The surgeons in this study do not fit into the traditional and stereotypical picture of the paternalistic and authoritarian physicians . On the The surgeons emphasized the importance of being personally involved with the patients by focusing on patients as persons and their quality of life as much as their medical treatment. However, they experienced the challenge of finding the balance between involvement and distance in the relationships, between caring for the patients and themselves, and in giving professional and neutral information. Distance based on knowledge, skills, and experience with previous cases and situations is necessary in order to help the patients in a professional manner ,46. PersIn their narratives, the surgeons focused on cooperation and the relationships with their colleagues. They experienced being listened to and together they seem to create and recreate a collegial environment where they can express their doubts and admit their errors of deliberation and decisions.The surgeons said that they experience taking difficult decisions alone as a burden. Working in a hospital is experienced as satisfying because they appreciate working together. They seemed to accept that they are mutually dependent on each other and appreciated the support they receive in dialogue with colleagues. Interdependence and exchange is a fundamental way of human lives according to the ethics of Løgstrup . He callTo be seen and listened to by colleagues, be taken seriously, and comforted when something goes wrong is an answer to fundamental human needs. Openness about personal doubts and failures also make the surgeons vulnerable. The interdependency among surgeons in this study is not experienced as a burden, but as mutual support. The surgeons' acceptance and appreciation of their collegial dependency may be an answer to why surgeons are able to stand in ethical difficult situations and live with them in a satisfying way. The dialogue with colleagues reduces the surgeons' doubts, although their doubts cannot and do not disappear.The surgeons receive social confirmation for being good surgeons through dialogues with patients, relatives, and colleagues. Their experience of being of use to society as a whole also confirms their identity as good surgeons. To be confirmed is to be seen, listened to, and accepted by other persons. A person's identity is dependent on other persons in good or bad relationships according to Ricoeur , as wellThe surgeons in this study emphasized the importance of dialogue with patients and colleagues. All identities are socially bestowed, socially sustained, and socially transformed and people make meanings of their actions by participating in communicative contexts. We all need recognition and social confirmation from others in order to construct our identities ,48. ThusThere is a close relationship between identity management and values in a society since human beings usually want to be something they find valuable. What constitutes morality is created, recreated and communicated in social relations ,49. NarrThe modern self is described as multi-voiced and dialogical and moral action is determined through a process of inner dialogue. To open up to the different voices within and enter into a dialogue, one can either reach consensus with oneself or experience conflict and dissatisfaction with oneself ,49. The The modernization and secularization of western societies emphasize the ideology of individual autonomy and freedom of choice. At the same time, the way in which social structures control and restrict individual performance and freedom becomes less visible. It is not in every person's or profession's power to choose, in other words, act as his/her conscience directs . The surAccording to the surgeons, their choices of actions and ways of being in relationships with patients and colleagues have to be accepted and confirmed by their inner moral selves. They speak about "having the courage of your own conviction", "taking a stand", "having a personal set of ethical values" as important in order to "live with" the ethical challenges of surgery. The surgeons in this study revealed their identities through their narratives about being in ethically difficult situations.Being a surgeon means having the necessary specialized knowledge, skills, and experience to perform complicated, extensive, and technically advanced operations in principally uncertain and unpredictable situations. This identity is socially sustained through dialogues with patients, relatives, and colleagues. To have an identity as a surgeon is also to understand that one is vulnerable and exposed in these relationships and to know what is at stake in one's own life as well as in the lives of the patients and colleagues.In this study uncertainty, fallibility, and humility seem to be equally important in the surgeons' identities as are their responsibility and confidence. The social importance and benefit of their work to patients and society is confirmed both socially and by their moral selves. This seems to outweigh their personal uncertainty and vulnerability. Thus, surgeons seem to appreciate their work and have learned to live with, and to a certain extent even appreciate, its most difficult dimensions. The meaning of being a surgeon is to be able to live with the tensions of contradictions, ambivalence, dilemmas, and paradoxes in their practice and to find workable solutions in these situations.The author(s) declare that they have no competing interests.KT participated in the design of the study, carried out the interviews, participated in the analysis and completed the manuscript.AN read the interviews, participated in the analysis and helped to draft the manuscript.VS participated in the design of the study, read the interviews, participated in the analysis and helped to draft the manuscript.All authors have read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


