PLoS GeneticsPLoS BiologyPLoS PathogensPerhaps more than any other biological discipline, the study of animal viruses is confined to the present. Virions are simply not the stuff of which robust fossils are made. Phylogenetic analysis can help by revealing deep relationships between extant viral lineages, yet such reconstructions lack detail , and molecular clock estimates are notoriously imprecise when applied to viruses Retroviral infection occasionally results in the deposition of a provirus in a host's germline DNA. While germline integration of a provirus may be an exceedingly rare event, across the great expanse of evolutionary time millions of ERV loci have accumulated in animal genomes. Because retroviruses replicate through an integrated DNA intermediate, it is not difficult to imagine how ERVs are generated. For other animal viruses, which do not normally integrate their genomes into host DNA, the formation of germline insertions should be far less likely. Nonetheless, reports of non-retroviral specimens being unearthed from the genomes of animal species are on the rise. Notable examples include functional expression of nudivirus-related structural genes in the genomes of parasitic wasps Two of the studies also took a closer look at a previously described class of EVEs, called EBLNs (for endogenous Bornavirus-like N genes) in trans, by retrotransposons or possibly retroviruses, may be a predominant mechanism of EVE formation. In fact, for RNA viruses that replicate in the cytoplasm , retrotransposition is the most plausible mechanism for EVE formation. In such cases, it will be interesting to determine whether the more abundant EVE sequences share some common feature(s) conferring a propensity for retrotransposition. In contrast, hepadnavirus “fossils” lack the hallmarks of retrotransposition (such as flanking insertion-site duplications and poly-A tails), and may instead have resulted from non-homologous end joining and insertion of viral DNA directly into the host genome As a group, viruses are polyphyletic, as evidenced by the variety of unique genome types and distinctive replication strategies they collectively employ. There are double-stranded DNA viruses and single-stranded DNA viruses, double-stranded and single-stranded RNA viruses, and viruses with segmented genomes; among those with single-stranded RNA, there are those with positive polarity (the genome resembles an mRNA) and those with negative sense genomes. Each genome type represents a different starting point for takeover of the host cell, and each requires a different strategy for achieving this fundamental task. For example, replication of some viruses is confined entirely to the cytoplasm, whereas others involve synthesis of DNA or RNA in the nucleus. While the fossil record is still dominated by retroviral sequences, the inventory of known EVE loci now appears to include representatives of all the basic replication strategies exemplified by modern viruses. Non-retroviral EVEs are typically subgenomic, derived from just one or a few viral genes instead of entire viral genomes. Insertion site duplications bracketing some EVEs suggest that retrotransposition When incorporated into phylogenetic trees, many EVEs group as sister taxa to their modern counterparts. Thus, they are not evolutionary intermediates on the path to extant viruses, but rather extinct lineages sharing a common ancestor with modern viruses. From this, one can infer that most of the distinctive replication strategies employed by modern viruses probably originated hundreds of millions of years ago. While virologists intuitively understand this (given the widespread distribution of viruses among living organisms), EVEs constitute direct, physical evidence that modern viral lineages have very ancient roots . That moThe catalog of EVEs is impressive for what it contains, but even more so for what it does not. Why? Because the known EVEs probably represent a minor and highly skewed sampling of viral prehistory. Minor, because the odds that infection of an individual organism will result in fixation of an EVE are exceedingly small . Skewed,The current EVE record may have other limitations. Just how far back does the EVE fossil record extend? Erosion due to the steady accumulation of mutations must impose an upper limit on how far back the viral fossil record can be deciphered, and theoretical predictions of that limit would be useful. Even in the absence of sequence degradation, some EVEs may be easier to detect than others. For example, the studies described here relied on known viral sequences as queries: if our genomes also harbor ancient viral sequences for which there is no modern counterpart, how would we recognize them for what they once were?


We show that when ecologists act as reviewers their reported rejection rates recommended for manuscripts increases with their publication frequency in high impact factor journals. Rejection rate however does not relate to reviewer age. These results indicate that the likelihood of getting a paper accepted for publication may depend upon factors in addition to scientific merit. Multiple reviewer selection for a given manuscript therefore should consider not only appropriate expertise, but also reviewers that have variable publication experience with a range of different journals to ensure balanced treatment. Interestingly since age did not relate to rejection rates, more senior scientists are not necessarily more jaded in reviewing practices. In the peer-review of publications, scientists alternate between two roles: one as author and the other as reviewer If objective assessment of potential publication by others is one of our principal activities, then the effect of experience as referees needs critical examination, particularly since assessment could be balanced by selection of different categories of referees if they exist. In several instances, it has been shown that ecologists who publish more papers experience higher rejection rates of their manuscripts As part of an NCEAS working group on publication bias, we conducted an online survey of ecologists to develop a profile of their experiences with publication and review. A total of 17 open-ended, multiple choice, and likert-scale questions relating to the publication process were included in the survey, however only those pertaining to this paper were analysed and reported here . SpecifiThe survey was posted online from May 4th, 2006 to November 4th, 2006 and was distributed to the Ecological Society of America (ECOLOG) and EvolDir mailing lists as well as promoted at international ecological and evolutionary conferences and posted on the working group website. These distribution lists were selected as a representative means to target ecologists and evolutionary biologists. The extent to which individual respondents subscribe to both list-serves was unknown hence the minimum (assuming there was complete overlap in subscribers to both list-serves) and maximum (where there was no subscription overlap) population sizes ranged from 6000 to 12 200. After removal of duplicates and incomplete surveys, the sample size was 1334 responses, representing between 11% and 22% of the total population solicited. We were unable to test for response bias as non-respondents could not be tracked due to the use of list-serves for survey distribution rs) to examine the association between the recommended rejection rates and reviewer's scientific age and the number of high impact factor journals in which he/she has published. Sensitivity analyses via exclusions were also used to ensure that a relationship detected was not a product of single individuals.Chi-square tests were used to compare the distribution of rejection rate categories among respondents with and without publication experience in high impact factor journals. We calculated Spearman rank correlation coefficients (Respondents reported significantly different recommended rejection rates of reviewed manuscripts depending on publication experience in high-impact-factor (IF) journals . Furtherper se, but that they do likely become more critical as they publish more in high-IF journals. The increase in recommended rejection rates can be as much as double or triple , or whether those with less experience are insufficiently critical (i.e. fail to notice significant shortcomings). Nevertheless, variation in rejection rate by reviewer attributes, as reported here, represents a potential reviewer bias, which is likely to affect community-level perception and assignment of relative merit in the peer-review process Appendix S1(0.03 MB DOC)Click here for additional data file.


