To fully define the grammar of American Sign Language (ASL), a linguistic model of its nonmanuals needs to be constructed. While significant progress has been made to understand the features defining ASL manuals, after years of research, much still needs to be done to uncover the discriminant nonmanual components. The major barrier to achieving this goal is the difficulty in correlating facial features and linguistic features, especially since these correlations may be temporally defined. For example, a facial feature  occurring at the end of the movement of another facial feature , may specify a Hypothetical conditional, but only if this time relationship is maintained. In other instances, the single occurrence of a movement  can be indicative of the same grammatical construction. In the present paper, we introduce a linguistic–computational approach to efficiently carry out this analysis. First, a linguistic model of the face is used to manually annotate a very large set of 2,347 videos of ASL nonmanuals (including tens of thousands of frames). Second, a computational approach is used to determine which features of the linguistic model are more informative of the grammatical rules under study. We used the proposed approach to study five types of sentences – Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed, and Assertions – plus their polarities – positive and negative. Our results verify several components of the standard model of ASL nonmanuals and, most importantly, identify several previously unreported features and their temporal relationship. Notably, our results uncovered a complex interaction between head position and mouth shape. These findings define some temporal structures of ASL nonmanuals not previously detected by other approaches. Sign languages provide a window for the study of what formal, highly abstract and minimally required properties constitute human linguistic knowledge e.g., e.g., head, brows, eye lids, eye gaze, nose, mouth, cheeks, chin, shoulders), the options available to each , and the multiple combinations in which they interact.. Thus, sorting through all the possibilities and testing each for what may be subtle differences in meaning is a complex problem with many variables. While it is well known how the handshape, hand movement and palm orientation form the fundamental building blocks of the manual component of the sign The sign language literature has made it clear that although affective and linguistic expressions may co-occur, they are nonetheless easily distinguished by their articulation onsets and offsets with respect to the signs made on the hands, with linguistic expressions tightly coordinated with the syntactic constituents that they relate to To better understand the need of computational tools for the linguistic analysis of nonmanuals, let us review their use in sign languages. The nonmanuals used in sign languages serve a variety of functions similar to those performed by intonation or word order changes in a spoken language like English. For example, to make a question from the English statement “Sarah is having a party this weekend,” the intonation pattern can be changed from falling at the end to rising at the end “Sarah is having a party this weekend?” (an echo question) or the word order can be changed to give “Is Sarah having a party this weekend?” (a yes/no question). To make similar questions, American Sign Language (ASL), like some spoken languages, does not use the option of changing the word order but instead adds nonmanual markers. In this example, the nonmanual marker is that of a “Yes/no question.” Such a marker is used to denote questions that can be readily answered with a simple “yes” or “no.” This is in contrast, for instance, to “Wh-questions” which start with a “wh”-word  such as “which,” “when,” “how,” etc; in ASL Wh-questions are made with both the addition of nonmanual markers and optional word order changes. But each of these markers, for “Yes/no question” or “Wh-question,” may consist of multiple articulations, the most prominent being the position of the eyebrows, but with secondary articulations that may turn out to have their own meanings which combine with the primary meaning, or that may have emphasizer effects on the primary meaning, or that may be signer-specific, or even accidental and irrelevant To identify nonmanual markers, sign language researchers will typically manually annotate head movements and facial expression changes observed in a large number of video sequences. Tools such as ELAN e.g., for conditionals, a sign with the meaning ‘if’ may be used but is not required) i.e., positive versus negative) seems to be marked with nonmanuals; there is no regular sign for indicating positive polarity as this is the default interpretation in all languages, and negative signs for negative polarity are optional if the nonmanual for negation is present To date, research in ASL has identified that Hypothetical conditionals, Yes/no questions and Wh-questions are marked primarily by nonmanuals and secondarily by optional signs , and first-order co-occurrences , as, for example, one facial or head articulation occurring before another . Note that the term “discriminant” goes beyond a characterization of the nonmanual. While characterization defines the production of a nonmanual, discriminant features are those produced during one grammatical construction  but absent elsewhere. This proposed approach will thus be used to test the hypothesis that nonmanual markers discriminate among the following nine classes of sentences: Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed, Assertions and their polarities (positive and negative).The present paper describes a linguistic-computational approach to This proposed approach not only validates some known nonmanuals but, most importantly, identifies a large variety of previously unsuspected nonmanual markers for each of the nine sentence types of ASL considered in the present paper. For example, as expected, our results show a systematic relationship between eyebrow position and grammatical constructions. As predicted by previous literature, ‘brows move up’ is prominent in Hypothetical conditionals (89.1%) and Yes/no questions (92.3%). Similarly, ‘brows move down’ occurs systematically in Wh-questions (89.5%) and Wh-questions with the Wh-sign postposed (99.2%). However, our results reveal a complex interaction between head position and mouth shape that has not been previously reported in the literature. This finding is extremely relevant because it shows how co-articulations of facial components are employed as grammatical constructions and hence emphasizes the importance of complex interaction of nonmanual markers in sign language.The results summarized in the preceding paragraph would have been difficult to attain using a visual analysis of manual annotations. In contrast, the proposed computational approach can search for all possible first-order feature relationships and calculate which consistently co-occur in a given grammatical construct but rarely happen elsewhere. The approach and algorithms described in this paper have been incorporated into ELAN and can hence be readily used by other researchers to replicate and expand on the results reported herein.e.g., spoken English and Turkish Sign Language both allow negative Yes/no questions We investigate the role of nonmanuals in five (5) types of sentences: Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed and Assertions; in addition we consider their polarities: positive and negative. This yields a total of 9 classes because Yes/no-questions are neutral, meaning they cannot be associated with a specific polarity , for a total of We recorded fifteen (15) Deaf native users of ASL signing more than The signers were recorded using two high quality Sony DCR-VX2100 cameras. These cameras are equipped with 3 1/3″ CCDs for fast capture of color images in our studio conditions. All human subjects signed a consent form, granting permission for the use of their video sequences in research and the replication of these in scientific articles. The research and consent forms were approved by the IRB boards at The Ohio State University and Purdue University.The first camera recorded the upper-body (including the head) of the signer. The second camera captured a close-up of the face. This second camera provides high-quality video of the nonmanuals, For consistency check, the annotations of each recorded sentence were visually validated by a native Deaf ASL signer and an experienced sign language researcher who were members of the American Sign Language Linguistics Laboratory at Purdue University. In particular, we made sure all video clips in the database correctly expressed its target sentence and that it was clearly visible and understood. Video clips not passing this test were eliminated from the database.The video clips and manual annotations described in this section will be made publicly available to those wishing to extend on the results reported herein.e.g., nose on top of the mouth), while second-order specify between-feature distances. Shape features means that facial features are in a specified position . These descriptions are correlated with facial movement that may also be defined using other coding systems Research in face perception has demonstrated that facial expressions are coded and recognized by the cognitive system using configural Similarly, sign language research has shown that such options as brow position, closed/open mouth and flat/round lips, teeth showing, and head turns are potential building blocks of nonmanual markers All video clips are displayed with the ELAN discriminative facial features. A possible solution is to treat a feature as a time varying function, where each category has some numerical value e.g., headshakes, left to right turns, etc. We resolve these problems using Allen's Temporal Logic (ATL).The qualitative manual annotations described above must then be quantified in order to determine the most event A happens before event Bbefore, meets, overlaps, equals, starts, during and finishes. To show the use of the above defined propositions, consider the examples in A and B. A is said to be before B, when A happens disjointly before B, A could be head turns right and B head turns left. Here, we would write head turns right before head turns left. This could be the case when a subject is signing a negative statement with negation marked with a headshake.ATL is a framework that allows us to analyze relative temporal information, such as A happens immediately before B, then A is said to meet B, before and meets is that before requires a non-empty time interval between both events. For example, when nodding, the head moves up and down without a visual pause, which could be written as, A meets B. Obviously, in practice, two events involving different articulations would only perfectly follow one another by chance. To accommodate for small natural variabilities , we define meets as B occurring after a very brief interval A. The value of In the case that A is said to overlap B when A starts before B and A finishes during B, equals means that both events, A and B, share the same time interval, e.g., to indicate that the brows move up once, as in Yes/no questions A finishes before B, then A is said to start with B, A and B finish at the same time but A starts after B, then A is said to finish at B, during means that A's time interval happens within B's time interval, When both events start at the same time but i.e., “Brad is cooking/cooks fish on the grill”). The resulting coding using ATL relations is shown in e.g., In summary, the Allen's Temporal Logic defined above is composed of a set of binary propositions. Formally, we denote this set as e.g., brows move up equals brows move down) giving a total The 17 feature categories  form a se.g., while a single headshake may not carry any grammatical meaning, multiple headshakes can be a marker of negation or Wh-questions It is also important to encode the number of consecutive occurrences for a given ATL relation. This might be important for some discriminant features, Formally, we represent a sentence as e.g., Yes/no-questions versus the others), we need to use a feature extraction algorithm that uncovers the features or combinations of them that best discriminate between sentence types. In pattern recognition, such approaches are called discriminant analysis The histogram representation of the ALT described thus far provides a convenient numerical representation of the nonmanual events we wish to study. To determine the time relations that best discriminate a grammatical