Accurate assessment of suicidality is of major importance in both clinical and research settings. The Scale for Suicidal Ideation (SSI) is a well-established clinician-rating scale but its suitability to adolescents has not been studied. The aim of this study was to evaluate the reliability and validity, and to test an appropriate cutoff threshold for the SSI in a depressed adolescent outpatient population and controls.218 adolescent psychiatric outpatient clinic patients suffering from depressive disorders and 200 age- and sex-matched school-attending controls were evaluated by the SSI for presence and severity of suicidal ideation. Internal consistency, discriminative-, concurrent-, and construct validity as well as the screening properties of the SSI were evaluated.Cronbach's α for the whole SSI was 0.95. The SSI total score differentiated patients and controls, and increased statistically significantly in classes with increasing severity of suicidality derived from the suicidality items of the K-SADS-PL diagnostic interview. Varimax-rotated principal component analysis of the SSI items yielded three theoretically coherent factors suggesting construct validity. Area under the receiver operating characteristic (ROC) curve was 0.84 for the whole sample and 0.80 for the patient sample. The optimal cutoff threshold for the SSI total score was 3/4 yielding sensitivity of 75% and specificity of 88.9% in this population.SSI appears to be a reliable and a valid measure of suicidal ideation for depressed adolescents. Accurate assessment of suicidality is of major importance in both clinical and research settings. Adolescent suicide occurs usually in the context of an active, often treatable, but unrecognized or untreated mental illness -3. The iSuicide attempts are complex acts for which no single set of clinical features can be expected to be a good predictor . SuicidaThe Scale for Suicidal Ideation (SSI)  was desiThe psychometric properties of the SSI have been evaluated in adult population and in inpatient children. Both in a sample of adult psychiatric inpatients and in a sample of inpatient children the internal consistency of the scale was good ,13. SSI The predictive validity of the SSI has been studied in a sample of hospitalised patients, where the SSI scores of those who committed suicide were not significantly higher than the scores of inpatients that did not . In a saSome instruments have evolved from the SSI, for example the Modified scale for suicidal ideation (MSSI)  that wasThe SSI has been used widely in adult psychiatric populations e.g. ,21], but, but21]]The study population consisted of two samples; a psychiatric outpatient sample of 218, and an age- and sex-matched control sample of 200 school-attending adolescents. The outpatients suffered from depressive mood disorder, were of ages 13 through 19, and took part in the Adolescent Depression Study (ADS). They were recruited between 1.2.1998 and 31.12.2001 from a consecutive sample of patients attending the outpatient clinics of the Department of Adolescent Psychiatry of Peijas Medical Health Care District covering approximately 210,000 inhabitants and comprising the cities of Vantaa and Kerava in the Helsinki metropolitan area, southern Finland.Of the eligible (appropriate age, knowledge of Finnish language and adequate cognitive capacity) 660 outpatients, 624 (94.5%) were screened during their first consultation visit by the Beck Depression Inventory (BDI)  and the The control sample was drawn from the enrollment lists in four schools in the corresponding geographical area. It was a random sample of age- and sex-matched students equating the distribution of the educational level of the outpatients.1) The Scale for Suicide Ideation (SSI) is a clinician-rating scale and is presented in a semi-structured interview format . It cons2) The Schedule for Affective Disorders and Schizophrenia for School-Aged Children-Present and Lifetime (K-SADS-PL)  is a widThe K-SADS-PL is considered internationally reliable and valid diagnostic instrument for adolescent population . It has 3) Clinical suicidality assessment (CSA): A three-point mutually exclusive grouping of suicidality  is a simplified version of the 5-item "Spectrum of Suicidal Behavior Scale" . It has After a description of the study, a written informed consent was obtained from the subjects. For subjects less than 18 years consent was also asked from the parents or other legal guardians. For the community sample the K-SADS-PL and the SSI were performed at the same day by an expert clinician. For the outpatient sample the K-SADS-PL was performed within variable time from the SSI rating. The CSA was performed for the patient sample by clinicians during the beginning of the treatment.Central tendencies of some data were reported using medians and quartiles because of non-normal distribution. Mann-Whitney U test was used to assess the significance of differences between the two samples.Internal consistency of the SSI was evaluated by calculation of Cronbach's α for the whole scale.Concurrent validity of the instrument was examined by comparing it with the K-SADS-PL with the CSA classifications. SSI total scores were first assessed in 5 classes of increasing suicidality derived from the K-SADS-PL responses in the following way: 1-no suicidal ideation or acts, 2-mild suicidal ideation (score 2 on item-1), 3-severe suicidal ideation (score 3 on item-1), 4-mild suicidal acts (score 2 on any of items 2–4 regardless of ideation), 5-severe suicidal acts (score of 3 on any of items 2–4 regardless of ideation).Then the SSI total scores were measured in 3 classes of increasing suicidal ideation severity, regardless of possible suicidal acts, derived from the K-SADS-PL