Dentinogenic ghost cell tumor (DGCT) is an uncommon locally invasive odontogenic tumor regarded by many as a variant of calcifying odontogenic cyst. The peripheral variant of this clinical rarity appears as a well-circumscribed mass mimicking a nonspecific gingival enlargement. Microscopic appearance of odontogenic epithelium admixed with focal areas of dentinoid formation and sheets of ghost cells giving the definitive diagnosis of dentinogenic ghost cell tumor imply that microscopic examination is compulsory for any gingival mass. Van Gieson histochemical stain further confirmed the nature of dentinoid-like material. A complete workup of a case of peripheral dentinogenic ghost cell tumor is presented in this paper and the current concept as well as the appraisal of literature is presented. Calcifying odontogenic cyst (COC) is a unique jaw lesion, first recognized as a distinct entity by Gorlin et al.  and hencThe term DGCT is commonly used, and the peripheral variant of this neoplastic entity is rare; only few reports with clinical, radiographic, and histologic documentation can be found in the English literature. A report of peripheral dentinogenic ghost cell tumor (PDGCT) and characterization of dentinoid material using Van Gieson special stain for the confirmation adds a new dimension to the diagnosis of DGCT.A 40-year-old male patient reported to the dental clinics at Manipal College of Dental Sciences, Manipal University, with a complaint of missing teeth. Clinical examination disclosed a swelling measuring about 5 mm in diameter in the region of lower left premolars which was non tender, and the over lying mucosa was normal in color. Clinically, a provisional diagnosis of epulis was made . The lesHistological examination revealed a solid well-circumscribed, encapsulated soft tissue mass surrounded by a dense fibrous connective tissue covered by stratified squamous epithelium . The tumDGCT is a distinct but a rare histological entity among odontogenic ghost cell lesions which have been recently classified into the simple cystic type or COC; cysts associated with odontogenic hamartomas or benign neoplasms; solid benign odontogenic neoplasm, which is same as COC but with dentinoid formation, the DGCT; malignant odontogenic neoplasm-ghost cell odontogenic carcinoma . The perThe usual presentation of the peripheral variant is a nodular swelling on the edentulous alveolar mucosa of denture wearers, a feature that implicates trauma/irritation. This clinical presentation could lead to the provisional diagnosis of epulis as was true in our case as well. Due to the dearth of documented cases, it is difficult to typify the exact location, age, and gender distribution of PDGCT. However based on the existing literature it appears to be more common in the canine-premolar region, with a predilection for the elderly age group , 14–23 . HirshbeBased on this histological diversity, the origin of this lesion has been attributed to cell rests of Serres or the surface epithelium , 26. TheDue to its biological behavior COC, and its variants are thought to resemble a benign odontogenic tumor rather than a cyst . PreviouIn our case as well, the presence of keratinizing ghost cells and mineralization was an outstanding feature. The lesion did not exhibit any cystic areas, and its features were consistent with those of DGCT. The calcifications seen as dentoid, frequently described in connection with masses of ghost cells, were a characteristic finding of this lesion. These calcified areas were thought to represent juxtaepithelial osteoid formation by granulation tissue due to induction by ghost cells . This viConservative but aggressive local resection has been the treatment of choice with no recurrences found in any patient. However patients with a DGCT should remain in long-term follow-up . Though


The HIV/AIDS epidemic in America is rapidly progressing in certain subpopulations, including African-American and Hispanic communities. Churches may provide a means for reaching high-risk minority populations with effective HIV/AIDS prevention. We report on a series of focus group interviews conducted with Utah clergy who primarily serve African American and Hispanic congregations.A total of three focus groups (two with Catholic clergy serving Hispanic congregations and one with protestant clergy serving African American congregations) were conducted with eleven participants, lasting approximately two hours each. Each focus group was audio-recorded and transcribed for analysis. Analysis of the data was conducted using a modified grounded theory approach.There were remarkable similarities in the attitudes and beliefs among all clergy participating in this study regarding HIV/AIDS and church-based prevention programs. All groups expressed concern about the diseases as a global epidemic and reported that the disease is highly preventable. Also, participants indicated a sense of responsibility to address the issues surrounding HIV/AIDS-related prevention, testing and care within their theological framework.HIV/AIDS prevention and care for the infected are seen as falling within the scope of religious organizations. Openness to expanding efforts in this regard was shared by clergy participating in this study. Approaching religious leaders with tailored approaches that respect the values and practices of their particular religions will be more effective than attempting to impose approaches that do not achieve this standard. After two decades of HIV/AIDS in America, the epidemic is rapidly progressing in certain subpopulations, including African-American and Hispanic communities. Adults and children in these communities have been disproportionately affected. According to the CDC surveillance reports for 2001, African-Americans and Hispanics together represent 57 percent of reported AIDS cases and 62 percent of reported HIV cases  as a problem.” However, the African American clergy stated that they knew of church members who were infected as well as members who had died from the disease. As such, African American clergy indicated more awareness and active engagement in addressing HIV/AIDS within their congregations.Both groups stated that members of their congregation engage in risky behaviors. They also discussed their belief that HIV/AIDS has a bigger impact on people outside of their congregation than on participating church members, and stated that those whose lifestyles put them at risk for HIV/AIDS may not attend or may feel ostracized from the church. Thus, they further indicated that outreach beyond their own church members was both necessary and part of their ministry. Included in this was a concern regarding HIV/AIDS among incarcerated individuals.All respondents professed compassion for those infected with HIV/AIDS and for those affected because of an HIV positive loved one. There was a distinction between teachings that condemn the behaviors and compassion for individuals engaged in these behaviors. When asked about current HIV/AIDS-related activities, the African American clergy discussed a number of established programs within their churches including HIV/AIDS information/awareness meetings, educational programs focused on youth, spirituality programs for those infected with HIV/AIDS, and outreach to prisoners and community members. The Catholic clergy discussed moral teachings targeted at high risk behaviors for youth prior to their Quinsañeras celebrations.Respondents were asked about the acceptability of a number of church-based HIV/AIDS prevention programs, and gave very similar answers. Both the Catholic and African American Christian clergy felt that sermons and youth services about abstinence and drug abuse, public workshops about HIV/AIDS prevention, support groups for people with HIV/AIDS and their family members, and outreach programs directed at people at risk for HIV/AIDS would be acceptable church-based activities. A number of participants stated that they would not discuss condom use or other non-abstinence-related prevention methods from the pulpit. Both groups felt that sermons and youth services about condom use, clean needle exchanges, and condom distribution would be unacceptable church-based activities.Some participants stated that discussion of such issues may arise during one-on-one interactions with church members or in church-sponsored activities outside of sermons. In each case, such comments were linked to concerns about balancing appropriate moral teaching with effective means of preventing infections. They were clear that such discussions needed to be handled with the utmost sensitivity and judgment.Ministers were eager to learn about means of improving their existing programs. Specifically, they were interested in learning more factual information about HIV/AIDS and developing programs that fit within their respective doctrines. They further discussed the need to be sensitive to doctrinal limitations, time constraints, and busy schedules in improving upon their current efforts. All were open to integrating their efforts with others addressing this epidemic as long as these same sensitivities were considered.With the continued emergence of HIV infections there is increasing evidence that preventive efforts are not sufficiently effective and that increased attention is needed to care for the infected. When addressing these issues, novel approaches such as church-based prevention programs may provide the means for increased success in both prevention and care. Our research indicates that religious leaders see themselves as having responsibility in addressing the HIV/AIDS epidemic. Further, they see themselves as a critical part of the multifaceted campaign to address HIV/AIDS related impacts.Specifically, clergy indicated that there are many ways in which their efforts related HIV/AIDS may be enhanced. From their perspective, collaboration with others that fit within the scope and boundaries of their ministries will likely lead to increased effectiveness in prevention and compassionate care. Further attention is needed for the development approaches to enhance clergy members’ capacity to be effective in their efforts as well as the design of evidence-based interventions that are consistent with clergy members’ primary ministerial responsibilities.Church-based programs may also be a means of reaching high-risk minority populations. Many outreach efforts are already targeting individuals at high risk, providing a natural platform from which to further extend HIV/AIDS related efforts. However, in the development of such programs, sensitivity to church doctrine, theological limitations, and cultural diversity are factors that must be addressed. With such consideration, HIV/AIDS prevention messages and promoting care for the infected can easily be incorporated into current church teachings and outreach programs.Academic and other social institutions have a role in working with religious organizations to integrate efforts as a means of creating synergy that can directly impact the HIV/AIDS epidemic and those infected. Specific programs can be designed and collaboratively implemented that combine the most current understanding of the HIV/AIDS biology and effective behavioral and therapeutic interventions that are within the scope of churches stewardships. We found that not only were the clergy of churches serving minorities open to such collaboration, they were anxious for partnerships that respected their theological boundaries. Rather than attempting to impose approaches that are contrary to church values, interventions need further development that will allow for enhancing the impact of efforts that are deemed to be appropriate.The primary limitations of this study include being geographically constrained and having a relatively small sample that may lack generalizeability. However, the primary intent of this study was an initial effort to explore the openness of religious clergy to engage in collaborative efforts related to HIV/AIDS. This work merely provides a glimpse of the potential to combine the influence of religious organizations with evidence-based approaches typically reserved for non-religious efforts targeting HIV/AIDS.HIV/AIDS prevention and care for the infected are seen as falling within the scope of religious organizations. Further, openness to expanding efforts in this regard was shared by clergy participating in this study. Critical next steps include more research to better understand the perspective of religious organizations and development of approaches that can be implemented within the context of their philosophical frameworks. Approaching religious leaders with tailored approaches that respect the values and practices of their particular religions will be more effective than attempting to impose approaches that do not achieve this standard. There was clear consensus among respondents that supportive partnerships rather than directive efforts are desired for increasing the effectiveness of HIV/AIDS related efforts.


A new mouse study provides experimental evidence that exposure to secondhand cigarette smoke during pregnancy may lead to weight gain in offspring as well as changes in lipid profiles that may increase the chances of cardiovascular disease later in life Oxidants in cigarette smoke have previously been shown to promote local and systemic inflammation and increase the risk of cardiovascular disease in both smokers and those exposed to secondhand smoke. Lipid oxidation in particular has been associated with cardiovascular diseases. Women have a higher risk of dying from cardiovascular disease than men and are more likely to die following a heart attack.The current study may shed light on this observed sex-specific difference. Female pups of mice that were exposed to cigarette smoke for 4 hours a day, 5 days a week, throughout pregnancy grew up to have a higher body weight than their unexposed peers and had significant increases in plasma high-density lipoprotein (HDL), low-density lipoprotein (LDL), and total protein. However, these differences were not observed when the adult female offspring were fed a high-fat diet instead of a regular diet. On the other hand, smoke-exposed male pups gained more weight and displayed altered lipid profiles compared with their sex-matched, unexposed counterparts when they were fed a high-fat diet but showed little evidence of an effect of smoke exposure when fed a normal diet.Although maternal exposure to cigarette smoke appeared to influence weight gain and lipid profiles in their offspring, lipid parameters in the dams themselves showed little change in response to smoke exposure. Additional work is necessary to understand why lipoprotein levels—which reflect cholesterol metabolism—are altered in the offspring in response to cigarette smoke exposure during pregnancy.Abnormal body weight and dyslipidemia  are among the best-established risk factors for cardiovascular diseases. Although the new study does not investigate the mechanisms of the observed changes, it does suggest that prevention programs that emphasize avoidance of cigarette smoke during pregnancy could reap long-range health benefits for the newborn.


Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment—previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches—yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our  Biological sequence alignment is one of the fundamental problems in comparative genomics, yet it remains unsolved. Over sixty sequence alignment programs are listed on Wikipedia, and many new programs are published every year. However, many popular programs suffer from pathologies such as aligning unrelated sequences and producing discordant alignments in protein (amino acid) and codon (nucleotide) space, casting doubt on the accuracy of the inferred alignments. Inaccurate alignments can introduce large and unknown systematic biases into downstream analyses such as phylogenetic tree reconstruction and substitution rate estimation. We describe a new program for multiple sequence alignment which can align protein, RNA and DNA sequence and improves on the accuracy of existing approaches on benchmarks of protein and RNA structural alignments and simulated mammalian and fly genomic alignments. Our approach, which seeks to find the alignment which is closest to the truth under our statistical model, leaves unrelated sequences largely unaligned and produces concordant alignments in protein and codon space. It is fast enough for difficult problems such as aligning orthologous genomic regions or aligning hundreds or thousands of proteins. It furthermore has a companion GUI for visualizing the estimated alignment reliability. The field of biological sequence alignment is very active, with numerous new alignment programs developed every year in response to increasing demand driven by rapidly-dropping sequencing costs. The list of approximately 60 sequence alignment programs on the wikipedia compilation provides a lower bound on the number of available tools and illustrates the confusing choice facing biologists who seek to select the “best” program for their studies. Nevertheless, the ClustalW program A key issue in understanding the popularity of ClustalW is to recognize that it is difficult to benchmark alignment programs. Alignments represent homology relationships among the nucleotides, or amino acids, of the genomes of extant species, and it is impossible to infer the evolutionary history of genomes with absolute certainty. Comparisons of alignment programs therefore rely on databases of structural alignments for proteins and RNA or on gene loci or simulated data for DNA. Each type of benchmark is vulnerable to manipulation and furthermore may not represent the problem setups which are most relevant to biologists. The result is that biologists are confronted with many programs and publications, but it is frequently unclear which approach will give the best results for the everyday problems which they seek to address.Adding to the difficulty of selecting software tools is the blur between programs and ideas. Developers of alignment programs make choices about the objective functions to optimize, the statistical models to use, and the parameters for these models, but the relative impact of individual choices is rarely tested In lieu of these issues, biologists have favored the conservative approach of using the tried and trusted ClustalW program, although they frequently use it in conjunction with software which allows for manual editing of alignments We therefore approached the alignment problem with the following goals in mind:An approach which seeks to maximize the expected alignment accuracy. Our approach seeks to find the alignment with minimal expected distance to the true alignment of the input sequences, where the true alignment is treated as a random variable, with the probability of each true alignment determined under a statistical model. Explicitly incorporating a statistically-motivated objective function, this “expected accuracy” approach to alignment allows us to visualize alignments according to estimates of different quality measures, including their expected accuracy, sensitivity, specificity, consistency and certainty. We therefore offer biologists a way to compare alignments that allows them to quantitatively judge differences in alignment quality when they are performing manual edits.A method which is robust to variation in evolutionary parameters. We sought a method which is robust to phenomena such as sequences of differing evolutionary distances and base composition. While “phylogenetic alignment” methods seek to accomplish this by explicitly modeling alignments on trees Robust results when faced with the wide range of alignment problems encountered today. We sought to create a single program which is capable of achieving high accuracies on protein, RNA and DNA sequences without additional input from, e.g., database homology searches. We additionally sought to make our approach fast enough for large-scale problems such as aligning many sequences or orthologous regions of genomes. Creation of a modular code base so that future improvements in one aspect of alignment could easily be incorporated into our approach. In particular, we aimed to create a collaborative infrastructure so that “bioinformaticians with expertise in developing software for comparing genomic DNA sequences [can] pool their ideas and energy to produce a compact tool set that serves a number of needs of biomedical researchers” The “distance-based” approach to sequence alignment, proposed in We have implemented our approach in FSA, a new alignment program described below. We give an overview of the structure of FSA and explain the details of its components below. input to FSA is a set of protein, RNA or DNA sequences. These sequences are assumed to be homologous, although FSA is robust to non-homologous sequence. The output of FSA is a global alignment of the input sequences which is a  optima of the expected accuracy under FSA's statistical model.The FSA first performs pairwise comparisons of the input sequences to determine the posterior probabilities that individual characters are aligned . While the number of possible pairwise comparisons is quadratic in the number of sequences being aligned, giving unfavorable runtimes for datasets of many sequences, FSA overcomes this problem by reducing the number of pairs of sequences that are compared. This is accomplished using a randomized approach inspired by the Erdös-Rényi theory of random graphs, thereby drastically reducing the computational cost of multiple alignment.After obtaining pairwise estimates of homology at the single-character level, FSA uses the sequence annealing technique The architecture of FSA reflects the inherent modularity of the distance-based approach to alignment. FSA's inference engine uses the flexible HMMoC code-generation tool Each of these components can be improved independently of the others, allowing for rapid future improvements in distance-based alignment. For example, FSA's entire statistical model could easily be altered to incorporate position-specific features or completely replaced with a discriminative or hybrid generative-discriminative model.The components described here correspond roughly to the simplest mode of operation for FSA, outlined in bold in FSA accepts FASTA-format input files and produces alignments in multi-FASTA or Stockholm format. The server also outputs PHYLIP and ClustalW formatted files.Distance-based alignment, relying on pairwise estimations of homology, operates on the posterior probability distributions that characters in two sequences are aligned. FSA uses the standard three or five-state pair hidden Markov model (Pair HMM) shown in The standard Forward-Backward algorithm on a Pair HMM has time complexity After calculating the posterior probabilities of alignment for characters in all sequence pairs, After estimating these posterior probabilities and sorting them, FSA creates a multiple alignment with the sequence annealing technique The distance fraction of positions for which they make identical homology statements. In contrast with traditional measures of sensitivity and specificity, accuracy takes into account all positions, rather than just those that are predicted to have a homolog. The alignment with the minimum expected distance to the truth is equivalent to the alignment with the maximum expected accuracy,The posterior probabilities over alignments Using this expected accuracy as an objective function for a greedy maximization, sequence annealing begins with the null alignment  and merges single columns  according to the corresponding expected increase in “The mathematics of distance-based alignment” in In FSA's definition of an alignment, an alignment consists solely of a specification of homology. This definition differs from the standard definition of a multiple alignment, which implies an evolutionary history of substitution and indel events. For example, FSA  considers the two alignments shown in This is problematic for comparative genomics analyses which use an alignment to infer evolutionary parameters such as indel frequencies across a clade. In order to output a single global alignment from which such evolutionary parameters can be inferred, we choose a topological ordering of the alignment POSET which corresponds to a maximum-parsimony interpretation of indel events. FSA outputs the global alignment with the minimum number of “gap openings” across the individual sequences  can give misleading results. Nonetheless, sequence alignment algorithms traditionally use a single model for all sequences.In order to overcome these difficulties, FSA uses “query-specific learning,” wherein a different model is learned for each pairwise comparison (the “query”). This is done in a completely unsupervised framework: FSA uses an unsupervised Expectation Maximization (EM) algorithm to estimate transition (gap) and emission (substitution) probabilities of the Pair HMM on the fly.aligned sequences; in contrast, we empirically observe good results with as little input data as two unaligned DNA or RNA sequences of length 60 nucleotides or four unaligned protein sequences of length 266 amino acids. These figures correspond to observing each of the independent parameters of a substitution matrix four times.Despite its unsupervised nature, FSA's query-specific learning needs remarkably little sequence data to effectively learn parameters. Standard alignment algorithms estimate parameters from thousands or tens of thousands of pairs of 2−1) = 15 free parameters, FSA can learn a different emission distribution for every pairwise comparison of all but the shortest RNAs or DNAs . In contrast, emission matrices over aligned amino acids have (202−1) = 3,999 free parameters, thereby preventing FSA from learning independent models for each pair of proteins. FSA therefore learns a single emission matrix using an all-pairs comparison for protein sequences.While FSA learns distinct transition parameters for every pair of query sequences regardless of the sequence composition, it uses different learning strategies for nucleotide and amino acid emission matrices. Because a pair emission matrix over aligned nucleotides has only  using a weak Dirichlet regularizer (prior) when estimating both transition and emission probabilities, and (2) terminating parameter learning