structure from the rest .Formally, RLDA finds the projection vector Solving for (1) yields, discriminative if its corresponding absolute magnitude in i.e., i.e., An ATL relation is hence defined as hypothesis is that nonmanual markers can be used to discriminate among the nine classes of sentences described above. More specifically, we hypothesize that first-order temporal relations of facial movements are sufficient to code for such grammatical structure. To test this hypothesis, we use all the video sequences in our database except one to find the discriminant facial features (as described in the Methods section) and test whether the resulting model correctly classifies the left out sentence. This approached is known as Leave-One-Sentence-Out (LOSO) test.Our i.e., Classification of the left out (test) sample In addition to the above, we included the commonly used sensitivity index d′ to measure the distance between signal and noise for the most discriminative features. Here, d′ measures the performance of a single feature in isolation and, hence, does not provide information on co-occurring features or their temporal structures.i.e., the discriminant features. To achieve this, we run a one-versus-all experiment. This means that, for each class , we use the linguistic-computational approach described in the Methods section to find the discriminant features that are common to that class but are not descriptive of the other classes.First, we wish to determine the nonmanuals that best discriminate each structure, The resulting discriminant features need to distinguish between the grammatical structures under study. These features are those providing the highest classification accuracies in the LOSO test described above. They are in i.e., i.e., i.e., In discriminant the feature is. Some discriminant features will of course be more common and, hence, will successfully discriminate more samples of finishes brows move up” in not a Hypothetical conditional (with classification accuracy at 97.6%). In comparison, “Brows move up” is a better nonmanual marker of conditionals , but is also employed elsewhere . Thus, this second nonmanual is not as robust as the previous one. As expected, the result of averaging the last two columns in The numbers in these last two columns (labeled “% Classification”) specify how many of our sentences can be correctly classified using each single feature Additionally, we tested for the statistical significance of our results. This was done by comparing our results with those given by a randomization of the class labels. That is, we compare the results obtained with the proposed approach to the results one observes when the class labels for each of the samples Let us now describe the results of this study in detail for each of the 5 classes under consideration.With respect to the Hypothetical conditionals , the higfinishes brows move up” in 19% of the Hypothetical conditionals suggests a head thrust at the end of the conditional clause Most notably, during brows move up,” which may reflect the establishment of a space to the left of the signer at head level to mark clauses containing content that is uncertain, hypothetical, or otherwise irrealis. The use of space for linguistic pragmatic functions has been recently reported for Catalan Sign Language (LSC) during brows move up” in Hypothetical conditionals is Lackner's observation of the signers' reference to a “mental” space or “space of thoughts,” which may be coded by pointing, gazing up, or moving the chin up.Another frequent head behavior is “head turns left during brows move up” occurs very frequently in clauses containing negation (negative polarity), as part of the negative headshake  teeth touch the (bottom) lip at the end of the articulation of “if.” In contrast, the high frequency of “teeth open” in non-Hypotheticals is not accompanied by high occurrence of “teeth touch lip during brows move up” and “teeth touch lip during mouth open.” Instead, “teeth open” is the result of the inclusion of lexical items such as FISH in the stimuli. As reported in e.g., pronouns, verbs). Thus, it is not unusual that a noun sign like FISH would be accompanied by the articulation of “fish” or at least the first part of it that involves articulation of “f” or “fi.” Both Hypothetical conditionals and non-Hypotheticals have a high occurrence of “teeth open” in From In contrast, “brows move up” occurs in few Wh-questions (10.6%) but is very frequent in other constructions (70.5%), which includes the Hypothetical conditionals discussed above and Yes/no questions (discussed below), both of which are associated with raised brows. “Brow move up” may also be associated with some occurrences of Wh-questions with Wh-sign postposed. This allows for very high classification rates of Wh-questions and other constructions even when they are using this single feature.starts brows move down,” which occurs frequently in Wh-questions (43.1%) but not in other constructions (0.5%). This cue is likely associated with the presence of mouthing of “who” at the beginning of some Wh-questions. This is also the case for “mouth shape round.”The remaining discriminative cue is “mouth shape round starts brows move down” for Wh-questions.From the results in meets brows move down,” with the brows up on the non-question part and the brows down on the Wh-word. This “brows up meets brows down” pattern in ASL Wh-questions postposed is noted in A “Wh-question postposed” is one in which the Wh-word has been produced at the end of the question instead of at the beginning  in Wh-questions postposed, and may be related to mouthing of other Wh-words, such as “which,” “why,” and “where.” Note the classification rate, for Wh-questions postposed and others is 94% when combining the features.The mouth is also active in relation to “brows move down,” with “mouth shape round overlaps brows move down” occurred in 16.9% of these as compared to only 2.5% in other constructions. Periodic blinks, the kind that are associated with eye-wetting, are well-known as a marker of the end of intonational phrases and syntactic constituents in ASL inside the clause. This supports the suggestion that they are deliberate blinks, which are used to emphasize a sign, because signs in final position in a clause are already emphasized/stressed One articulation in Wh-questions postposed that did not show up in other constructions is the occurrence of blinks. “Blink Yes/no questions are distinguished primarily by “brows move up,” although this cue also occurs frequently in other constructions, which include Hypothetical conditionals  and Assebefore brows move down” does not occur in Yes/no questions, since the brow raise is expected to span the entire question before brows move down” does occur in other constructions, namely those in which a Topic or Hypothetical conditional clause (brows up) precedes a Wh-question.Note that, as expected, “brows move up starts brows move up” occurs in 33.5% of Yes/no questions but only 6.9% of other constructions. Half of the Yes/no questions are preceded by a topic; according to “Head moves up finishes brows move up” occurs in 32.9% of the Yes/no questions as compared to only 3.4% of the other constructions, with a clear classification accuracy for the latter (97.2%). This is a truly surprising result which undoubtedly suggests further investigations in this direction as, to our knowledge, no function for flat mouth in ASL has been assigned in the existing literature. Since it spans the full duration of brows up  and ends when the brows up ends, these results suggest that this is a question mouth marker, although the issue is then raised as to why it is only not more frequent.“Mouth shape flat Assertions have been traditionally viewed as not marked by specific nonmanuals, leaving the articulators free to reflect ones that accompany nonmanually marked lexical signs as well as to reflect the signer's emotional status. The cues identified as distinctive in i.e., Hypothetical conditionals, Wh-questions, Wh-questions postposed and Assertions.The study of polarity follows the same procedure described above. The discriminant features selected by the LOSO approach are given in Here, we also performed the statistical significant analysis described in Experiment 1 section. All our results were again statistically significant with: Let us look at each of these results in more detail.From When we dig into the details of the temporal behavior of head turns, we identify linguistic interactions that have not been available to impressionistic analysis so far. We believe this is an improvement our algorithm has made possible for sign language research. In this sense, the findings with the ordering and the relation of head turns alert us to two previously unrealized findings about negative polarity in ASL.meets the opposite head turn” which kinematically correlates to a fast paced headshake. That the defining relation is “meets” rather than a head turn preference on either side of the relation is proved when we compare meets head turns right” discriminant feature. On the other hand, what gives us the fast paced headshake in meets head turns left” discriminant feature. The commonality turns out to be the abstract linguistic relation “a head turn meets the opposite head turn.” The kinematic realization of this abstract linguistic property is a fast paced headshake.The first finding is that the defining relation for negative polarity is “a head turn meets the opposite head turn.” There is a widespread linguistic assumption that Assertions are the most basic, simplest clause type, and this is where we see the negative headshake start with “head turns right.”The second finding is that we can generalize that negation normally begins with “head turns right.” Because this does not always occur, we state the general nonmanual marking as “a head turn during brows move up” is the discriminant feature for conditionals. As we will see in discriminant features for polarity in assertions, the primary indicator of fast paced negative headshake “head turns right meets head turns left” in Assertions, the most basic clause, starts with head turn to the right. In Hypothetical conditionals, the “head turns left” dominates the negative, and the fast paced negative headshake is modified to start on the left, yielding “head turns left meets head turns right”, the most active nonmanual marker in negative Hypothetical conditions , leading to In addition to these two findings we also need to note that the headshakes reflected by “head turns right/left Beyond the results above, our results further highlight the role of the mouth in nonmanuals. Note the frequency of “mouth shape other”  during (overlapping with) “head turns right” in a large number of negative Hypothetical conditionals.meets head turns right” gives us a strong cue for differentiating negative polarity from positive polarity in the conditional sentences. When this result is evaluated with “head turns right overlaps mouth shape other,” we come up with the pattern in As we noted above, the fast paced “head turns left Next, note that the percentage of “mouth shape other” (46.3% vs. 17.9%) is strong enough not to be associated with a combined effect of lexical mouth-shapes of random signs in negative sentences. The contrast in discriminant percentages indicates that the mouth is actively involved in the expression of negation in ASL. This finding  is consistent with results reported in The fact that “mouth shape other” is not as frequent as headshake is another interesting finding. There are two ways to interpret this finding. First, although “mouth shape other” is present for almost half of the negative sentences, it could be a redundant or secondary prosodic cue, similar to the findings in The discriminant features that distinguish negative and positive polarity in Wh-questions are more varied than those of Hypothetical conditionals and seem to be less clearly reflective of general negative marking. That is, they generally do not indicate head turns. Instead, a number of the features relate to mouth and teeth positions. In addition, there is no clear pattern of occurrence such as that seen with Hypothetical conditionals, where strong markings were seen for negatives as compared to positives. Here, sometimes a mouth or teeth feature is more prevalent in negatives and sometimes the reverse is true. This suggests that while Wh-questions can be clearly marked by brows down, when Wh-questions are negative, nonmanuals alone may not be able to carry both semantic functions. Such a conclusion is in keeping with two other observations in the literature. One is that both Wh-marking and negation use headshakes; the negative headshake is somewhat larger and slower starts mouth open” is highly classificatory (91.9%) for positive Wh-questions by its absence. While “brows move down” is clearly related to Wh-questions, mouth open could be related to some of the Wh-words being mouthed  and given the higher occurrence in negatives, possibly also ‘not.’ Another mouth cue with a high classification value (89%) for positives by its absence, “teeth open overlaps head turns right,” is almost three times more prevalent in negatives than in positives. Similarly, “mouth closed meets teeth open” is twice as prevalent in negatives as in positives and has a high classification value – its absence from positives yields correct classification 90.2% of the time despite its rare occurrence in Wh-questions in general. When such negative evidence (9.8%) is combined with positive evidence (30.8%), we may thus suggest that “mouth closed meets teeth open” is a candidate to discriminate between negative and positive polarity in Wh-questions. The computational model of this interaction is given in Moreover, the current results define several interesting interactions in Wh-questions and polarity. “Brows move down As we have discussed in the section above regarding negative conditionals, there is evidence of “mouth closed” as a marker of negation. The fact that it meets “teeth open” 30.8% of the time suggests that this cue may be interrupted by some lexical interference (mouthing of English words) tucked into the flow of prosody due to certain lexical items.Another mouth feature that has a high classification value for negative Wh-questions is “teeth touch lip,” which occurs in 25.2% of positives versus only 6.7% of negatives. This is likely the result of three of the positive Wh-questions containing signs that can be accompanied by mouthing of English words beginning with ‘f’ .In contrast to regular Wh-questions, there is a clearer pattern to negative marking for Wh-questions postposed, with discriminant features all occurring more frequently in the negatives than in the positives. This pattern seems to support the argument above concerning regular Wh-questions. The basic difference between Wh-questions with and without Wh-sign postposing is that when the Wh-sign occurs at the end of the question, the material that occurs before the Wh-sign does not have to be covered by Wh-marking. As discussed in discriminant features for polarity in Wh-questions, the material prior to the Wh-sign can sometimes be considered an Assertion, meaning that Wh-marking and negation marking would not come into conflict. Hence, Like regular Wh-questions, we see increased prominence of mouth and teeth positions which will require further research to explain, such as the interaction of mouth gestures with mouthing the English words when certain signs are produced The results for polarity marking of Assertions also show clear nonmanual marking of negation, as all discriminant features occur more often in negatives than in positives. The primary cue in all discriminant features is head turn, reflecting negative headshakes. The only other discriminant cue is “brows move up,” which occurs before “head turns right;” this is the result of those Assertions that begin with a topic or are preceded by a conditional clause, both of which are marked with brows up, followed by a negative Assertion marked with headshake.In sum, with the exception of Wh-questions, the marking of negative polarity is clear on the constructions included in this study, and Wh-questions themselves are known to differ from the other constructions in needing a manual Wh-sign most of the time. The surprises in the data are related to mouth and teeth positions, which seem to gain prominence as nonmanual marking becomes more complex when multiple semantic functions are expressed simultaneously.Uncovering the discriminant features of the linguistic model governing nonmanuals in sign languages has proven to be an extremely hard problem. The present paper shows how this can be resolved using a linguistic-computational approach. In this approach a linguistic representation of the face is first obtained. A computational approach is then employed to determine the combination of these features consistently observed in each class but not with others. The resulting linguistic model proves to be able to discriminate between nine different classes of sentences – Hypothetical conditionals, Wh-questions, Wh-questions postposed and Assertions in their two polarities and Yes/no questions in positive polarity.The analyses described above strongly suggest that there are discriminant features that can be used to separate conditionals from non-conditionals, Yes/no questions from non-Yes/no-questions, Wh-questions and Wh-questions with postposed Wh-signs from non-Wh-questions, and Assertions from non-Assertions. In addition, for each of these except Yes/no questions which do not form negative in ASL, the discriminant features separate the negative structures from their positive counterparts. From the model , the resi.e., a faster paced headshake.In addition, the algorithm gives temporal relations that are striking with respect to head turns, where there are both expected and important novel results. The use of multiple head turns as headshakes has been well-documented for ASL and other sign languages as a major nonmanual marker of negation i.e., headshake, may very well be instantiated in more than one articulatory combination given the left and right directions of articulation, as well as temporal possibilities; a priori there is no reason to expect other sign languages which employ “headshake” as the major nonmanual cue to behave the same way as ASL does. On the big picture, this path also opens up an exciting agenda, both for ASL and cross-linguistic research, for quantitatively detecting nuances in the behavior of certain nonmanual markers which look the same on the surface even to the eye of an experienced sign language annotator.This opens a new venue for the study of headshakes. For instance, with regard to negative head turns it will be important to determine whether all negative headshakes are faster under all conditions across multiple sign languages. This possibility is raised in observations on Austrian Sign Language In addition to the insights about negation reported here, the approach presented in the present work also revealed that head turn left is a discriminant feature in conditionals. Again, work on Austrian Sign Language Lastly, the results also highlight the important role that the mouth and teeth play in negation. It is noted in As a final note, it should be noted that the methodology described herein  will most probably find applications beyond the studies of sign language. Elan is a generic tool used in several disciplines and the statstistical analysis described in the present paper is equally valid in these studies.Appendix S1Supporting Tables S1–S5.(TEX)Click here for additional data file.


Sarcoidosis is a multisystem disease which is most commonly manifested in the pulmonary system. However, extrapulmonary manifestations have also been frequently reported. Isolated occurrence of sarcoidosis in the genital system is rare and poses a diagnostic and therapeutic dilemma. Uterine sarcoidosis can present with cervical erosions, endometrial polypoid lesions, and recurrent serometra. In majority of cases, it is diagnosed by endometrial curettage, but it has also been detected by examination of hysterectomy, polypectomy, and autopsy specimens. Nonnecrotizing granulomas are the characteristic pathologic finding of sarcoidosis. However, many infectious and noninfectious etiologies including certain neoplasms can produce similar granulomatous reactions in the female genital tract. These conditions affect the female genital tract more commonly than sarcoidosis, and therefore it is important to rule out these conditions first before making a diagnosis of sarcoidosis. Treatment of sarcoidosis is different from treating these other conditions and the most commonly used systemic or local corticosteroids can be hazardous if the underlying cause is infection. In this case report, the clinical presentation, histopathology, clinical course, and treatment of a patient with isolated uterine sarcoidosis are described, and a brief literature review of sarcoidosis of the female genital tract is provided. Sarcoidosis is a multisystem disease of unclear etiology. Any organ system in the body can be affected by sarcoidosis, and the classic pathologic finding is the presence of noncaseating granulomas in the involved organs. Pulmonary sarcoidosis is the most common manifestation of the disease, accounting for 90 percent of the cases . Extra p3 with an endometrial thickness of 6 mm. It also revealed an anterior body mural fibroid with a submucosal component measuring 4.3 × 3.7 × 4.4 cm3 and a fundal fibroid measuring 2.9 × 2.7 × 2.9 cm3; her ovaries were normal. She received a short course of high dose oral contraceptive pills. Punch biopsies from the vulvar lesions revealed high grade squamous intraepithelial lesions with features of human papillomavirus infection. Therapeutic endometrial curettage was performed, and the histopathological examination of the endometrial tissues revealed menstrual phase changes, strands of smooth muscles suggestive of uterine myoma, and numerous nonnecrotizing epithelioid giant cell granulomas , and with a past medical history significant for schizophrenia and chronic obstructive pulmonary disease presented to our facility with menorrhagia. She was recently treated for latent syphilis with penicillin, and she also has genital warts and herpes virus 2 infections. Three years prior, she presented with mediastinal adenopathy and thick walled pulmonary cavities involving both the upper lobes. Flexible bronchoscopy with bronchoalveolar lavage and transbronchial biopsies from the right upper lobe revealed nonnecrotizing granulomas consistent with sarcoidosis. They were negative for AFB and fungal stains. A diagnosis of primary cavitary pulmonary sarcoidosis was made, and she was treated with systemic steroids for twelve months. She responded well to steroids with complete clinical and radiographic resolutions Figures . Fourtee Figures . Stains Sarcoidosis of the female genital tract is probably the rarest form of all the extra pulmonary sarcoidosis, accounting for less than 1% of cases . Based oOvarian sarcoidosis is probably the second most common manifestation of female genital tract sarcoidosis. Winslow and Funkhouser in 1968 described a case of a 28-year-old female who underwent total abdominal hysterectomy with bilateral salpingoophorectomy for a cervical lesion . HistopaInvolvement of the fallopian tubes commonly occurs in conjunction with sarcoidosis of the other parts of female genital tract. In 1954, Cowdell described an autopsy finding of sarcoidosis involving the fallopian tubes of a 21-year-old female who died of cardiac sarcoidosis , 38. SubNonnecrotizing granulomas are the characteristic pathologic finding of sarcoidosis. However, this finding is not pathognomic of sarcoidosis and many infectious and noninfectious etiologies including certain neoplasms can produce similar granulomatous reactions in the female genital tract. Infectious etiologies include tuberculosis, atypical mycobacteria, endemic mycosis, actinomycosis, and parasites. Noninfectious causes like foreign body reaction, Crohn's disease, medications, lymphoma, and other neoplastic conditions and postprocedure or postsurgical granulomas can also mimic sarcoid granulomas –48. ThesIn conclusion, female genital tract sarcoidosis is rare and its presentation can mimic other conditions that commonly affect the female genital tract. Diagnosis is mainly based on identification of noncaseating granulomas in the involved organs and ruling out other conditions that can have a similar histopathology finding. It can affect any age group but usually occurs in the reproductive age group. Like other extra pulmonary manifestations of sarcoidosis, the majority of the patients have pulmonary involvement and the Black population seems to be affected more frequently than other races. Increased incidence of uterine sarcoidosis may just reflect a sampling bias as most of these cases had concomitant involvement of other structures of the female genital tract. Endometrial curettage or even pap smear may be sufficient to make the diagnosis of uterine sarcoidosis; involvement of other structures will need a biopsy. Isolated cases may just require observation but systemic and symptomatic patients may be given a trial of systemic steroids.