responses on item 1: 1-no ideation, 2-mild ideation, and 3-severe ideation. Severe ideation (score 3) in this item was considered as "clinically significant suicidal ideation".Finally the SSI total score was assessed in the three classes of the CSA: 1-no suicidality, 2-suicidal ideation, 3-suicidal or self-harming acts.The statistical significance of the between-class differences was evaluated by Kruskal-Wallis test. For the analyses of concurrent validity only SSI-measurements in a range of 30 days from the K-SADS-PL and the CSA were included.Construct validity was measured by performing a principal component analysis (PCA) with varimax rotation in the outpatient sample. The internal consistencies (Cronbach's α) of the extracted components as well as the originally reported factors  were calROC-analysis was performed to evaluate the screening properties of the SSI, and the cutoff threshold for the instrument was defined by optimal trade-off between sensitivity and specificity (Youden's index ). The K-SPSS 11.0 (Chicago, Illinois 60606, SPSS Inc) was used for the statistical analysis.Eighteen percent (n = 40) of the outpatient sample were boys and 82% (n = 178) girls, in the community sample the percentages were 18.6% (n = 37) and 81.4% (n = 162), respectively. The subjects' mean age was 16.4 (SD 1.6) in the outpatient sample and 16.5 (SD 1.6) in the community sample. The median SSI total score for the patient sample was 0 (Q1–3 = 0–6) and for the community sample 0 (Q1–3 = 0-0) (z = -9.6, p = 0.000). The median SSI total score for subjects aged 13–15 was 0 (Q1–3 = 0–1) and those aged 16–19 0 (Q1–3 = 0–1) (z = -0.685, p = 0.493). The median time distance between SSI and K-SADS-PL was 21.5 days (Q1–3 = 9–36) for the patient sample and 0 days (Q1–3 = 0-0) for the control sample (z = -18.0, p = 0.000). The median time distance between SSI and the CSA was 6 days (range 0–35).Forty-seven (21.6%) outpatients and one (0,5%) control subject had current clinically significant suicidal ideation (p = 0.000) according to the K-SADS-PL.Cronbach's α was 0.95 for the whole sample, 0.81 for the community sample and 0.95 for the outpatient sample.146 (67%) of the outpatients and 199 (99.5%) of the controls were included in the analyses for concurrent validity, as their measurements were within the required range of 30 days.2 = 111.6, df 4, p = 0.000).The median SSI sum scores in the five suicidality classes derived from the K-SADS-PL were class-1 = 0 (Q1–3 = 0-0); class-2 = 5.5 (Q1–3 = 0–8); class-3 = 13 (Q1–3 = 0–18.5); class-4 = 4 (Q1–3 = 0–17.3); class-5 = 8 (Q1–3 = 0–13). The differences were significant (χ2 = 132.6, df 2, p = 0.000).The median SSI sum scores in the three classes of suicidal ideation derived from the K-SADS-PL were class-1 = 0 (Q1–3 = 0-0); class-2 = 4 (Q1–3 = 0–8); class-3 = 13 (Q1–3 = 4–18). The differences were significant (χ2 = 57.9, df 2, p = 0.000).The median SSI sum scores in the three clinical suicidality evaluation classes (only the outpatient sample) were class-1 = 0 (Q1–3 = 0–1); class-2 = 10 (Q1–3 = 5–18); and class.3 = 15 (Q1–3 = 13.3–16.6). The differences were significant  and the sample of patients was large compared to earlier similar studies in adult populations, and probably representative of adolescent psychiatric outpatients with depressive disorders. The main finding was that the SSI appeared to be a reliable and valid instrument for evaluation of suicidal ideation in a depressed adolescent population. Its internal consistency and different aspects of validity were good and similar to what has been reported among adults.The construct validity of the SSI was checked by Principal Component Analysis, which yielded 3 theoretically meaningful and coherent factors, only slightly different from the original ones, with good internal consistencies. This suggests good construct validity. The first factor  was nearly identical to Beck's original one . The secThe SSI converged theoretically meaningfully with both the three-class K-SADS-PL suicidal ideation-item and the clinical suicidality assessment (CSA); growing SSI scores were found within categories with increasing severity of suicidality. As to the convergence with the 5-class K-SADS-PL suicidality instrument, the results were more complex. The Kruskal-Wallis test yielded significant differences between the SSI scores in the different categories as expected, but the SSI-scores in the K-SADS-PL classes 4 and 5, with the supposedly most severe suicidality were not higher than in class 3. Classes 4 and 5 inquire about suicidal acts, and may represent a partly separate domain from suicidal ideation, which may be related to the presence of comorbid personality traits or conduct disorders. The SSI was designed to tap suicidal ideation and it may not satisfactorily tap features related with suicidal acts. In accordance with the theory of multidimensional nature of suicidality , severe The authors are not aware of previous empirical estimations of clinically relevant cutoff for the SSI in adolescents. In this study ROC analysis of the whole sample yielded a reasonable result, but the validity coefficients for the different cutoffs of the SSI were somewhat difficult to interpret. In the community sample, there was only one subject with K-SADS-PL-diagnosed clinically significant suicidal ideation, which may have biased the analyses made with the whole sample. The results for both the whole sample and the patient sample suggest that a cutoff threshold score of four or more might be optimal for adolescents. Depending on the purpose the SSI is used, however, the emphasis between sensitivity and specificity may change, and a different threshold may be useful. For example, if the purpose is to detect the maximum number of potential suicides the cutoff threshold should be lowered to minimize the number