before the EM algorithm converges. By default the Dirichlet emission priors are scaled such that total number of pseudocounts for aligned characters is equal to the number of free parameters in a symmetric pair emission matrix. As is the case for other machine-learning algorithms, it can be shown that termination before convergence of query-specific learning is equivalent to a form of regularization .If there is insufficient sequence data for effective learning, then FSA does not estimate parameters and instead uses default parameters to construct an alignment. The default parameters values, as well as seeds used for the learning algorithm, are discussed in While FSA can align hundreds or thousands of sequences on a single computer, it can handle truly large-scale problems by running in a parallelized mode on a computer cluster. FSA's distance-based approach to alignment gives the multiple alignment a natural independence structure: each pairwise alignment is independent of all other pairs, allowing dramatic runtime reduction by distributing the individual pairwise computations to different processors.Two factors were considered for the parallelization of FSA : (1) communication overhead between nodes, and (2) workload distribution over the different processors. For example, distributing jobs in very small batches may reduce processor idle time but lead to high overhead; in contrast, using large batches may increase idle time but minimize overhead. FSA's parallelization mode uses the “Fixed-Size Chunking” strategy described in While the pairwise comparisons can be naturally parallelized, sequence annealing does not have the same obvious independencies. Therefore, even when running in parallelized mode, FSA performs sequence annealing on a single node. The parallelization of the annealing step is a future aim for this project. A schematic of the current parallelization strategy is given in As a greedy algorithm, sequence annealing is only guaranteed to find a local optima of the expected accuracy. FSA therefore uses an iterative refinement strategy after sequence annealing terminates to locally improve the alignment. For each round of iterative refinement, FSA looks at every character's position in the multiple alignment and sees whether the objective function can be improved by moving it to another position . FSA assembles a list of such candidate character shifts, orders the list by the expected change in the objective function, and then performs the shifts. Iterative refinement terminates when there are no candidate shifts which improve the objective function.FSA's included GUI permits the user to visually assess alignment quality under FSA's statistical model according to estimates of different measures, including expected accuracy, sensitivity, specificity, consistency and certainty. This permits biologists and bioinformaticians to incorporate reliability measures into downstream analyses, such as evolutionary rate measurements and phylogenetic reconstruction. Incorporating such information can produce distinctly different results. For example, over-aligned non-conserved sequence can cause a systematic bias towards long branch lengths; this can be ameliorated by incorporating the expected accuracy statistics produced by FSA into reconstruction algorithms. FSA's GUI can color alignments according to five different measures of alignment quality, which are approximated under its statistical model. Characters Accuracy: The expected accuracy with which Sensitivity: The expected sensitivity with which Specificity: The expected specificity with which Certainty: The certainty with which Consistency: The consistency of the many pairwise comparisons used to construct the multiple alignment and the implied optimality of the alignment of See The GUI also provides a visual and statistical guide when manually editing alignments.We benchmarked FSA against databases of multiple alignments compiled from reference structural alignments, including protein databases  sequence. This is a realistic setup for biologists who might want to decide whether a sequence is orthologous to a particular protein family. With the exception of FSA, the tested alignment programs suffered a false-positive rate increased by over 25% on this BAliBASE 3+fp dataset, indicating that they aligned the random sequence with the homologous set. In contrast, FSA left the random sequence unaligned and had an essentially-unchanged false-positive rate.BRAliBase 2.1 was assembled from the RFAM The Consan mix80 dataset of alignments of Small and Large Subunit ribosomal RNAs, assembled from the European Ribosomal RNA database Drosophila DNA sequences. FSA produced higher-accuracy alignments than the other programs on the two Drosophila datasets and only Pecan gave better alignments of the mammalian sequences.Drosophila described in Drosophila genomic alignments were created by parameterizing the DAWG and simgenome programs using whole-genome alignments produced by Pecan for The simulated alignments of nonfunctional DNA sequences from nine mammals  were created by Blanchette et al. FSA's strong performance on all three datasets of simulated long DNA sequences indicate that it is a useful and accurate tool for genomic alignment.In order to further test the appropriateness of using popular alignment programs to detect homology between sequences, we conducted a large-scale random-sequence experiment. We generated datasets of random sequences to simulate unrelated protein, short DNA, and genomic (long) DNA sequences. The results, shown in Saccharomyces cerevisiae identified as having orthologs in the six related yeast species S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri Click here for additional data file.


Artemisia annua) and are well established for the treatment of malaria, including highly drug-resistant strains. Their efficacy also extends to phylogenetically unrelated parasitic infections such as schistosomiasis. More recently, they have also shown potent and broad anticancer properties in cell lines and animal models. In this review, we discuss recent advances in defining the role of artemisinins in medicine, with particular focus on their controversial mechanisms of action. This safe and cheap drug class that saves lives at risk from malaria can also have important potential in oncology.Artemisinins are derived from extracts of sweet wormwood ( The remarkable story of the discovery of artemisinin a and estin vitro, including protozoa that are phylogenetically unrelated to apicomplexan parasites such as the Plasmodium species that cause malaria. Artemisinins also act against metazoan parasites such as Schistosoma spp. Their anti-disease properties include potent anticancer activity in in vitro studies and in an in vivo model of colorectal cancer. Taken together with case reports describing benefits in diverse cancers, a recently published clinical trial of short-term use in lung cancer, their established record of safety in children and adults with malaria, and their permissive cost, there are compelling reasons to study their contribution to management of tumours that require adjuvant and neo-adjuvant therapies. This selective review focuses on rapidly advancing areas of artemisinin science and usage and illustrates why artemisinins have the potential to rival acetylsalicylic acid in the breadth of their anti-disease properties.Artemisinins have also been submitted to studies aimed at exploring other uses for this drug class. Artemisinins are active against other parasite species in vitro reactions of some artemisinins, including their decomposition in aqueous solutions.There is considerable debate regarding the mechanisms of antimalarial action of artemisinins. An endoperoxide bridge  lies at Plasmodium spp. or are there multiple targets? Fully synthetic trioxolanes that contain an endoperoxide bridge but lack other features of artemisinins have increased complexity of the debate on mechanisms of action of artemisinins One issue focuses further discussions: is there a single important target for artemisinins in Plasmodium chabaudi infection in mice identified a locus linked to artemisinin resistance that is stable after mosquito passage Rodent malarias are also useful models for understanding possible mechanisms of resistance to different classes of antimalarials Plasmodium falciparum multiplies in red blood cells, and digestion of haemoglobin during its 48 h asexual life cycle is essential for parasite survival  between parasiticidal activities of artesunate and OZ277 tested against field isolates, with no correlation between OZ277 and other classes of antimalarial such as quinolines Further evidence for the irrelevance of parasite pigment in the action of artemisinins comes from their potent activity against non-pigment-producing apicomplexan parasites (see later). There is also divergence between some As a variant of the haem hypothesis, reaction with a histidine-rich protein of parasites HRPII;  might alin vitroin vivo kinetic studies using bioassays of artesunate and its active metabolite, DHA, show approximately tenfold higher plasma concentrations in α-thalassaemic subjects when areas under the time–concentration curves were assessed in vitro activities of artemisinins related to the haemoglobin status of host erythrocytes, thalassaemia is not an influential co-variate in population pharmacokinetic analysis of rectal artesunate used to treat Plasmodium vivax or P. falciparum infections. Additionally, antimalarial activities of artemisinin against P. falciparum parasites cultured in the presence of carboxy-haemoglobin are significantly higher than in the presence of oxy-haemoglobin. This increase in artemisinin activity is unexpected if Fe2+ is important in activating artemisinins because carboxy-haemoglobin inhibits haem-Fe2+ reactivity, indicating that haemoglobin iron plays no part in activating artemisinin for antimalarial activity and that competitive degradation of the artemisinin by haemoglobin actually attenuates its antimalarial activity Understanding interactions between haemoglobins and artemisinins is complicated by alterations in iron status associated with haemoglobinopathies. Higher concentrations of free iron in haemoglobin-E-containing and thalassaemic erythrocytes reduces parasiticidal potencies of artemisinins when assayed P. falciparum SERCA orthologue, as a target for artemisinins have been reviewed recently 50 value >20-times higher for artemether (indicating artemether resistance) compared with parasites without this mutation The supportive arguments for PfATP6, the in vitro assays used in the earlier publication P. falciparum multidrug resistance gene 1 (pfmdr1) ex vivo assays of susceptibility to artemisinins with the Xenopus oocyte model. An African isolate carrying the Ser769Asn mutation was still susceptible to DHA, and data for susceptibility to artemether were not reported  decreases susceptibility to DHA, although data are only available from two isolates . when carbon sources such as glycerol or ethanol are not metabolized by glycolysis) Recent studies with Baker's yeast indicate that mitochondrial membrane potential can be disrupted by artemisinin when grown in nonfermentable conditions  recently died because