Circulating immature platelet fraction (IPF) reflects real-time thrombopoiesis and correlates with platelet recovery from thrombocytopenic presentations. To understand the dynamics of IPF in platelet transfusions, we quantified the %-IPF in single-donor platelet components (SDP) during prolonged storage. %-IPF significantly increased from baseline by day 5 post-donation. Absolute IPF counts (A-IPC) had similar significant increments. However, gamma-irradiation suppressed the increments of %-IPF and A-IPC by >50%. Ultrastructural analysis of SDP units at day 10 showed well preserved morphology of immature platelets. Our findings suggest that IPF might actively expand ex-vivo and may have a longer shelf life than their mature counterparts. Closer study of IPF may be of critical clinical importance for transfusion practices. Circulating immature platelets are newly released from the bone marrow, contain higher concentration of RNA than mature platelets, and are measured by automated hematology analyzers equipped with a reticulocyte detection channel as the percent immature platelet fraction (%-IPF) The clinical significance of %-IPF and A-IPC in platelet transfusion has not been elucidated. A recent report showed that transfusion of hematopoietic-progenitor-cell transplanted children with IPF-rich platelet units significantly reduced the overall number of platelet transfusions required by patients compared to those receiving IPF-poor units SDP specimens were obtained from our local blood suppliers: American Red Cross  and LifeShare Community Blood Services . All units were from healthy volunteers, leukoreduced, collected by apheresis, stored in PVC bags  with ACD-A (10–15%) as anticoagulation TM controls  were measured after the analysis of every 50 samples. XbarM control program was also applied to re-assure the equipment's quality control as recommended by the manufacturer . A-IPC and H-IPF counts (H-IPC) were obtained by multiplying the %-IPF or %-H-IPF times the optical platelet count respectively.All aliquots were tested for optical platelet (fluorescent) count, mean platelet volume (MPV), platelet-large cell ratio (P-LCR), %-IPF and %-High (H)-IPF within 1 hour of sampling using the Sysmex hematology analyzer XE-5000 according to manufacturer's protocols . Sysmex e-Check (XE)Three 1 mL aliquots from day 3 and three from day 10 were fixed by immersion in quarter-strength Karnovsky fixative solution for 2 hours at room temperature. After washing, specimens were post-fixed for 2 hours in an unbuffered 1:1 mixture of 2% osmium tetroxide and 3% potassium ferrocyanide. After rinsing with distilled water, specimens were soaked overnight in an acidified solution of 0.25% uranyl acetate. Specimens were then rinsed in distilled water, dehydrated in ascending concentrations of ethanol, passed through propylene oxide, and embedded in a Poly/Bed 812 embedding media . Thin sections were cut on a RMC MT6000-XL ultramicrotome . These were mounted on Gilder square 300 mesh nickel grids  and sequentially stained with acidified methanolic uranyl acetate and stable lead staining solution. Sections were subsequently coated on a Denton DV-401 carbon coater , and examined in a JEOL 1200EX electron microscope .t test. All p values are two-sided with a type I error rate of 5% and a p<0.05 set for significance.All statistics were performed using Prism 6 . Results are presented as mean ± SD unless otherwise specified. Intergroup data comparisons were performed using the Student 9/L) was 20.0±4.0. As shown in 9/L) were stable and did not significantly decrease until day 7 . On the contrary, %-IPF and A-IPC (×109/L) significantly increased by day 5 compared to day 0  and %-IPF further increased on day 7 while A-IPC seemed to reach a plateau .%-IPF on day 0 was 1.58±0.3% similar to the reference range we established for the Sysmex XE-5000  which correlates with ranges reported for other analyzers To test if the %-IPF/A-IPC increment in storage was due to random variation among units or A-IPC expansion ex-vivo, we followed %-IPF and A-IPC changes of SDP from five donors for 14 days. As shown in 9/L) in the five SDPs also increased by day 10 . Analysis of additional parameters obtained with each run showed significant increments of MPV and P-LCR . On day 5 irradiation did not affect platelet counts; however, %-IPF, A-IPC, %-H-IPF, and H-IPC were significantly reduced by 50% in the irradiated group .To understand IPF morphology in SDP during storage, we performed SDP ultrastructural analysis focusing on the internal structure and granule integrity of immature platelets using transmission electron microscopy. As shown in Together %-IPF and %-H-IPF increments in the same units followed for two-weeks suggest ex-vivo expansion as a plausible explanation. A recent report indicated that the increment of %-IPF in storage represents non-specific artifacts of platelets degranulation Analysis of other parameters using our analyzer showed increments of %-H-IPF and H-IPC which implies that immature platelets are capable of expansion ex-vivo. Alternatively, a less mature platelet fraction than H-IPF might exist in peripheral blood that replenishes H-IPF but cannot be detected by the analyzer used. However, increases in both PLCR and MPV at day 10 along with data obtained through TEM showing morphologically intact immature platelets in day 10 samples lend support to the ex-vivo expansion or the greater stability of this platelet fraction in prolonged storage. It will be of interest to determine if the immature platelets observed on day 10 samples are still functional and capable of giving origin to mature platelets. Along these lines, the optimal growth/preservation conditions required by immature platelets in storage need to be elucidated.Ionizing irradiation is known to damage DNA and RNA and inhibit protein synthesis. However, ionizing irradiation of apheresis platelets has not been shown to have a clinically significant or demonstrably adverse effects on platelet function L degradation that antagonizes the pro-apoptotic effect of Bak How immature platelets give origin to mature ones is not understood but it has been shown that ex-vivo generated murine megakaryocytes infused into mice generate up to 200 platelets/cell in as little as 5 minutes Platelet transfusions prevent bleeding in patients with thrombocytopenia, but the clinical significance of %-IPF requires scrutiny. Animal studies have shown that newly formed murine immature platelets have increased hemostatic activity compared to mature ones as demonstrated by their increased response to thrombin and higher expression of surface P-selectin


In this study, a novel method of graphite chemical exfoliation to create graphene oxide (GO) is reported. Here, new oxidants were examined: a mixture of perchloric and nitric acids and potassium chromate. Furthermore, an effect of oxidation time, temperature of oxidation, and ultrasonication on graphite exfoliation degree was investigated. The obtained GOs were next reduced with glucose, used as a reducing agent. Detailed analysis of the materials indicated that when graphite was oxidized for 24 h at 50 °C, 5-layered graphene was prepared. An effect of sonication process was also examined, and it was found to enhance the exfoliation to bilayer graphene. Furthermore, when time and temperature were increased to 48 h and 100 °C, respectively, graphite was exfoliated to single-layer graphene. Therefore, it is believed that the proposed route can be applied for the preparation of graphene or few-layered graphene with defined number of layers upon the process parameters optimization and in a bulk scale. The materials were characterized with atomic force microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, and X-ray diffraction. Perchloric acid, nitric acid, hydrochloric acid, and ethanol were obtained from Chempur. K2CrO4 (6 g) was added. The mixture was then heated to 50 °C and reaction was operated for 24 h. The obtained mixture was next filtrated through polycarbonate (PC) membrane (Whatman 0.2 μm) and washed three times with ethanol (200 mL) and 10 % hydrochloric acid (200 mL) to remove residual metal ions, and finally with distilled water until pH of the solution was 7. Finally, the material was dried in air at 100 °C for 24 h.Here, three types of graphene oxides (GOs) were prepared. In the first procedure of GO1 synthesis, 1 g of graphite was dispersed in a mixture of perchloric and nitric acids , and next, K2CrO4, an