of false negatives.Several methodological limitations should be noted, some suggesting caution in interpreting the findings. Inter-rater and test-retest reliabilities, which would have given a complete picture of the reliability of the SSI, could not be evaluated in our setting; they would have required repeated SSI measurements for each subject. However, the alpha-coefficients are a marker of internal consistency, which is one indicator of reliability.Although large and representative, the sample was a pure outpatient sample with age- and sex-matched controls, and females were over-represented. The absence of inpatients may have caused us to see the spectrum of suicidal ideation narrower than in real clinical situations. The sample was limited to an urban area in southern Finland, the generalizability of our findings to rural areas, or to other countries, is not known.The use of K-SADS-PL as a standard for clinically significant suicidal ideation and behavior may be criticized, as the authors are not aware of a data on its validity. It is used, however, as one of the best available standards in adolescent mood disorder diagnostics, and taps suicidality with 4 relevant items.The same rater rated the K-SADS-PL and the SSI, which is a weaker test of concurrent validity than correlating measures rated by separate raters.The SSI can safely be used to evaluate suicidal ideation in adolescents where it seems to perform as well as in adults, where it is considered to be well established. When screening clinically significant suicidality in adolescents, a total score threshold of 3/4 may be useful.Suicidal acts may occur among adolescents with only "mild" suicidal ideation. Thus, prevention of suicidal acts cannot rely solely on the SSI, which does not seem to tap them accurately. Furthermore, questionnaires should be only an adjunct to the clinical evaluation of suicidality.SSI appears to be a reliable and a valid measure of suicidal ideation at depressed adolescents, with a cutoff threshold value of four or more of total SSI score being an appropriate for detecting significant suicidal ideation.The author(s) declare that they have no competing interests.MMH analyzed the data and wrote the paper. MP interviewed patients, participated in planning the study and analyses, and writing the paper. LK, TR, HH and VT participated in planning the study, interviewed patients, and commented on the manuscript. OK participated in planning the study and the analyses, and commented on the manuscript. MM supervised the study, interviewed patients and participated in planning of the study and analyses, and writing the paper. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:


The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue.With the goal to assemble a first genome-wide reference transcriptome of the adult mammalian retina, referred to as the retinome, we have extracted 13,037 non-redundant annotated genes from nearly 500,000 published datasets on redundant retina/retinal pigment epithelium (RPE) transcripts. The data were generated from 27 independent studies employing a wide range of molecular and biocomputational approaches. Comparison to known retina-/RPE-specific pathways and established retinal gene networks suggest that the reference retinome may represent up to 90% of the retinal transcripts. We show that the distribution of retinal genes along the chromosomes is not random but exhibits a higher order organization closely following the previously observed clustering of genes with increased expression.The genome wide retinome map offers a rational basis for selecting suggestive candidate genes for hereditary as well as complex retinal diseases facilitating elaborate studies into normal and pathological pathways. To make this unique resource freely available we have built a database providing a query interface to the reference retinome . The mammalian retina is a highly structured tissue developmentally originating from neuroectodermal evagination of the diencephalon and subsequent invagination processes resulting in the formation of two cellular layers which ultimately give rise to the inner neural retina and the outer retinal pigment epithelium (RPE) monolayer . In the Recent progress in retinal research has greatly enhanced our current understanding of basic functional processes in the adult retina e.g. ,5). A gr. A gr5])Despite these advances, a remaining challenge is to obtain a reference genome-wide expression map of the retina/RPE transcriptome, further facilitating the identification of retinal susceptibility genes, but most importantly, offering an invaluable resource for functional genomics studies. Initial analyses of human ,10 and mIn recent years, a number of approaches and technologies were adopted to identify genes expressed in the retina/RPE of human, cow, dog and mouse including data-mining and assembly of publically available expressed sequence tag (EST) information -23, sequBased on a comprehensive survey of data available from 27 independent studies applying a wide spectrum of gene identification approaches we have now assembled a first genome-wide reference transcriptome of the adult mammalian retina/RPE. This reference transcriptome comprises 13,037 non-redundant transcripts and likely reflects up to 90% of the mammalian retinome.A total of 481,137 primary datasets on gene transcripts from the adult mammalian retina/RPE tissues have been generated in 27 independent studies  to be specifically expressed in the retina/RPE (category I, n = 43) , liver (5,343/5,780) and prostate (6,471/7,018). A total of 2,330 genes are expressed in all tissues and represent putative "housekeeping" genes  versus the number of human non-redundant syntenic gene predictions (SGPs) (43,109)  along 61RP29 locus contains 28 SGPs of which 5 are present in the reference