of probable toxicity Using artesunate to treat severe malaria in adults has been emphasized in recent publications Curiously, oral artemether and DHA are more commonly used in fixed-dose formulations rather than artesunate. Artesunate might have more favourable properties, both in terms of stability and ease of co-formulation when compared with DHA, and in terms of adverse effects in animal models when compared with artemether Toxoplasma gondii is a somewhat more tractable parasite than Plasmodium spp., particularly for studies using genetic manipulations or imaging technologies. Early work showed toxoplasma to be susceptible to artemisinins, albeit requiring concentrations within the micromolar range to kill parasites (T. gondii can be killed by nanomolar concentrations of artemisone in in vitro models and that TgSERCA (the PfATP6 orthologue) is susceptible to inhibition by artemisinin when expressed in yeast in vivo and after heterologous expression). They also indicate that a glutamic acid residue predicted in transmembrane segment 3 of TgSERCA is permissive for artemisinin susceptibility Studying the susceptibility of non-plasmodial apicomplexans to artemisinins affords new therapeutic opportunities and provides new mechanistic insights. If organisms within the crown eukaryotic group are susceptible to artemisinins, then the simplest mechanistic interpretation is that they function in a similar way against these phylogenetically related organisms. For example, arasites . Now stuBabesia species are tick-borne intraerythrocytic parasites that can infect humans in addition to a variety of domestic animals, depending on the species of parasite. Unlike plasmodial infections, babesia do not generate a parasitophorous vacuole and do not digest haemoglobin to make haemozoin Schistosoma spp. is reviewed elsewhere Leishmania spp. are also killed by micromolar concentrations of artemisinins , matrix metalloproteinase-9 (MMP9), thrombospondin-1 (THBS1) and hypoxia-inducing factor α (HIF1A). The fact that sensitivity and resistance of tumour cells can be predicted by mRNA expression levels of angiogenesis-related genes indicates that artemisinins reveal their antitumour effects, at least in part, by inhibition of tumour angiogenesis. Overexpression of enzymes associated with modulation of oxidative stress such as glutamylcysteine synthetase, glutathione S-transferases and the endothelial growth factor receptor reduce susceptibility of tumour cells to artemisinins in vitro studies have also shown that for some cancer lines, delivery of iron, for example by the use of holotransferrin, enhances the anticancer properties of artemisinins mRNA expression of 30 out of 90 angiogenesis-related genes correlated significantly with the cellular response to artemisinins in vitro properties against cancers but have not been studied sufficiently to warrant more extensive clinical studies? Probably not, for many reasons. First, artesunate is a cheap, safe, easily administered and orally bioavailable compound that acts at targets different to those of many current cancer chemotherapeutic agents and is unlikely to interact adversely with existing anticancer interventions . Second, study of an animal model carrying a human colorectal cancer cell line confirms that artesunate has independent antitumour activity and can shrink primary tumours and reduce the risk of hepatic metastases developing Should artemisinins remain relegated to the large category of compounds that have interesting in vitro studies, several groups have reported that artemisinins have antiviral properties. Artemisinins reduce replication rates of hepatitis B and C viruses Pneumocystis carinii in vitroin vivo studies in immunosuppressed rats In Artemisinins are firmly established in combination therapies


This case study examines the automation and process change options available to emerging discovery/development stage pharmaceutical companies when considering implementing sophisticated high-throughput screens. Generally there are both financial and personnel constraints that have to be addressed when implementing state-of-the-art screening technology in smaller companies which generally are not as significant as in large pharmaceutical companies. When NPS Pharmaceuticals considered installing a Molecular Devices FLIPR™ for high-throughput cell based screening it became clear that, to make the best decision, the whole screening process at NPS Pharmaceuticals from screen development and validation, tissue culture, compound distribution, data handling and screening had to be re-examined to see what automation options were possible and which, if any, made sense to implement. Large scale automated systems were not considered due to their cost and the lack of in-house engineering infrastructure to support such systems. The current trend towards workstation based laboratory automation suggested that a minimalist approach to laboratory automation, coupled with improved understanding of the physical process of screening, would yield the best approach. Better understanding of the work flow within the Biomolecular Screening team enabled the group to optimize the process and decide what support equipment was needed. To install the FLIPR™, train users, set up the tissue culture protocols for cell supply, establish high-throughput screening database protocols, integrate compound distribution and re-supply and validate the pharmacology on four cell based screens took the team 3 months. The integration of the screening team at the primary, secondary and tertiary screening stages of the target discovery project teams at NPS has enabled us to incorporate minimal automation into the Biomolecular Screening Group whilst retaining an enriching work environment. This is reflected in our current consistent throughput of 64 96-well microplates per day on the FLIPR™, a figure that is comparable with that achieved within most major pharmaceutical companies. This case study suggests that process optimization coupled with modern stand alone automated workstations can achieve significant throughput in a resource constrained environment. Significantly greater throughput could be achieved by coupling the process improvement techniques described above with 384-well microplate technology.


There are some common occupational agents and exposure circumstances for which evidence of carcinogenicity is substantial but not yet conclusive for humans. Our objectives were to identify research gaps and needs for 20 agents prioritized for review based on evidence of widespread human exposures and potential carcinogenicity in animals or humans.For each chemical agent (or category of agents), a systematic review was conducted of new data published since the most recent pertinent International Agency for Research on Cancer (IARC) Monograph meeting on that agent.Reviewers were charged with identifying data gaps and general and specific approaches to address them, focusing on research that would be important in resolving classification uncertainties. An expert meeting brought reviewers together to discuss each agent and the identified data gaps and approaches.Several overarching issues were identified that pertained to multiple agents; these included the importance of recognizing that carcinogenic agents can act through multiple toxicity pathways and mechanisms, including epigenetic mechanisms, oxidative stress, and immuno- and hormonal modulation.Studies in occupational populations provide important opportunities to understand the mechanisms through which exogenous agents cause cancer and intervene to prevent human exposure and/or prevent or detect cancer among those already exposed. Scientific developments are likely to increase the challenges and complexities of carcinogen testing and evaluation in the future, and epidemiologic studies will be particularly critical to inform carcinogen classification and risk assessment processes. Forty-five years after the World Health Organization recognized cancer as a world health problem by creating the International Agency for Research on Cancer (IARC), carcinogenic exposures in the workplace remain a concern. Many known and suspected carcinogens are found in today’s workplaces, and uncertainties about the health effects of exposure to these hazards have delayed regulatory action and the search for safer alternatives. In this review we focus primarily on chemicals, metals, dusts, and physical agents for which there is widespread human exposure, predominantly in occupational settings, and we address unresolved questions regarding carcinogenicity. Most of these agents are in IARC Groups 2A and 2B—agents for which there is sufficient evidence of carcinogenicity in animals but limited evidence for carcinogenicity in humans.A project to systematically identify data gaps was initiated by the National Occupational Research Agenda team of the U.S. National Institute for Occupational Safety and Health (NIOSH) to enhance occupational cancer research and involved joint planning with IARC, the American Cancer Society, the U.S. National Institute of Environmental Health Sciences, and the U.S. National Cancer Institute. In this review we present the results of this effort and identify opportunities for further research that would resolve classification uncertainties for selected high-priority agents. The process included a meeting to identify high-priority agents; expert reviews of each agent to update the literature since the last Monograph evaluation and to identify research priorities; and a workshop to discuss the identified data gaps and approaches. Expert reviewers were selected by the planning committee based on expertise in epidemiology and toxicology and on knowledge of the agents. For many agents, we recognized that opportunities for cohort studies would be limited, and reviewers were encouraged to consider possible experimental studies to elucidate carcinogenic mechanisms and molecular epidemiologic studies to develop intermediate biomarker data that could be used in classification.Full reviews and recommendations will be published in an IARC technical report. Here, we summarize recommendations for each of the agents and address some overarching topics pertaining to several agents or categories of agents.in vivo in experimental animals or humans. Genetic changes can be broadly defined to involve either inherited or somatic changes in the DNA sequence. Epigenetic modifications generally involve modification  of DNA or histones in chromatin or the binding of microRNAs (noncoding RNAs 21–23 bases) to homologous sequences in mRNA, resulting in a double-stranded structure that can decrease production of the corresponding protein , epigenomics (studying epigenetic regulation of gene expression), proteomics , and metabolomics . Omic technologies can be used to study the effects of the same chemicals in experimental animals and in human cells Oxidative stress has been invoked as a mechanism in the carcinogenicity of a number of agents, including some metals and particles. Oxidative damage to cellular DNA, the epigenome (including proteins), and lipids can occur when reactive oxygen species (ROS) escape cell antioxidant and repair mechanisms . ProposeImmunomodulation is also associated with