ultrasonication process was performed for 6 h at room temperature. After oxidation process, the purification, filtration, and drying steps were realized as in the first procedure, and finally GO2 was obtained.In the second method, prior heating a mixture of graphite, perchloric acid, nitric acid, and KIn the third route, the time and the temperature of oxidation process were increased to 48 h and 100 °C, respectively. The sonication, purification, filtration, and drying steps were carried out as in the second procedure to obtain GO3. After the purification process of the each graphene oxide, the content of impurities was determined with thermogravimetric analysis. It was estimated that GO1, GO2, and GO3 contain 0.11, 0.19, and 0.08 wt% of contaminants, respectively (data are not presented here).Reduced graphene oxide (RGO) was synthesized with glucose using as a reducing agent  . The measurements were done in air under ambient conditions. Raman measurements were performed on an In-Via Raman microscope (Renishaw) with excitation laser wavelengths of 785 nm. Raman spectra were obtained from individual flakes deposited on SiO−1. The peaks between 1,190 and 1,380 cm−1 are related with C–OH stretching vibration  of GO1, GO2, and GO3 is 3.7, 3.6, and 3.7 Å, respectively. It is enhanced compared to that of graphite (3.4 Å)  at the Brillouin zone center  determines relative defect content in the carbon lattice  preparation, glucose was used as a reducing agent. The obtained materials  were analyzed with Raman spectroscopy to characterize their structure, in terms of number of graphene layers and lattice defects. Figure 2/Si with approximately 1 nm rms roughness, would be 0.8–1.2 nm. The enhanced thickness of monolayer graphene may be attributed to the interaction between the sample and the tip (Gupta et al. To confirm the morphology of RGO1, RGO2, and RGO3, atomic force microscopy was applied. Figure In summary, novel method of chemical exfoliation of graphite was presented. Here, novel oxidants were examined: a mixture of perchloric and nitric acids and potassium chromate, and an effect of oxidation time, temperature of oxidation, and ultrasonication in exfoliation degree were investigated. The presented methodology leads to creation of graphene with controlled number of layers: single-, bi-, and 5-layered graphene in a bulk scale.


In this work micro temperature and humidity sensors are fabricated to measure the junction temperature and humidity of light emitting diodes (LED). The junction temperature is frequently measured using thermal resistance measurement technology. The weakness of this method is that the timing of data capture is not regulated by any standard. This investigation develops a device that can stably and continually measure temperature and humidity. The device is light-weight and can monitor junction temperature and humidity in real time. Using micro-electro-mechanical systems (MEMS), this study minimizes the size of the micro temperature and humidity sensors, which are constructed on a stainless steel foil substrate (40 μm-thick SS-304). The micro temperature and humidity sensors can be fixed between the LED chip and frame. The sensitivities of the micro temperature and humidity sensors are 0.06 ± 0.005 (Ω/°C) and 0.033 pF/%RH, respectively. They are favored because of their high reliability, low power consumption, and little-to-no-maintenance requirements. They have been adopted for a long time in various devices and computers as visual indicators of signal integrity and operational status. An LED is a solid-state semiconductor device that directly converts electrical energy into light. It is a strong candidate for the next generation of general illumination applications. Following further improvements, LEDs have recently been identified as illumination devices. High-power, high-brightness light emitting diodes are being used in an increasing number of lighting applications because of their excellent color saturation and long lifetimes. Preventing them from overheating is challenging task for thermal designers. The thermal management of packages depends on external cooling mechanisms, heat dissipation, and thermal interfaces. Under a fixed cooling condition, the rate of increase of the junction temperature of an LED increases with thermal resistance, reducing the luminescent efficiency declines. Therefore, the effective thermal design of LED packages with low thermal resistance is essential to improving the performance of LEDs  estimateAs well as temperature, humidity factor significantly influences LED packaging. Moisture causes delaminating in electronic packages. LED packages are molded using polymeric materials. Such moisture diffuses into the package, which therefore swells. The package swells after absorbing moisture. Furthermore, the mismatching coefficients of moisture expansion (CMEs) induce hydro-mechanical stress in the package . Tan 6]6] invest2.2.1.In this study, the micro temperature sensor was a resistance temperature detector (RTD). Among the various advantages of an array of thin film RTD sensors include a small volume, high accuracy, short response time, and mass production capacity. As Pt and Au are the conventionally adopted sensing materials in temperature sensors, the former is expensive while the latter has a higher conductivity and flexibility. Therefore, in this work, Au is used in the device . As the tR represents the resistance at t °C; iR is the resistance at i °C, and αT is the sensitivity (1/°C).When the temperature of the RTD varies linearly, the relationship between the measured resistance and the change in temperature can be expressed as:2.2.C is capacitance (F); ε0 is the dielectric constant of a vacuum; ε is the dielectric constant of the environment; A is cross-sectional area of the electrode (m2), and d is distance between the two electrodes (m).The three main classes of humidity sensors are ceramic, electrolyte-based and polymer-based. Polymer-based sensors are either of the capacitance type or of the resistance type. Although the measurement range of the polymer-based sensor is not as large as that of the ceramic-based sensor, it is simply fabricated, low-cost, and highly accurate because of the high degree of polymer polymerization. It is useful for developing rapid IC processes. The polymer must have high resistance and a low dielectric constant. As the amount of vapor that is absorbed by the polymer increases, the dielectric constant increases and the increase in the capacitance can be derived using Hα is the sensitivity of the humidity sensor (C/%RH) [ (C/%RH) .3.The frame of the LED is a very important conductor of heat in an LED chip, so an insulating medium is installed between the frame of the LED and the LED chip to increase thermal resistance. The authors’ earlier study involved the development of a flexible micro temperature sensor that could be installed between an LED chip and the frame. The design in the present work is based on that earlier work . In this4.2 and the sensing area of the micro humidity sensor was 18,900 μm2. Flexible micro temperature and humidity sensors were fabricated using MEMS. Such micro sensors have the advantages of (1) small size, (2) mass-producability, (3) multi-functionality, and (4) flexible but precise measurement positions.In The junction temperature of the LED can be determined from the voltage based on the thermal resistance measurement theory. A CREE® EZ1000 chip and input currents ranging from 0 to 350 mA were used. Data obtained by thermal resistance measurement differed from those obtained using a micro temperature sensor. The data experimented is shown in In the humidity portion, the capacitance that was measured by the humidity sensor was 21.98 pF both before and after packaging. This result suggests that the LED in this study was well-packaged.5.In this study, flexible micro temperature and humidity sensors that could be set between an LED chip and an LED frame was developed, and a 40 μm-thick stainless steel foil was used to conduct heat between the LED chip and the frame. Flexible micro temperature and humidity sensors were fabricated using MEMS. These sensors have the advantages of: (1) small size, (2) high sensitivity, (3) mass-producability, (4) multi-functionality, and (5) flexible but precise measurement positions. A future study will adopt flexible micro temperature and humidity sensors to evaluate the operating parameters of LEDs and thus could improve their design and performance.