retinome including GPM6A, WDR17, FLJ22649, VEGFC, AGA). The number of possible candidates is further reduced in the "retinome-enriched" transcript category to GPM6A and VEGFC. To make the information on the reference retinome available, we have created the interactive RetinaCentral database, a research portal which collects and stores information on genes and proteins functionally relevant to the retinal tissues [To provide positional candidates for syndromic and non-syndromic hereditary retinopathies, the 13K reference retinome as well as the "retinome-enriched" transcripts (5,051 transcripts) were superimposed onto the disease intervals of 42 thus far uncloned retinal disorders (Table  tissues  which arCompiling the transcriptome of a cell or tissue is arguably more demanding than establishing the number of gene loci encoded by a given genome sequence . This maRHOK, MTATP6, CHM, LRAT, RIMS1) not included in the 13K retinome. Similarly, an additional three genes (RHOK, LRAT, GPRK7) involved in the vitamin A/phototransduction pathway are part of the 15K but not the 13K retinome. With additional transcription data on the retina/RPE becoming available, a second generation retinome map will need to address this issue.The present meta-analysis has integrated information from 27 studies employing diverse technologies to identify retinal/RPE transcrips. Among these, SAGE represents a sensitive tool to detect low level transcription  while thThe estimation of transcriptome size represents one of the fundamental questions in molecular biology. Early studies using reassociation kinetics have calculated the number of distinct mRNA transcripts present in various mouse tissues to be between 11,500 and 12,500 . Initialany of the partial transcriptomes revealed overlapping gene profiles between 92 % and 95 %. This would suggest that only a minor proportion of retinome transcripts is indeed unique to the retina/RPE. Thus far, we have identified a group of so called "retinome-enriched" genes comprising 5,051 transcripts which are not present in the partial transcriptomes of heart, liver and prostate. This group most likely contains additional "housekeeping" or tissue-restricted transcripts and needs further adjustment by more refined in-silico normalization to comprehensive reference transcriptomes of other tissues.Another point of interest concerns the proportion of retinome transcripts which is uniquely expressed in this tissue. Brentani et al.  estimateHighly expressed genes including those with a ubiquitous or a tissue-specific transcription profile, have been shown to cluster in chromosomal regions of increased gene expression (termed RIDGEs) ,56. FuncRP28 or VRNI, we have similarly integrated the "retinome-enriched" transcripts. This also accommodates for the fact that approximately 50% of retinal disease genes are retina/RPE-specific [AIED, COD4, CORD8, CRV, LCA5, RP28, and USH2B, the number of candidates may still exceed capacities of most laboratories for direct analysis. For other disease loci (e.g. BCD, BBS3, COD2, CYMD, MCDR4, OPA4, PRD, RNANC, RP24, RP29, RP6, WFS2 and WGN1), a restricted number of candidates are now available  sources  were retrieved (as of December 2003) and chromosomally mapped to the reference sequence of the human genome (July 2003) utilizing the USCS Genome Table Browser . Based oCORD1, CORD4 and RCD1) are insufficiently mapped on the respective human chromosomes and were therefore not included in the analysis.Mapped loci of retinal dystrophies with unknown genetic basis (n = 45) were taken from RetNet, January 2004  and placTo determine if either of the two datasets, the 43,109 human non-redundant SGPs and the 13K retinome transcripts, is distributed in a non-parametric and distribution free manner over the genome, the Kolmogorov-Smirnov Goodness-of-Fit Test was used . StatistHLS participated in the design of the study, collected and processed the information from the published reports related to the retina and RPE genes. TG conceptually developed the RetinaCentral database and is involved in the curation of the site. JK carried out the statistical analyses and helped with the computational handling of data. BHFW was involved in all aspects of data assembly and prepared the manuscript. All authors read and approved the final manuscript.Retina/RPE genes reported only in a single study List of genes expressed in the retina or RPE reported only in one studyClick here for fileGene list of the reference retina / RPE transcriptome List of 13,037 genes expressed in the retina/RPEClick here for fileList of genes identified exclusively in retina studiesClick here for fileList of genes identified exclusively in RPE studiesClick here for filePartial list of genes known to be expressed specifically in the retina and/or RPEClick here for filePartial list of genes known to be involved in the vitamin A cycle and phototranduction pathwayClick here for filePartial list of genes known to encode retina / RPE proteinsClick here for fileList of known genes involved in retinal diseasesClick here for filePartial gene list of the heart transcriptomeClick here for filePartial gene list of the liver transcriptomeClick here for filePartial gene list of the prostate transcriptomeClick here for fileList of genes present in the reference retinome and partial transcriptomes of heart, liver, prostateClick here for fileList of genes present in partial transcriptomes of heart, liver, and prostate but not in reference retinomeClick here for fileList of retinome transcripts mapping to retinal disease intervals.Click here for fileData sources used to compile the retina / RPE transcriptomeClick here for fileData sources used to compile partial transcriptomes of heart, liver, and prostateClick here for file