cancer in humans and plays a particularly important role for some lymphomas  and otheAddressing the role of genetic susceptibility to carcinogenic exposures is also important; however, the stable and reproducible associations are few. Examining genetic polymorphisms related to carcinogen metabolism and/or DNA repair may facilitate identification of higher cancer risks in susceptible subgroups and clarify the role of specific agents in mixed exposures. However, the magnitude of such associations may be modest and involve multiple genes or metabolic pathways, making them difficult to detect.2), in products.Some agents considered in this review may occur as extremely small particles with at least one dimension between 1 and 100 per unit mass than larger particles of the same composition, and the smaller particles appear to be more biologically reactive, toxic, and carcinogenic than larger-size particles. Thus, their toxic effects may need to be evaluated separately from larger particles of the same chemical composition . CriticaIn occupational settings where many Group 2 carcinogens are used, levels of exposure may be relatively low and potential for multiple exposures high. High-quality exposure assessment will be required to assess quantitative exposure response for specific agents while accounting for other potentially carcinogenic exposures. Historical monitoring data, when available, may be used to create a job-exposure matrix. Biomarkers of exposure to agents with long biological half-lives, such as serum levels of PCBs , may be Some agents discussed here are used primarily in small businesses with high turnover, where it is difficult to assemble large study populations. Alternative approaches include use of union records, national census records, or records of individuals licensed to perform certain work , case–control studies with enhanced exposure assessment, and cross-sectional surveys examining intermediate markers. It may be possible to recruit participants outside of the workplace through the media and then use a validated biomarker to confirm and quantify recent exposure.Epidemiologic studies using death certificates may fail to identify excesses in cancer sites with high survival rates or excesses in specific morphologic types of cancer. The ability to study cancer incidence rather than mortality—linking occupational cohorts with regional or national cancer registries—would improve detection of cancers with high survival rates, the accuracy of diagnostic information, and more timely identification of carcinogenic hazards. In several Nordic countries, national cancer registries that are linked to census occupational data (and in Norway to a serum bank) have been an important resource for studies of occupational and environmental exposures. Such resources could be developed in other countries.Interpretation of evidence for excesses in lymphohematopoietic cancers (LHC) for several agents has been complicated by inconsistencies in specific tumor sites. These differences may result from inaccuracy of death certificate diagnosis as well as from changes in LHC classification and grouping over time. Epidemiologic and animal studies may consider morphologically distinct hematologic cancers as separate end points, even though they may share common cellular origins. As knowledge of hematologic malignancies evolves, it is important to reexamine approaches to disease categorization in epidemiology and animal toxicology. Over time, there has been growing recognition of close relationships and overlap of such morphologically diverse disorders as chronic lymphocytic leukemia and multiple myeloma, now considered subclassifications of mature B-cell neoplasms .The agents, exposure circumstances, and prior IARC Monograph evaluations of the agents considered are listed in the Supplemental Material (doi:10.1289/ehp.0901828).a) assessment of the correlation of blood lead measurements with cumulative exposure as measured by bone lead; b) assessment of whether Helicobacter pylori infection is associated with higher blood lead levels; and c) evaluation of genetic susceptibility factors, such as polymorphisms in the δ-aminolevulinate dehydratase (ALAD) gene. Further experimental research is needed to evaluate the mechanisms by which lead may cause cancer, with particular emphasis on oxidative stress/apoptosis and the roles of cellular defense mechanisms, signaling pathways, and intracellular lead-binding patterns.Although the occurrence of lead in the environment has decreased greatly because of the elimination of most leaded gasoline, substantial occupational exposures continue primarily via lead in the battery industry and lead pigments in paints . EvidencIntratracheal installation of indium phosphide causes pulmonary inflammation and high incidences of lung tumors in experimental animals . No epidThe evidence for carcinogenicity of cobalt with tungsten carbide in humans comes from studies finding increased lung cancer risks among workers in the hard-metal industry in France and Sweden . The prein vitro and in vivo studies have shown welding fumes to be genotoxic .Recent subchronic studies in rats confirm earlier findings that particle size  and coatings can influence pulmonary responses  to TiO2 , 2007 anace area . The obs nucleus , suggest nucleus . EpidemiTwo meta-analyses estimated the summary risk for lung cancer and diesel engine exhaust (DE) exposure to range from 1.33   to 1.47 2, which can aggravate effects of inhaled fibers. The impact of fiber length on carcinogenicity should also be investigated.Refractory ceramic fibers (RCF), which have replaced asbestos as high-temperature insulation, induce benign and malignant lung tumors in rats . Only onThe validity of negative dose–response data in rats after inhalation exposure to RCF is questionable because there are indications that the sensitivity of the rat inhalation model with man-made fibers is relatively low . Future In 2008, a U.S. National Toxicology Program (NTP) expert panel reviewed styrene, finding limited evidence in humans but sufficient evidence of animal carcinogenicity from multiple studies in mice by multiple routes . EpidemiSince the last IARC review , only onFormaldehyde has been classified by IARC as a Group 1 carcinogen based on sufficient evidence for nasopharyngeal cancer in humans . Both IAALDH2) deficiency or low aldehyde dehydrogenase (ADH1B) activity   . These sCYP) pathway to oxidative metabolites and by the glutathione (GSH) conjugation pathway to genotoxic metabolites; incorporation of data on genetic polymorphisms in glutathione S-transferase and CYP2E1 would be useful in this regard.Since the IARC review , numerouSince the IARC review , severalInhalation exposure to DCM causes lung and liver tumors in mice and mammary tumors in rats . EpidemiChloroform causes cancer in rats and mice, most likely through a mechanism involving cytotoxicity , and theIdentifying research gaps for PCBs is considerably more difficult, because a large volume of epidemiologic and mechanistic data has been published since the last IARC evaluation . MoreoveTetOff (which expresses the human receptor only in liver) or hPPARαPAC  may elucidate the role of human PPARα in DEHP carcinogenesis. Further characterization of DEHP exposures in industry is needed and could be carried out in established cohorts in PVC-processing factories using mono-2-ethylhexyl phthalate and mono(2-ethyl-5-carboxypentyl) phthalate as sensitive and specific biomarkers of DEHP exposure.Although extensive human exposure to DEHP occurs through its use as a plasticizer of polyvinyl chloride (PVC), definitive epidemiologic studies are not available because of the difficulty in identifying highly exposed workers in retrospective cohort or case–control studies. Since the previous monograph review, which concluded that liver cancer in animals resulted from induction of peroxisome proliferator-activated receptor-α (PPARα) and that peroxisome proliferation activation was not relevant to humans , severala) a better definition of what is meant by shift work and related exposure metrics; b) studies of markers of circadian disruption in non–day workers; c) better descriptions of controls and their exposure to light at night; and d) investigation of the effect of variations in expression of circadian genes on cancer in shift workers. An emerging area of interest is the relative toxicity of occupational chemical exposure depending on time of day of that exposure. The marked circadian variations in cell division and DNA repair during the daily cycle are controlled by the circadian genes  renewed interest in this field; b) training, career, and funding opportunities; and c) advances in addressing legal–ethical barriers to accessing worksites, study populations, and personal/medical data. If measures are not taken to stem declines in this area of research, we will continue to have an extremely limited epidemiologic knowledge base for the evaluation of potential carcinogens.In this review we discuss only a small fraction of potentially carcinogenic agents—generally those for which there is substantial evidence for animal carcinogenicity but as yet inconclusive evidence of human carcinogenicity. For most other agents, there exists little or no evidence by which to evaluate animal or human carcinogenicity because neither adequately designed animal bioassays nor human studies have been done. However, even the modest research agenda outlined here will be difficult to achieve given current trends. Although objective evaluation of trends in research funding and productivity related to environmental/occupational risk factors for cancer is difficult, there is a general sense that funding for occupational cancer research has declined over the past two decades and that fewer and fewer epidemiologists, exposure assessment experts, and toxicologists are attracted to careers in this area. A more formal evaluation of these trends could consider what measures could encourage