Phaeocystis, respectively low and high DMSP producers. On an annual basis, the particulate DMSP (DMSPp) production simulated in 1989 is mainly related to Phaeocystis colonies (78%) rather than diatoms (13%) and nanoflagellates (9%). Accordingly, sensitivity analysis shows that the model responds more to changes in the sulfur:carbon (S:C) quota and lyase yield of Phaeocystis. DMS originates equally from phytoplankton and bacterial DMSP-lyase activity and only 3% of the DMS is emitted to the atmosphere. Model analysis demonstrates the sensitivity of DMS emission towards the atmosphere to the description and parameterization of biological processes emphasizing the need of adequately representing in models both phytoplankton and bacterial processes affecting DMS(P) dynamics. This is particularly important in eutrophied coastal environments such as the SNS dominated by high non-diatom blooms and where empirical models developed from data-sets biased towards open ocean conditions do not satisfactorily predict the timing and amplitude of the DMS seasonal cycle. In order to predict future feedbacks of DMS emissions on climate, it is needed to account for hotspots of DMS emissions from coastal environments that, if eutrophied, are dominated not only by diatoms.We developed a module describing the dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) dynamics, including biological transformations by phytoplankton and bacteria, and physico-chemical processes (including DMS air-sea exchange). This module was integrated in the MIRO ecological model and applied in a 0D frame in the Southern North Sea (SNS). The DMS(P) module is built on parameterizations derived from available knowledge on DMS(P) sources, transformations and sinks, and provides an explicit representation of bacterial activity in contrast to most of existing models that only include phytoplankton process (and abiotic transformations). The model is tested in a highly productive coastal ecosystem  dominated by diatoms and the Haptophyceae  Dimethylsulfide (DMS) is a volatile sulfur (S) compound that plays an important role in the global S cycle and may control climate by influencing cloud albedo through the emission of atmospheric aerosols a), nutrients, irradiance or mixed layer depth) are uncertain and generally regional in scope In marine ecosystems, phytoplankton are the primary producers of dimethylsulfoniopropionate (DMSP), the precursor of the DMS e.g. . HoweverSeveral mechanistic models of different biological complexity  that is one of the most intense DMSP producers Phaeocystis globosa that develops between the spring and summer diatom blooms  bacterial transformation, and DMS emissions as field observations also report important DMS concentration Accordingly, we integrated a module describing the DMS(P) cycle into the existing ecological MIRO model oms e.g.  in respoa.In this paper, we first describe the concepts behind the DMS(P) mathematical model and its coupling with the ecological MIRO model (MIRO-DMS). The model is then applied in the SNS to describe the seasonal evolution of DMS(P) and the associated DMS emission to the atmosphere, and provide an annual budget of DMS(P) fluxes. Sensitivity tests on parameters are conducted to identify key microbial controls of DMS(P) production and how these change the emission of DMS to the atmosphere. Finally, we test the applicability of several published empirical relationships that predict DMS from other variables such as Chl Phaeocystis colonies The MIRO-DMS model results from the coupling between a module describing the DMS(P) dynamics and the existing ecological MIRO model developed to represent the dynamics of the ecosystem of the North Sea dominated by Phaeocystis colonies), two zooplankton FT (meso- and microzooplankton) and one bacteria FT involved in the degradation of dissolved and particulate organic matter (each with two classes of biodegradability) and the regeneration of inorganic nutrients 4) in the water column and the sediment. Equations and parameters were formulated based on current knowledge of the kinetics and the factors controlling the main auto- and heterotrophic processes involved in the functioning of the coastal marine ecosystem .The ecological MIRO model, describing C, N, phosphorus (P) and silica (Si) cycles, assembles four modules describing the dynamics of three phytoplankton Functional Types  cycle  and its Phaeocystis colonies (OP) expressed in mgC m−3) as in the MIRO model and a specific DMSP:C quota (SC) is attributed to the three phytoplankton types. The DMSPp (in mmolS m−3) state equation is:The DMSPp is a constitutive compatible solute produced by phytoplankton cell nμ represents the growth of different phytoplankton types (in mgC m−3 h−1), nlysis is the phytoplankton lysis (in mgC m−3 h−1)  derived from the literature (nsed correspond to the loss of DMSPp due to diatoms and Phaeocystis colonies sedimentation (in mgC m−3 h−1)  and diatoms (DA) (in mgC m−3 h−1)  are not subject to grazing where flux1+2,  and SCn terature . sedn co) flux4, . In the ) flux3, . Phaeocy−3) is:nlysis  and uptakeDMSPd is the bacterial uptake of DMSPd (in mmolS m−3 h−1)  for their C and S needs: BC is the bacterial biomass, bmx is the bacterial growth, SBC are monomeric C substrates available for bacteria and sbck is the half-saturation constant for the bacterial consumption of SBC (in mgC m−3).The description of Sneed, flux5, BCy is the bacterial growth efficiency and BCSC is the bacterial S:C ratio  state equation is:DMS is produced from enzymatic cleavage of DMSP by phytoplankton 1, nlysis is the phytoplankton cellular lysis (in mgC m−3 h−1), bacterial_lyase is the enzymatic cleavage of DMSPd in DMS by bacteria   flux9, .43-Although bacterial degradation of DMS is important uptakeDMS) will cover the bacteria S needs if uptakeDMSPd (Eq. 3) is not sufficient. In the model, uptakeDMS is described from the consumption of carbon by bacteria and the DMS content of bacterial C substrates, according to:Based on that, we assume that bacterial uptake of DMS , K0 is the photooxidation rate in the surface Z is DMS at depth z. As a first approximation, the ultraviolet A (UVA) penetration in the water column is considered equal to that of photosynthetic active radiation (PAR), as PAR attenuation in the studied coastal area is mainly governed by detrital particulate and colored dissolved organic matter. This assumption corresponds to a maximum water penetration of UVA and tends to overestimate the DMS loss by photooxidation. surface  and kD iDMS) is determined based on the surface DMS concentration and the gas transfer velocity (k) of DMS at in-situ temperature (kDMS):The DMS air-sea flux  of 600 and ScDMS is the Sc of DMS computed according to Saltzman et al. where kT is sea surface temperature (°C).where k600 (cm h−1) was computed from a parameterization (u10 in m s−1) that we derived from the binned data reported by Yang et al. rization  as a funu10 data were extracted from the National Centers for Environmental Prediction (NCEP) Reanalysis Daily Averages Surface Flux (http://www.cdc.noaa.gov/) for one station in the North Sea (3.75°E 52.38°N).http://saga.pmel.noaa.gov/dms/) and correspond to data available in the SNS between 51.0°N–52.5°N and 1.5°E–4.5°E For this application, the MIRO-DMS model was implemented in the SNS using a multi-box 0D frame delineated on the basis of the hydrological regime and river inputs  [60]. InValidation of the MIRO ecological model is given by Lancelot et al. Phaeocystis colonies, and summer diatoms  concentrations are analyzed in parallel to the evolution of the planktonic compartments (phytoplankton and bacteria) . The phy diatoms . Spring Chla m−3  in April 1 month . In asso 1 month .Phaeocystis bloom  concentrations show low values except during the spring is bloom . Simulat1 month, , i.e. ines bloom  and reac mgC m−3  correspo−3; The time lag of about 10 days between the simulated DMSPp and DMSPd  representing a DMS flux similar to bacterial DMSP-lyase activity. The importance of phytoplankton DMSP-lyase was previously reported in the area by Stefels and Dijkhuizen Phaeocystis bloom MIRO-DMS estimates the total annual phytoplankton production of DMSPp at 50 mmolS mPhaeocystis, which in itself releases almost 50% of DMSPp throughout the year. The sedimentation of DMSPp amounts to 4.3 mmolS m−2 y−1. Bacterial uptake accounts for the majority the removal of both DMSPd and DMS inducing a rapid decrease of their concentrations in the water column. The consumption of DMSPd is sufficient to sustain the total bacteria S need (10.8 mmolS m−2 y−1), and provides up to 16% of bacteria C requirements. In agreement with previous findings −2 y−1 and results in S products other than DMS (mainly SO42− and MeSH). Although only 8% (3.2 mmolS m−2 y−1) of the DMSPd consumed by bacteria is cleaved to DMS, this flux represents 50% of annual DMS input and is similar to phytoplankton DMSP-lyase activity (DMSPd results from phytoplankton cell lysis (68%) and zooplankton grazing (32%). The dominant process is the cell lysis of activity .