To evaluate the validity (study 1) and the reproducibility (study 2) of an interviewer-administered food frequency questionnaire (FFQ).Study 1: The FFQ was compared against a 3-day food record (2 week-days and 1 weekend-day), at week 0, 6 and 12 of a nutritional intervention. Study 2: In order to evaluate the reproducibility of the FFQ, 2 registered dietitians administered the FFQ 4-weeks apart among subjects who were not part of the nutritional intervention.The FFQ was designed at Laval University and contains 91 items and 33 subquestions. Study 1: Mean values for intake of most nutrients assessed by the FFQ and by the 3-day food record were not statistically different. Energy-adjusted correlation coefficients for major macronutrients ranged from 0.36 for proteins to 0.60 for carbohydrates (p ≤ 0.01). Agreement analysis revealed that on average, 35% of the subjects were classified in the same quartile when nutrients were assessed by either the 3-day food record or the FFQ. Study 2: Significant associations were observed between dietary measurements derived from the two FFQs administered 4 weeks apart. Correlation coefficients for the reproducibility of macronutrients ranged from 0.66 for carbohydrates to 0.83 for lipids after energy adjustment. On average, 46% of the subjects were classified in the same quartile when nutrient intakes were assessed by either FFQ.These data indicated that the FFQ developed has a good validity and is reproducible. There is increasing evidence that nutrients may be important in the development of chronic diseases such as coronary heart disease (CHD) and type 2 diabetes. In the late 60s, the Mediterranean diet became a topic of interest primarily because of results of the Seven Countries Study, which demonstrated that the 15-y mortality rate from CHD in Southern Europe, was two to threefold lower than in Northern Europe or United States . ReliablAccurate assessment of dietary intakes, when based on self-report in free-living populations poses significant scientific challenges. All standard dietary assessment methods including food records, dietary recalls and list-type methods such as food frequency questionnaires (FFQ), are subjected to considerable error and bias, and none of these can be considered as a 'gold standard' measure . FFQ hasIn Québec, no validated FFQ was adapted for the needs of our nutritional intervention design. In fact, in the context of our nutritional intervention we wanted to use a FFQ to evaluate a Mediterranean food pattern in a North-American context that would contain foods available in Québec and also foods characteristic of the Mediterranean diet. In order to improve the precision in quantifying reported intakes we decided to use and interviewer-administered FFQ to facilitate the determination of portion size using food models. Thus, we decided to design an interviewer-administered FFQ to assess the dietary changes among a French-Canadian population in a nutritional intervention promoting the Mediterranean food pattern. The first purpose of the present study was therefore to test the validity of this interviewer-administered FFQ. In order to reach this objective, nutrient intakes derived from the FFQ were compared to intakes obtained by the 3-day food record. Comparisons were performed for baseline as well as for post-intervention values. This allowed us to determine whether our FFQ would permit to identify similar changes in nutrient intake in response to the intervention as the ones measured by the 3-day food record. As a second objective, we also wanted to estimate the short-term reproducibility of this FFQ in a control group who did not receive the nutritional intervention.This paper reports results of two studies: 1) a study on validity of the FFQ tested against a 3-day food record during a nutritional intervention program promoting the Mediterranean food pattern and 2) a study on reproducibility of the FFQ in a control population.For the validation study, women from the Québec City metropolitan area were recruited through the Laval University newspaper during the summer of 2001. Women included in the study were aged between 30 to 65 years . To be eFor the reproducibility study, 20 men and 19 women from the Québec City metropolitan area were also recruited through the Laval University newspaper during the summer of 2002. Men and women included in the study were aged between 25 to 70 years. Three men and 4 women did not complete the second FFQ for personal reasons. Therefore, 17 men and 15 women were included for the reproducibility analyses. The study was approved by the Ethics Committees of Laval University.The interviewer-administered FFQ developed inquired on the food habits during the last month and is based on typical food items, which are available in Québec. It contains 91 items among which 27 had between 1 and 3 subquestions. The FFQ was structured to reflect Quebecers' food habits and food items were listed in food groups . Because of the nature of our nutritional intervention, our FFQ was designed to make sure to document with enough details consumption of typical items of the Mediterranean diet such as type of oils, whole grain products and legumes. The 30-minutes FFQ was administered face-to-face by one of the 3 registered dietitians involved in the study. During the interview, the dietitians used food models for a better estimation of the real portion consumed by the subject. Participants were questioned about frequency of intake for different foods during the last month and were asked to report the frequency of these intakes in terms of day, week or month. The subquestions allowed a better definition of the food items consumed. For example, following the question "How often do you eat yogurt?" subjects were asked about the fat percentage and brand of the yogurt consumed. An open question at the end of the FFQ allowed individuals to report any other frequency