Takeo Watanabe and Yuko Yotsumoto explore the implications of a new study that shows that for perceptual learning of visual features involving multiple stimuli to occur, the brain needs to temporally "tag" the features, a learning process that requires paying attention. Experts show amazingly high perceptual skills. Experienced jewelers routinely classify diamonds that appear very similar to the uninitiated into different grades with high precision. Within a few seconds, airport baggage security officers can detect forbidden inconspicuous materials through x-ray images. Such feats are possible because the experts' “eyes” are trained through practice and experience. Long after most aspects of brain development have ceased, repeated exposures or trainings improve our perceptual/sensory abilities, and cause neural reorganizations in the brain. Such experience-induced improvement, called perceptual learning , and theWe are constantly exposed to an overwhelming amount of sensory signals, most of which are not noteworthy. To function normally in the world, we must react quickly and precisely to the important signals, while ignoring or discounting the less important, just as organisms must do in the natural environment to survive. By directing attention only to important signals or being repeatedly exposed to signals in an important context, our sensory systems learn to process important signals more efficiently than the less-important signals. Reflecting this fundamental role of perceptual learning, studies have been conducted to examine mechanisms of perceptual learning and neural plasticity with various kinds of tasks and stimuli by using behavioral measurements ,3 and neTo explore the mechanism of perceptual learning, here we focus on visual perceptual learning. Visual processing consists of many different stages leading from eyes to cortical areas for cognitive processes such as decision making . It is uEarly stage, local network model: Adini et al.  defined attention as assemblies of three different subsystems: alerting, orienting, and executive attention. Alerting is characterized as achieving and maintaining an alert state. Orienting is characterized as selection of information from sensory input by directing attention to a cued spatial location. Executive control of attention is characterized as resolving conflict between signals that do not induce the same response. For example, the executive control selects signals relevant to a given task while filtering out task-irrelevant signals that conflict with the relevant signals. While these subsystems often operate simultaneously with some interactions, basically they are orthogonally constructed systems that can operate independently .In the study by Zhang et al. , successSeitz and Watanabe have suggested that when a stimulus is presented concurrently with internal alertness elevation, perceptual learning of the stimulus occurs . PerceptClarifying the role of attention in perceptual learning provides clues to elucidate the underlying neural mechanisms of perceptual learning. Seitz and Watanabe  pointed Another potential future extension of the stimulus tagging model would be whether it can be generalized to other modalities. Although the tagging model is based on results of visual perceptual learning, it would be highly interesting to examine how well the tagging model fits with learning models associated with other sensory modalities, including audition and tactics, that have a hierarchical signal processing structure and top-down modulation just like the visual system.The study by Zhang et al.  has not


Predator attraction to prey social signals can force prey to trade-off the social imperatives to communicate against the profound effect of predation on their future fitness. These tradeoffs underlie theories on the design and evolution of conspecific signalling systems and have received much attention in visual and acoustic signalling modes. Yet while most territorial mammals communicate using olfactory signals and olfactory hunting is widespread in predators, evidence for the attraction of predators to prey olfactory signals under field conditions is lacking.Mus domesticus, which primarily communicate through olfaction. Olfactorily-hunting predators were rapidly attracted to mouse scent signals, visiting mouse scented locations sooner, and in greater number, than control locations. There were no effects of signal concentration on predator attraction to their prey's signals.To redress this fundamental issue, we examined the attraction of free-roaming predators to discrete patches of scents collected from groups of two and six adult, male house mice, This implies that communication will be costly if conspecific receivers and eavesdropping predators are simultaneously attracted to a signal. Significantly, our results also suggest that receivers may be at greater risk of predation when communicating than signallers, as receivers must visit risky patches of scent to perform their half of the communication equation, while signallers need not. The arms race in tactics of detection and evasion between predators and their prey has profoundly affected the life-history and behavioural strategies adopted by both parties All individuals emit odours as the inevitable consequence of metabolic processes combined with genetic individuality, hormonal fluxes, and microbial activity. These odours may be deposited in the environment unavoidably, for example as volatiles released from the body surface into the atmosphere, or deposited onto the substrate via footprints Mustela nivalis) prefer the scents of estrous over diestrous prairie deer mice (Peromyscus maniculatus bairdi), and Sundell et al. et al. Myodes glareous) and field (Microtus agrestis) vole. All three studies were conducted in small, relatively enclosed areas and controlled conditions where predator behaviour was focussed on the experimental trials. Consequently, the potential risks that prey scent pose in the wild remain largely assumed but unknown For mammalian systems, only three studies have looked at predator attraction to prey scents. Cushing Mus domesticus), for example, trade-off the social benefits of receiving signals with the perceived risk of predation: mice reduce receiving of low social value signals when the perceived risk of predation is high, while still maintaining rates of receiving of high social value signals There is evidence, however, that olfactorily communicating species are sensitive to increased risks of predation when receiving olfactory social signals. Male house mice , and also introduced mammalian feral predators such as cats (Felis catus) and foxes (Vulpes vulpes). Dingoes (Canis lupus dingo) and their introduced counterpart, the dog (Canis lupus familiaris), may also use olfaction to hunt mice.If the scents deposited by prey species such as house mice are used by predators searching olfactorily, we predicted that 1) significantly more locations treated with prey scents would be visited by a predator than unscented locations, and that 2) locations treated with prey scents would be visited sooner than unscented locations. We used patches of mouse scents to test this prediction in the mallee wheatlands of southeastern Australia. This area supports both house mice and a number of predators thought to hunt using olfaction, including a native predator, the brown snake (p = 0.01). Overall, predators visited significantly more mouse-scented locations than control-scented locations . There was no difference in the patterns of predator visitation to scents from two or six mice . No dingo/dog prints were detected on plots, however they are likely to be at low densities in the study area due to the low abundance of preferred prey (e.g. rabbits). Consecutive plots were never visited on the same day, and plots were therefore assumed to be independent of one another.Cats, foxes and snakes were rapidly attracted to scent plots, visiting more than 50% of scented locations within just two days . In contScent plots were also inspected for mouse prints: none were detected. Although mice will typically be attracted to conspecific odours, this finding was not unexpected as an extended drought had contributed to very low population densities of mice in remnant vegetation habitats (<1 mouse per 100 trap nights).These results provide the first definitive evidence of predator attraction to prey scent signals in the field. The predators' rapid detection of prey scents suggests that, like the acoustic and visual signals studied so far, the use of olfactory signals will expose individuals to predator mediated selection pressures. Importantly, however, it is not only the signalling individuals that will be at risk of predation from eavesdroppers. All individuals will be at an increased risk of predation when receiving a signal, irrespective of whether they are typically classified as “signallers” or “receivers”. Although dominant males are the primary signallers in many olfactorily communicating species, including mice, most individuals inspect scent marks, some frequently. This intimate association of both signallers and receivers with predator-attracting scent signals therefore suggests that in olfactory signalling systems, a wider range of individuals will be at an increased risk of predation when receiving signals than for other signalling modes Olfactory cues are more difficult to conceal than visual or auditory cues because they are long lasting and are necessarily focal points of activity of potential prey. Our findings suggest prey could adopt a variety of strategies to reduce the risks of predator attraction to patches of scent signals. Firstly, prey could distribute their scents to ensure concentrations at patches are below a predator's minimum threshold of detection. Alternatively, prey that perceive an elevated risk of predation could disperse their scent marks away from discrete patches, de-valuing scent patches as cues to predictable prey behaviour. This strategy would, however, necessitate an increase in prey activity when the risk of predation is greatest. As scents are preferentially concentrated around valued resources or boundaries where the likelihood of intrusion is greatest, these strategies are expected to have substantial consequences for resource and territory defence. Finally, prey could alter their activity in relation to scent signals to reduce their risk of predation The Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (1997), and with the approval of the University of New South Wales Animal Care and Ethics Committee (Permit Number 05/98A).All work was conducted in accordance with 2); areas of remnant Eucalyptus woodland are largely confined to roadsides and nature reserves. Mice are the only small mammal found throughout much of this highly modified landscape, and the diets of foxes We established a large-scale experiment in the mallee wheatlands of northwestern Victoria, Australia  during November 2007. This landscape is dominated by large fields  around buildings on surrounding farms and housed them in familiar groups of two or three. We held mice in standard mouse cages (48×26×15 cm), with a local sand substrate and shredded paper for bedding, and fed them an We established two mouse-scent treatments by collecting the scents produced by groups of two mice and of six mice over a 24 hour period. This number of individuals is representative of the range of mice known to visit a single burrow within 24 hours within this landscape 2. We selected roads based on the presence of roadside vegetation, a sandy substrate, patchy herbaceous vegetation and infrequent use. Cats and foxes are also known to use roads when moving through these landscapes; plots were at least 500 m apart to maintain independence We established scent plots in remnant vegetation beside roads within a study area of approximately 80 kmPlots were checked every 24 hours and tracks or scats were recorded. Tracks were identified to the species level using species-specific characteristics We used a contingency table to test whether more mouse-scented plots (two mice and six mice pooled) were visited than control-scented plots after two days and also by the end of the sampling period. We also used Kaplan-Meier survival analyses with log rank tests to examine differences in the time to visitation of scent plots receiving different treatments. We classified scent plots as right-censored if they were discontinued before the maximum time. All analyses were run in JMP7 (SAS Institute).