−2 y−1) of the DMS pool is consumed by bacteria and transformed in SO42− or DMSO. Kiene and Bates DMS represents <1% of the DMSPp production in the water column in agreement with Archer et al. Bacteria also consume directly DMS and about 83% (5.3 mmolS mk600 parameterization). In particular, the impact of phytoplankton S:C quota determining the maximal DMSP production of the ecosystem, the importance of phytoplankton DMSP-lyase that represents the direct transformation pathway of DMSP into DMS and the DMS(P) bacterial uptake and lyase activity were tested.Annual S budget simulated in the BCZ points both phytoplankton and bacteria as key controlling factors of the DMS production. However the relative importance of these processes will results from their description and parameterization in the model. Sensitivity analyses were then carried out to estimate the impact on the atmospheric emission of DMS of the description of several biological processes compared to physical processes , but also within a FTs (spring versus summer diatoms).In our model, phytoplankton S:C quotas were fixed, corresponding to the mean values of measurements for Haptophyceae and diatoms reported by Stefels et al. r factor  without r factor , any modr factor ; 8a and tor . For low phytoplankton S:C ratio  similar to the DMS flux that comes from bacterial enzymatic cleavage  with little impact on DMSPd concentration.In the model, DMSPd is released in the water column by phytoplankton lysis and grazing processes (Eq. 2). The modification of the phytoplankton DMSP-lyase activity affects the F Test 8,  will decDMS. However, as shown in Sensitivity tests were then conducted by varying the bacterial S:C quota between extreme values reported in the literature i.e. 1∶37 and 1∶196 molS:molC . In our DMS increases  and 375 µmolS m−3 and 40 µmolS m−3 for a fraction of 50%. The simulated DMS emissions to the atmosphere also increase with an annual FDMS of about 0.24 and 0.32 mmolS m−2 y−1, respectively, compared to 0.19 mmolS m−2 y−1 in the reference simulation (−2 y−1 compared to 3.2 mmolS m−2 y−1 in the reference simulation), and the increase of FDMS mainly results from the decrease of bacterial DMS uptake and the accumulation of DMS in the water column. This is confirmed by results obtained by modifying only DMSPd (Test 15) or DMS bacterial uptake (Test 16). These results are consistent with the observations that suggest that bacterial DMS uptake may be a quantitatively important sink for DMS from the surface ocean In a third series of tests, we modified the percentage of bacteria able to use DMSPd and/or DMS as S source. The hypothesis of 100% used in the reference simulation was based on the observation that most marine bacteria have the genetic capability to demethylate DMSP ncreases . The maxncreases  simulatemulation . This inDMS.In the model, bacterial cleavage of DMSP in DMS represents 10% of the uptake of DMSPd not assimilated by bacteria. To test the importance of bacterial DMSP-lyase activity, this fraction was set to 25% inducing an increase of almost two fold of both the concentration of DMS and FDMS resulting from the maximal hypothesis of bacterial uptake (RatioBCS = 1). This is particularly important for the direct bacterial uptake of DMS. Similarly, the bacteria state variable lumps both bacteria and Achaea that might also be important for the demethylation/demethiolation processes Due to their importance on both DMSPd and DMS transformation, bacterial processes need to be accurately described and/or parameterized in ecosystem models. Note that in the present version of the model we only considered one bacterial community, and we did not individually represent the DMS- or DMSP-consumers although this simplification also induces possible uncertainties and underestimation of FDMS is also function of the k600 that depends on the intensity of wind speed and how it is translated into turbulence (depending on the parameterization). Additional tests were performed to estimate the sensitivity of the simulated atmospheric emission of DMS to wind speed and k600 parameterization  release experiments in the SNS, and this parameterization has been shown to be also applicable in open ocean conditions k values of Yang et al. DMS by eddy-covariance during 2 experiments in the Pacific Ocean and 3 experiments in the Atlantic Ocean. The k600 values of Nightingale et al. 10>8 m s−1  wind speed is low , the annual average of k600 computed from the Yang et al. −1) is only ∼9% lower than the one computed using the Nightingale et al. −1).The net annual Fry close . The two>8 m s−1 , and suc the SNS  when [DM the SNS . Since wDMS, several empirical relationships have been derived from DMS field data and variables such Chl a, NO3−, T, primary production, solar radiation, or mixed layer depth that can be derived at higher spatial and temporal resolution from climatologies, remote sensing or models. We tested if some of these empirical relationships that are assumed universal and generic were applicable to the SNS that is representative of a temperate eutrophied coastal system. Several empirical parameterizations that allow to compute DMS concentration in marine waters  and compared to DMS concentration obtained with the MIRO-DMS, and with the available DMS observations in area  used in these relationship was computed based diatoms and non-diatoms (nanoflagellates and Phaeocystis colonies) Chl a simulated by the MIRO-DMS model. Results obtained with both relationships largely overestimated DMS concentrations in the area during Phaeocystis bloom , well below the maximum values in the SNS, up to 25 µg L−1  but also within a FT (spring versus summer diatoms) to describe DMSP and DMS concentrations in marine ecosystems. Due to their elevated S:C quota and their major contribution (50%) to the annual primary production, Phaeocystis colonies are responsible of 78% of the annual production of DMSP in the BCZ. This work is an additional modelling effort to explicitly include bacterial processes in transforming DMS(P), and shows their contribution in processing DMSP and as a sink of DMS that is much higher than DMS removal by photooxidation and FDMS.The application in the BCZ of the newly developed biogeochemical model MIRO-DMS shows that modelled Faa values were related to diatoms unlike eutrophied coastal environments such as the SNS where high biomass is not associated to diatoms. Therefore, future projections of FDMS and the investigation of the potential feedback on climate require to use modeling tools that accurately represent DMS(P) dynamics in coastal environments that are hotspots of DMS emissions, in particular, in eutrophied coastal environments dominated by high biomass non-diatom blooms. Further, bacterial processing of DMS(P) needs to be correctly represented in models. The potential feedbacks of DMS emissions on climate will depend on the impact of climate change on the phytoplankton composition and biomass, as postulated by the CLAW hypothesis versus bacterial consumption/transformation).Current empirical relationships to predict DMS from Chl


TTC28 using deep coverage WGS data from 92 CRC tumor-normal sample pairs. In two cases the event had targeted NOVA1 gene (p=0.025). In addition, a germline retrotransposition event from TTC28 to GABRA4 was found to be a common polymorphism in the Finnish population. Thus while some events may be tumorigenic, others are likely to be neutral. Our data contradict a recent study where a similar signal in TTC28 was interpreted as a common inactivating translocation. While much work remains to be performed to understand the biological significance of retrotranspositions in cancer, accurate identification of these events is a prerequisite for success.L1 element retrotranspositions have been found to alter expression of genes neighboring the insertion sites, potentially involving them in tumorigenesis and tumor progression. In colorectal cancer (CRC), L1 insertions have been found to target genes with a role in tumorigenesis. Structural changes such as L1 insertions are identifiable by whole genome sequencing (WGS). In this study, we observed frequent somatic L1 retrotranspositions originating from  The role of transposable elements (TEs) in tumorigenesis and tumor progression is, despite active research -4, stillODZ3, ROBO2, PTPRM, PCM1, and CDH11 that have a role in tumorigenesis [L1 retrotranspositions have been reported in several tumor types including colorectal cancer , 13. Theigenesis .TTC28 intron 1 - that was recently reported to be the site for the most frequent structural change in CRC  is a state-of-the-art method for analyzing structural variations in the genome  and is gf cases; ). The chTTC28  WGS in the first intron of TTC28 were observed in WGS data of 52 out of 92 (57%) CRC cases. Deep sequencing coverage (>40x) facilitated identification of multiple retrotransposition events in some of the cases. A total of 17 cases with two separate retrotransposition events were identified. In addition, we observed four cases that harbored three events, and two cases with four events. Insertion sites are illustrated in Figure 2=54.2, df=1, p=1.81e-13), compatible with previous literature on retrotranspositions [neuro-oncological ventral antigen 1 (NOVA1) (p=0.025).A total of 83 somatic L1 insertions originating from a specific L1 element residing in the first intron of SGIP1, NOVA1 and ARHGEF4. In each case, we identified two PCR products of varying length: one matching the expected wild type allele size and a larger one representing the allele containing also the L1 insertion. In two cases (SGIP1 and NOVA1), we were able to see sequence corresponding to the truncated 5' end of the L1 element. In SGIP1 case, we observed 449 bp of L1 sequence originating from 5484 bp downstream from the start of ORF1. Similarly in NOVA1, 246 bp of inserted L1 sequence originating from 5472 bp downstream from ORF1 start was identified. For the ARHGEF4 case, we observed 235 bp of sequence from 6162 bp downstream from ORF1. Finally, in SGIP1 and ARHGEF4 cases, we also observed a poly(A) tail at the 3' end.We successfully validated three somatic L1 insertions by Sanger sequencing. Insertion sites of the validated somatic events were in introns of TTC28 were observed in WGS data; at GABRA4 and rp11-136O12  were found to share significantly longer haplotypes around the insertion locus than other cases, indicating a shared founder haplotype . As expected, evidence for shared haplotypes at TTC28 (chr 22) were not observed in cases sharing the TTC28-GABRA4-retrotransposition . The 3/92 (3.3%) WGS cases with the germline L1 insertion at rp11-136O12 (chr 8) were found not to have a significantly longer haplotype , suggesting more ancient or independent origins.The four WGS cases sharing the germline retrotransposition at TTC28 L1 element  observed by TCGA [TTC28 was depicted as a frequent target for inactivating translocations [TTC28 are in fact L1 retrotranspositions, based on the evidence presented here.The frequent breakpoint signals in  by TCGA  and thosocations . The intNOVA1. Given the large number of potential insertion sites, even two hits to a single gene was somewhat unexpected (p=0.025) and might reflect selective value. NOVA1 has been identified as a splicing factor playing a role in neuronal splicing program, but it is also expressed in fibroblasts [SRSF6 have been associated with colorectal cancer [NOVA1 in CRC remains to be studied. We also found that TTC28-GABRA4 retrotransposition is a common polymorphism in the Finnish population. Thus this particular event is not likely to be oncogenic.Retrotranspositions may have oncogenic effects , or theyroblasts . Other sl cancer . The posTTC28 aberrations in CRC, as well as provides a valuable lesson in interpretation of WGS data. The TTC28 events that we observed are frequent, and some may be involved in tumorigenesis while others are likely to be neutral. Much work remains to be done to unravel the biological consequences of retrotranspositions