eaten foods not listed in the FFQ and provide details about usual recipes used in order to quantify better intakes of individual food items.Estimates of basal metabolic rate (BMR) were calculated from the Harris-Benedict formulas based on height, weight, age and sex . Energy st, the 6th and 12th weeks of the intervention in order to evaluate the changes and to select further objectives for increasing the adherence to the Mediterranean food pattern. Three registered dietitians were trained to provide a standardized intervention.The methodology of the nutritional intervention has been described previously . BrieflyEach participant completed a 3-day food record, 2-week days and 1-weekend day, at week 0, 6 and 12. At screening of the nutritional intervention, a dietitian provided 15 minutes of instructions to each participant on how to complete the food records. Written copies of record examples were provided to each subject. Also, participants were encouraged to consume usual amounts of typical foods and drinks for the completion of the food record. Participants were not required to weight foods but were asked to measure the volume of foods consumed with household measurements (cups, tablespoons) or to indicate the weight of commercial products when it was possible to assess portion sizes. The food record included a section for recording information recipes. After completing the food record, participants met with the dietitian to review all the information for record accuracy and completeness and portion size of individual items on the food record were reviewed when needed by using food models.At weeks 0, 6 and 12, body weight and height were measured according to the procedures recommended at the Airlie Conference on the Standardization of anthropometric measurements  and bodyThe 32 participants of the reproducibility study were distributed into two groups. In the first group, dietitian #1 administered the FFQ and 4 weeks later dietitian #2 administered the FFQ for the second time. Inversely, in the second group of participants, dietitian #2 administered the first FFQ and 4 weeks later dietitian #1 administered the FFQ for the second time. An interval of one month was chosen to reduce any training effect and memory influence of the method. Both dietitians were taught to use the FFQ similarly, using the same examples of portion size, and asking similar questions.At the first visit, body weight and height were measured according to standard procedures  and BMI Evaluation of nutrient intakes derived from the FFQs and food records was performed using the Nutrition Data System for Research (NDS-R) software version 4.03, developed by the Nutrition Coordination Center, University of Minnesota, Minneapolis, MN, Food and Nutrient Database 31, released in November 2000 . This daIn the validation study, means and standard deviations for nutrient intakes were calculated from the FFQs and from the food records. Student t-tests were performed to determine the differences between nutrient intakes assessed by the FFQ and by the 3-day dietary record. Since many variables were not normally distributed, Spearman correlations were used to put into relationship nutrient intakes from FFQ with those from the food record. Student t-tests were also performed to determine the differences between changes in nutrient intakes in response to the nutritional intervention assessed by the FFQ and by the 3-day dietary record. Agreement analyses were performed to verify the concordance of different nutritional variables among quartiles of the distribution between FFQ and the 3-day food record. In the reproducibility study, Student t test was performed to assess the differences between both FFQs. Spearman correlations were used to put into relationship the nutrients reported in the first and the second FFQ. Agreement analyses were assessed to verify the degree of concordance in classifying subjects among quartiles of the distribution between both FFQs. For both studies, the dietary variables were log transformed when necessary to achieve a normal distribution, and the formula log(x + 1) was used for alcohol because some subjects had a value of 0 g for alcohol intake. In addition, to make the comparisons based on absolute nutrient intakes, correlations were also made using energy-adjusted variables. Adjustment for total energy intake was achieved by using the residual method proposed by Willett and Stampfer . Residua2 and a mean age of 46.8 ± 7.9 y. Average daily nutrient intakes derived from FFQ and the 3-day food records are shown in Table Women had a mean BMI of 25.8 ± 3.9 kg/mSpearman correlations between values of nutrient intakes measured by the 3-day food record and those assessed by the FFQ at week 0 of the nutritional intervention are shown in Table Table st tertile) and from 27.8% for CHO to 55.6% for alcohol for the highest intakes (4th tertile). When considering all nutrients studied, it was found that, on average, 35.1% of subjects were categorized exactly in the same quartile by the FFQ and by the 3-day food record and 5.1% of the subjects were misclassified in extreme quartiles i.e. subject in the first quartile according to one method and in the fourth quartile according to the other (not shown).Agreement between quartile classification of FFQ and 3-day food record is show in Table 2 for women and 27.6 ± 5.1 kg/m2 for men. The mean age was 42.5 ± 10.4 y for women and 41.2 ± 11.9 y for men.The 32 subjects in study 2 had a mean BMI of 23.9 ± 3.6 kg/mst FFQ) showed similar variation in nutrients intakes between FFQ1 and FFQ2 than subjects from the 2nd group (in which dietitian #2 administered the first FFQ).Table st FFQ. In addition, similar correlations were observed when analyses were computed within each gender separately (not shown).Table st quartile) and from 37.5% for SFA and