A 25-year-old youth presented with inability to close his right upper eyelid completely since two days following suturing of an eyebrow laceration, which was done elsewhere. The wound was due to impact against the handle bar following a bicycling accident. On examination, there was wound in his right eye brow, which was closed with continuous interlocking sutures , the bitThe word lagophthalmos is derived from the Greek word for hare eye. It is a 3Hemostatic sutures are applied in situations to control bleeding following acute trauma and are done by variety of suturing techniques such as continuous sutures with or with out inter locking and interrupted simple or mattress sutures. Though the techniques are not significant in hidden areas such as hair bearing scalp, they are significant in face which is a cosmetically sensitive area and in areas near landmarks such as side burns, eyebrow, lips, nasal ala or eyelids, where interrupted simple sutures are preferred with proper approximation of the matching points on either side of the wound so as to control the bleeding as well as to get a cosmetically acceptable scar. During the repair of eyelids after traumatic injury, thorough lavage of the wound with saline, avoiding excessive debridement and approximation of anatomical layers with fine suture materials help in preventing lid shortening where as during elective surgeries, avoiding the extension of the incision far too medially or laterally avoiding excessive removal of the eyelid muscle and orbital fat help in reducing the scar formation in postoperative period.Excessive scarring of tissues causes contracture and lid shortening resulting in lagophthalmos. The condition is managed by:Conservative methods such as application of artificial tears (eye drops or ointment), physiotherapy, use of protective sunglasses and eye shields. The conservative methods are adopted when the condition is temporary or partial or till definitive surgical procedure is carried out.Surgery when there is complete inability to close the eyelids, with failed nonsurgical treatment to protect the cornea, and when there is possibility of long-term lid closure impairment.Surgical methods to correct lagophthalmos including lateral tarsorraphy, temporalis fascial sling, ipsilateral and crossed facial nerve grafting, facial re-animation with gracilis neuro muscular free flap or application of gold weights (for pat


Tinnitus is a frequent condition with high morbidity and impairment in quality of life. The pathophysiology is still incompletely understood. Electromagnetic fields are discussed to be involved in the multi-factorial pathogenesis of tinnitus, but data proofing this relationship are very limited. Potential health hazards of electromagnetic fields (EMF) have been under discussion for long. Especially, individuals claiming themselves to be electromagnetic hypersensitive suffer from a variety of unspecific symptoms, which they attribute to EMF-exposure. The aim of the study was to elucidate the relationship between EMF-exposure, electromagnetic hypersensitivity and tinnitus using a case-control design.Tinnitus occurrence and tinnitus severity were assessed by questionnaires in 89 electromagnetic hypersensitive patients and 107 controls matched for age-, gender, living surroundings and workplace. Using a logistic regression approach, potential risk factors for the development of tinnitus were evaluated.Tinnitus was significantly more frequent in the electromagnetic hypersensitive group (50.72% vs. 17.5%) whereas tinnitus duration and severity did not differ between groups. Electromagnetic hypersensitivity and tinnitus were independent risk factors for sleep disturbances. However, measures of individual EMF-exposure like e.g. cell phone use did not show any association with tinnitus.Our data indicate that tinnitus is associated with subjective electromagnetic hypersensitivity. An individual vulnerability probably due to an over activated cortical distress network seems to be responsible for, both, electromagnetic hypersensitivity and tinnitus. Hence, therapeutic efforts should focus on treatment strategies  aiming at normalizing this dysfunctional distress network. Tinnitus, the perception of sound in the absence of an external sound, is a frequent disorder of auditory perception, which is very difficult to treat Even if the pathophysiology of tinnitus remains incompletely understood, there is growing evidence that dysfunctional neuroplastic processes in the brain are involved. In particular, it is assumed that tinnitus might be the correlate of maladaptive neuroplastic changes due to distorted sensory input There has been an ongoing debate, whether tinnitus might be related to exposure to electromagnetic fields (EMF) Besides the hypothesized involvement in the generation of tinnitus, EMF-exposure has also been related to a variety of unspecific health symptoms . Despite a huge amount of studies investigating the health impact of EMF, no clear relationship between EMF-exposure and these unspecific health symptoms could be established and the majority of provocation studies failed to demonstrate such a relationship Due to the large sample size, the detailed clinical and neurobiological characterization and the control group, which was matched for age, gender and either living surroundings or workplace (as very rough proxies for EMF-exposure), this study population The study has been approved by the local ethics committee of the University of Regensburg. All participants gave written informed consent.Tinnitus occurrence and severity have been assessed in a sample of subjects who claimed themselves to be hypersensitive to electromagnetic fields (EMF-sensitive). Subjective electromagnetic hypersensitivity was defined by the occurrence of unspecific health complaints interfering with daily living and the subjective belief that these complaints are caused by named electromagnetic emission sources  Tinnitus occurrence and duration in the study population were assessed by the following questions: (1.) Do you currently perceive tinnitus? (2.) If yes, since how long? Furthermore, in all tinnitus sufferers tinnitus severity was assessed by a German translation in = 0.05, pout = 0.10) as model building strategy. The following variables were evaluated: (1) age at study entry; (2) subjective hypersensitivity to EMF, ability to differentiate electromagnetic evoked sensory stimuli, number of complaints in the Regensburg-EMF-complaint-list as an indicator of severity of subjective electromagnetic hypersensitivity; (3) gender; (4) measures of cortical excitability as determined by standard procedures with transcranial magnetic stimulation , anxiety disorder  and somatoform disorders  were significantly more frequent in the EMF-sensitive group compared to the control group . Furthermore, electromagnetic hypersensitive patients had a higher EMF-complaint level and a worse sleep quality . ElectroUsing a logistic regression analysis the following four items were found to be independent predictors for tinnitus . These wSince an association between tinnitus and sleep disorders is well known Interestingly, a reduced ability to discriminate real from sham magnetic pulses, which is typically diminished in subjectively electromagnetic hypersensitive subjects The primary aim of this study was to elucidate whether a potential relationship exists between EMF-exposure, electromagnetic hypersensitivity and tinnitus. The main finding is that tinnitus is much more frequent in subjectively electromagnetic hypersensitive patients compared to control subjects. Independent predictors of tinnitus occurrence were subjective belief of being electromagnetic hypersensitive, being male, a reduced sleep quality, and a reduced ability to discriminate real from sham electromagnetic evoked sensory stimuli. In contrast, no evidence for a relationship between EMF-exposure and tinnitus has been found.The observed prevalence of tinnitus of 17.5% in the control group is in accordance with findings from various epidemiological studies showing similar rates A new finding is the surprisingly high prevalence of tinnitus among the electromagnetic hypersensitive patients. Since the study design at least partially controlled for environmental EMF-exposure by recruiting patients and controls from the same private and working environments, the increased prevalence in the EMF-sensitive group can hardly be explained by differences in environmental EMF-exposure. Furthermore the utilization of mobile phones did not show any significant relationship to tinnitus. Our data thus indicate that the increased prevalence of tinnitus may rather be due to other factors raising the question about the nature of this relationship. One possibility is that tinnitus just represents another unspecific health symptom of subjectively electromagnetic hypersensitive patients. Another possibility is that tinnitus and subjective electromagnetic hypersensitivity share a common pathophysiology. A key feature repeatedly found in subjectively electromagnetic hypersensitive patients is reduced discrimination ability for magnetic pulses With the failure to prove a causal relationship between EMF-exposure and symptoms in subjectively electromagnetic hypersensitive patients The dysfunctional over-activation of this cortical neural network might be related to a disturbed representation of external and internal perceptions, which in turn could explain the reduced ability to discriminate real from sham electromagnetically evoked stimuli of electromagnetic hypersensitive patients Taken together these results point to a shared pathophysiology of subjective electromagnetic hypersensitivity and tinnitus. It may be hypothesized that these changes represent a key feature of somatoform disorders, which should be addressed in future studies.Although this study thus provides some interesting new findings, it is not without limitations. First, data were cross-sectional and correlation analyses were used, which makes it difficult to determine the exact nature of the relationships between the variables of interest. Hence, prospective, longitudinal studies are needed to establish the precise nature and the directions of the relationships explored in this study. Second, self-report measures were used for tinnitus assessment. Such measures may not accurately capture the phenomena under investigation. Third, the study design aimed at minimizing the influence of environmental physical  and social stressors. We are well aware that this design cannot guarantee equivalent EMF-exposure between both groups. However, it is noteworthy that the discrimination ability to differentiate real from sham magnetic stimuli, which was shown to be diminished in subjective electromagnetic hypersensitive patients and tinnitus sufferers, has been assessed under laboratory conditions in a double-blind, randomized design In conclusion, this study has shown that tinnitus is much more frequent among subjective electromagnetic hypersensitive patients whereas there is no hint for a relationship between tinnitus and exposure to electromagnetic fields. Rather, the correlation between tinnitus and electromagnetic hypersensitivity might be due to an individual vulnerability. Neurobiological characteristics of this increased vulnerability such as an oversensitive cortical distress network and an impaired discrimination ability for electromagnetically evoked sensory stimuli might be involved in the pathophysiology of both tinnitus and electromagnetic hypersensitivity and possibly also in other related perception disorders. Nevertheless, this hypothesis derived from our epidemiological study has to be confirmed in further studies by e.g. intervention studies aiming for a normalization of the postulated over-activated distress network in subjectively electromagnetic hypersensitive (e.g. cognitive behavioral therapy, which has been shown to be successful in electromagnetic hypersensitivity


The responses of SiHa tumours, which have essentially no transient hypoxia, were compared to the responses of WiDr tumours, which contain chronically and transiently hypoxic cells. We found that relatively modest increases in net tumour perfusion increased tumour cell radiosensitivity in WiDr tumours to a greater extent than in SiHa tumours. Moreover, redistribution of blood flow within WiDr tumours was observed on a micro-regional level that was largely independent of changes in net tumour perfusion. Through fluorescence-activated cell sorting coupled with an in vivo–in vitro cloning assay, increases in the radiosensitivity of WiDr tumour cells at intermediate levels of oxygenation were observed, consistent with the expectation that a redistribution of tumour blood flow had increased oxygen delivery to transiently hypoxic tumour cells. Our data therefore suggest that drug-induced changes in tumour micro-perfusion can alter the radiosensitivity of transiently hypoxic tumour cells, and that increasing the radiosensitivity of tumour cells at intermediate levels of oxygenation is therapeutically relevant. © 2001 Cancer Research Campaign


Nuclear membrane assembly is an essential step in the cell division cycle; this process can be replicated in the test tube by combining Xenopus sperm chromatin, cytosol, and light membrane fractions. Complete nuclei are formed, including nuclear membranes with pore complexes, and these reconstituted nuclei are capable of normal nuclear processes. Current Protocols in Cellular Biology.The complete text protocol for this experimental approach is available in