in cancer. Accurate identification of these events is a prerequisite for success.To summarize, our study sheds light on the nature of In total, 92 familial CRC cases from 89 families  fulfilling the following criteria were included in this study: (i) at least one CRC case in a first degree relative, (ii) negative for any known high penetrance CRC mutation, and (iii) availability of sufficient amount of DNA, and (iv) microsatellite stable tumors. Seventy-nine of these 92 cases, and the additional 90 cases, used in the validation are part of a previously described population-based collection of Finnish CRC cases , 25. TheThe study has been reviewed and approved by the Ethics Committee of the Hospital district of Helsinki and Uusimaa (HUS). Signed informed consent or authorization from the National Supervisory Authority for Welfare and Health has been obtained for all the study participants.www.bioinformatics.babraham.ac.uk/projects/fastqc). Paired-end sequencing data was aligned using BWA 0.6.2 [Whole-genome sequencing was performed on the Illumina HiSeq 2000 platform with paired-end reads of length 100 bp. Each normal and tumor DNA sample was sequenced to at least 40x median coverage. Sequencing data quality was evaluated with FastQC . Here it was observed that the presumed translocation calls corresponded to insertions of sequence originating from the TTC28 locus elsewhere in the genome, instead of a translocation. Whole-genome sequences of all tumor and normal samples at the breakpoint position were visually inspected in RikuRator. An L1 insertion to a specific locus was called when at least three paired-end reads supported the insertion. This inspection also revealed the germline insertions that were initially removed by the above somatic filtering.The most frequently involved gene in DELLY translocation calls was TTC28 were examined by first calculating the sequencing coverage in tumors around the 3' end of the L1 element  was validated by Sanger sequencing in four samples. Primer pairs comprising each insertion junction were designed using Primer3Plus ([http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/); primer sequences and PCR conditions are available upon request. Fragments were amplified with AmpliTaqGoldVR  and the PCR products were purified using the ExoSAP-IT PCR purification kit . Sequencing reactions were performed using the Big Dye Terminator v.3.1 kit (Applied Biosystems) and electrophoresis was run on 3730xl DNA Analyzer (Applied Biosystems) at FIMM Genome and Technology Centre, Finland. The sequence graphs were manually analyzed using FinchTV v.1.4 .One germline L1 insertion site candidate  were successfully validated by Sanger sequencing. Primers flanking the insertion breakpoints were designed, as previously described. The PCR was performed using Expand Long Template PCR system . The PCR products were run in standard low-melting agarose gel. DNA band corresponding to the allele with the L1 insertion, was extracted from the agarose gel using QIAquick Gel extraction Kit . The sequencing reaction and the analysis of the sequences were performed as previously described.Additional three somatic L1 insertion candidates  or intergenic region (59%). In case of an event targeting a gene, the target gene was uniformly selected from 51573 genes, including protein-coding genes, short and long non-coding RNAs and pseudogenes (Ensembl 71.37). A total of 1000000 permutations were performed. An empirical p-value was derived as the fraction of permutations where any gene was hit two or more times.Significance of


Takayasu arteritis (TA) is a chronic vasculitis of unknown origin, affecting mainly the aorta and its main branches. As a result of the inflammation, stenosis, occlusion or dilatation of the involved vessels may occur and cause a wide range of symptoms. It has been described in association with various auto-immune disorders (mainly inflammatory digestive tract diseases). However, only few cases of TA associated with sarcoidosis have been reported, raising the question of an association by chance.R).We report a case of a 34 year-old woman, with one year history of sarcoidosis, who presented with asymmetric high hypertension revealing inflammatory humeral, axillary and subclavian arteritis related to TA, successfully treated by steroid and immunosuppressive therapy(MethotrexateTA and sarcoidosis may be related, rising the hypothesis that TA or Takayasu arteritis-like granulomatous vasculitis may be, in fact, a complication of sarcoidosis. Takayasu arteritis (TA) is a chronic inflammatory disease of large arteries which progressively develop stenosis, occlusion or aneurismal degeneration. The clinical presentation is characterised by an acute phase with constitutional symptoms, followed, months or years later, by a chronic phase in which symptoms relate to fibrosis or occlusion of vessels. Angiography is the gold standard for diagnosis and for topographical classification and it correlates with symptoms and prognosis. Proinflammatory cytokines and, among these, tumor necrosis factor-alpha  are increased and play a pathogenetic role in the development of disease. Laboratory findings are non-specific. Treatment of active disease is primarily based on corticosteroids but other immunosuppressive drugs are frequently needed. Anti-platelets agents, statins and antihypertensive drugs are frequently considered .Sarcoidosis, too, is a systemic inflammatory disease which can affect virtually any organ system. The lungs are most commonly affected, but often there is also affection of the musculoskeletal system, the cutaneous and central nervous systems, and the heart. Histology shows granulomas consisting of a central zone with macrophages, epithelioid cells, and multinucleated giant cells in addition to activated CD4 lymphocytes, and a peripheral zone with macrophages, fibroblasts, and CD4 and CD8 lymphocytes. Inclusion bodies are commonly found. Vasculitis may be found occasionally in patients with sarcoidosis. It has not been confirmed, however, whether vasculitis is a true manifestation of the disease or an occasional, incidentally concurring abnormality.Concurrence of sarcoidosis and TA were reported in few cases.A 34 year old woman was admitted to the hospital with dyspnea, submandubular gland tumefaction and parotid swelling.On physical examination, we found the tumefaction of the parotid and the submandibular gland. The respiratory frequency was 24 cycles per minute. The rest of the clinical examination was without abnormalities.Laboratory results were as follows: Haemoglobin 10 g/dl, white blood cell count (WBC) 11 200/mm3, platelets 450 000/mm3, erythrocyte sedimentation rate (ESR) 76 mm/h, calcium 12 mg/dl . Muscle enzymes, ANA, rheumatoid factor, VDRL, and complement components C3 and C4 were negative. The angiotensin converting enzyme (ACE) level was 135 UI/L.Chest radiography showed "Bilateral interstitial involvement". Thoracoabdominal CT scan showed "Multiple mediastinal and retroperitoneal lymphadenopathy, with moderate hepatomegaly". The respiratory functional test showed the presence of a restrictive syndrome.The lung fibroscopy was normal. The biopsy confirmed the presence of a non caseating granuloma in the bronchial mucosa. The bronchoalveolar lavage showed a predominantly lymphocytic cell with the elevated Cd4/CD8 ratio.Ophthalmological examination confirmed the presence of dry eye syndrome. There was no uveitis. The salivary gland biopsy confirmed the presence of a granuloma without caseous necrosis.Sarcoidosis was diagnosed, and the patient received prednisolone 60 mg/day. After 1 month of treatment, all complaints have been resolved.Seven months later, when she received 10 mg/day of prednisolone, she consulted for respiratory distress. Her left brachial and radial pulses were absent, and her blood pressure was 180/120 mm Hg as measured from the left arm. Bruits were audible over the course of the left carotid artery and the left and the right subclavian artery. The patient had elevated ERS (100 mm/H).An Ultra Sound Colour Doppler (USCD) was performed showing a circumferential parietal swelling interesting the left subclavian artery reducing his superficies of 76%, demodulating the Doppler spectrum and edema of the vessl wallFigure . These dWe diagnosed the patient having TA associated with sarcoidosis. She received prednisolone 40 mg/day with Methotrexate 10 mg/week and amlodipine 5 mg/say.As a response to treatment, blood pressure was normal 2 weeks after. The USCD control confirmed the therapeutic benefice showing a reduction of the parietal anomalies.About a dozen cases of the association TA and sarcoidosis were reported in the literature. -6; some TA can be associated with Crohn's disease , RCH, syThe association between sarcoidosis and TA or other forms of aortitis may be rare. However, TA or similar forms of aortitis are too rare to indicate that the reported concurrence with sarcoidosis is merely governed by chance. In fact, all these patients had several common features: (a) usually sarcoidosis preceded TA; (b) the time between the diagnosis of sarcoidosis and that of TA was several years (eight or more) in most of the patients; (c) the aorta and/or its major branches was affected; (d) 50% of the patients had uveitis, which is much less common in frank sarcoidosis; and (e) all patients responded to glucocorticoid treatment.Association of TA and sarcoidosis raise a number of questions of a possible link between these 2 diseases. Vascular injury (or "granulomatous vasculitis), and especially the location in the aorta thoracic and/or its branches, could be a complication in the course of sarcoidosis -3,10. HoThe association between sarcoidosis and TA are rare but not accidental; complete vascular clinical examination should be performed in those patients in order to detect asymptomatic underlying inflammatory arteritis.The relatively low prevalence of sarcoidosis, and even more so the rarity of aortitis, suggests that this number is relatively high and too high to be a coincidence; can we say that sarcoidosis and TA appears to be 2 related diseases or that Takayasu arteritis or Takayasu arteritis-like granulomatous vasculitis may be, in fact, a complication of sarcoidosis?Informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.The authors declare that they have no competing interests.AH, RK, OH, OB and SM: Diagnosis the disease and monitoring the patient RS and MG: Have carried out the radiological explorations.All authors read and approved the final manuscript.