MUFA to 75.0% for energy, proteins, CHO and alcohol for the highest intakes (4th quartile). When considering all the nutrients studied, it was found that on average, 45.7% of subjects were categorized exactly in the same quartile by both FFQs and 2.6% of the subjects were misclassified in extreme quartile (not shown).Table Accurate assessment of dietary intakes and dietary changes plays a central role in nutritional studies. Each tool used to evaluate dietary intakes has some strengths and limitations. Also, all standard dietary assessment methods are subjected to bias such as underreporting . In our In the validation study, coefficients of correlation between values derived from the FFQ and those obtained by the 3-day food record ranged from 0.30 to 0.60 for macronutrients and from 0.19 to 0.56 for micronutrients at week 0. It has been previously reported that correlation coefficients for validation studies ranged from 0.4 to 0.7, similar to our results after energy adjustment . Also, oDespite the fact that we obtained similar values for energy intake with both dietary methods, we can not exclude the possibility that both tools are subjected to underreporting and therefore underestimate usual dietary intakes. It has been previously suggested that subjects may tend to underreport actual food intake by as much as 20% when completing a weighted dietary record . It has In a nutritional intervention, interpretation of the study outcomes with regard to dietary changes will depend not only of the validity and the reproducibility of the method used but also of the sensibility of the method to detect dietary changes in response to the intervention. In our nutritional intervention study, conducted in a sample of healthy women, both diet assessment methods detected similar dietary changes over the duration of the intervention. These findings suggested that our FFQ is sensitive to dietary changes in response to our intervention and could be used to assess dietary changes during a nutritional intervention. Our results are in agreement with study that showed that in response to a nutritional intervention a FFQ measured similar dietary changes as compared to 24-hour recalls  or 4-dayThe major differences between the two methods in our study were noted for total lipids and MUFA intakes. Our FFQ was designed to assess precisely lipid intake and many questions were asked about types of fat used to spread or to cook. The more important differences between FFQ and 3-day food record for MUFA and lipids could therefore be explained by the fact that it was difficult for participants to report precisely their lipid consumption when completing the FFQ. It has also been reported in obese men that underreporting of food record is usually specific to lipid intake  and it iThe agreement in quartile classification was acceptable for selected nutrients with a mean of 35.1% of subjects who were in exact agreement and 5.1% who were misclassified in extreme quartiles. This finding is similar to previous observations ,19,32,33When analyses were performed at week 6 and 12 after the beginning of the nutritional intervention, coefficients of correlation were slightly higher than at week 0. We suggest that this finding be partly explained by the intervention effect. As previously reported  subjectsIn a nutritional intervention, it is important to use a reproducible method to insure that dietary changes observed are due to the intervention effects and not to the instrument error. Our study suggests that the FFQ presents a good degree of reproducibility. In fact, in reproducibility studies the coefficients of correlation generally ranged from 0.5 to 0.7 . In our In our reproducibility study, lower mean energy intake and nutrient intakes were found at the second administration of the FFQ as compared to the first FFQ (difference of approximately 10%). However, relatively high and uniform correlation coefficients for values derived from the two FFQs were observed. Riley et al  also repIn conclusion, the FFQ that we developed to estimate usual average daily energy and nutrient intakes in subjects from the Québec City metropolitan area is valid and reproducible. Mean energy and nutrient intakes were estimated accurately by our FFQ compared to the 3-day food record. The fact that our FFQ was administered by a dietitian trained to insure a standardized administration of FFQ was important to optimize the validity and reproducibility of the method. We also showed that both methods appeared to underestimate energy intake in a large proportion of subjects. Usually, food records are considered as the gold standard method to assess dietary intakes. It is however important to recognize that food records also have their own limitations. In nutritional studies, an interviewer-administered FFQ, as the one we used in the present study, can be used to assess energy and nutrient intakes and requires less time to compute dietary informations than food records. FFQ also decreases the possibility of interpretation by the coding person. Finally, there is still a need to develop other efficient methods to measure dietary intakes that will permit to more closely match habitual dietary intakes of individuals in their living environment.CHD: coronary heart diseaseFFQ: Food Frequency QuestionnaireBMR: basal metabolic rate (BMR)BMI: body mass indexNDS-R: Nutrition Data System for ResearchCHO: carbohydratesSFA: saturated fatty acidsMUFA: monounsaturated fatty acidsPUFA: polyunsaturated fatty acidsEPA: eicosapentaenoic acidDHA: docosahexaenoic acidNone declared.JG participated to data collection, performed data analysis and drafted the manuscript. GN and AL participated to data collection. BL and SL conceived the study, and participated in its design and coordination. All authors read and approved the final version of the manuscript.