dataesr/scientific-paragraphs-categorization huggingface dataset:
This score reflects several criteria including the predicted hybridization quality, GC content and steric hindrances (Additional file 2: Table  S2 ). A total of 56 % of probes displayed a BC_score of BC_1, 22 % of BC_2 reflecting the highest quality of predicted hybridization and a stable and consistent duplex with their targets. Only a small fraction of the probes were scored as BC_3 (11 %), BC_4 (11 %) and no BC_Poor were detected. Using the ROSO software we designed probes for the 208 of the remaining sequences. The final CAZyChip was constructed using 180,000 probes, targeting 55,220 GHs able to detect 117 GH families on the 133 available in the CAZy database (www. cazy. org). We included 4848 positive and negative control probes. Non-bacterial families and GH7, 22 and 133, for which thermodynamical parameters did not provide specific probes, were not represented on the CAZyChip.
The color intensity indicates the degree of variation in expression the middle of the phase 2 (day 5), where enzymatic activities were high (Fig. 3 ). A limma t test revealed that 2567 GHs were expressed in the two time points: day 3 and day 5 (Additional file 6: Table  S4 ). Both samples displayed a common group of 257 expressed GHs. The two sample points also displayed GH expression unique to the specific time point, with the day 3 sample containing the expression of an additional GH belonging to the GH66 family (accession number AFH61494), and the day 5 sample containing expression of 2309 additional GH's. Among the total 2566 GHs that were expressed at day 5, only 2 were down-regulated on day 5 compared to day 3 (Additional file 6: Table  S4 ). The weighted differentially expressed genes, and those present at day 5, belong to 96 GH families and are displayed on Fig.
Hum15 Human feces Xylanase CE15-GH8, CE6-GH95, GH10, GH115, GH31, GH43 (1) , GH43 (2) , GH43-CE1, GH97 Rum14O19 Cow rumen Mannanase GH26, GH28, GH63, GH43, GH4 Rum33M21 Cow rumen β-glucanase GH5, GH42 Bold data correspond to GHs detected with the cazychip of plant cell wall polysaccharide degradation. While focusing on GH families involved in enzymatic activities necessary to reach 25 % of wheat straw degradation  [36] , we observed an increase of the genes differentially expressed between day 3 and day 5, from GH families containing cellulase, xylanase, exoglucanase and betaglucosidase activities in accordance with  [36]  (Table  2 ). We observed an enhanced expression of GH1, GH3 and GH5, which according to CAZy, some members of these families are beta-glucosidases and exoglucanases (for GH1 and GH3) or cellulases (for GH5) (Table  2 ).
Discussion DNA microarray is one of the most popular technologies for gene expression profiling used in the past 15 years  [28, 42, 46, 50, 68]. In this study we presented the development and the validation of the microarray CAZyChip dedicated to analyze the bacterial glycoside hydrolase expression. This is the first high throughput tool, based on DNA microarray technology, allowing the rapid characterization and exploration of the GHs arsenal of complex microbiota at the transcriptomic level. For design purposes, we first collected all sequences of bacterial GHs available in the CAZy data base, belonging to cultivated species, as well as some metagenomic sequences issued from uncultivated species. We then performed a probe bioinformatic design using eArray and ROSO softwares, which took into account the thermodynamics and specificity regardless of the secondary structures that probes can adopt.
Functional metagenomic has been proven to be useful tool to achieve this screening of GH's activities (see review  [27, 58] ). However, like any screening related technology they face the paradigm "you get what you screened for". In this context, the CAZyChip allows the observation of the enzymatic arsenal developed by microbial consortia on complex substrate, and could represent a decisive support before choosing a sample for further analysis. As few CE sequences were included in the CAZyChip, in the near future, others CAZymes (i. e. glycosyltransferases, polysaccharide lyases, or auxiliary activities) could be detectable on the CAZyChip with the same approach. Thanks to its flexible design, this biochip will be able to accommodate additional probes  [9]  and could be upgradable, taking into account the regular updates of the CAZy database.
Acknowledgements and funding This work was supported by the  IDEX Transversality program  from  Toulouse University  (grant number:  2014-628 ) and by the  French National Institute for Agricultural Research (INRA , ' Meta-omics of Microbial Ecosystems ' research program, and  AIP Biotechnology 2011 ). A. Abot, was funded by a grant from the  Conseil Régional Midi-Pyrénées  (grant number  12053333 ). We thank  S. Bozonnet  for helpful discussion, our colleagues L  Ufarté ,  P. Alvira ,  B. Guyez ,  M. Abadie ,  S. Ladevèze , and  S. Comtet-Marre  ( INRA, UR454 Microbiology, Centre Auvergne-Rhône-Alpes, Saint Genes Champanelle; Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand; Lallemand Animal Nutrition, Blagnac, France ) for technical assistance, and fruitful discussion. The  GeT-TQ and GeT-Biochip Platform from Toulouse Genopole  are acknowledged for skillful technical assistance.
Constraining the past response of marine terminating ice streams during episodes of deglaciation provides important insights into potential future changes due to climate change. This paper presents new 36 Cl cosmic ray exposure dating from boulders located on two moraines (Glen Brittle and Loch Scavaig) in southern Skye, northwest Scotland. Ages from the Glen Brittle moraines constrain deglaciation of a major marine terminating ice stream, the Barra-Donegal Ice Stream that drained the former British-Irish Ice Sheet, depending on choice of production method and scaling model this occurred 19. 9 ± 1. 5 -17. 6 ± 1. 3 ka. We compare this timing of deglaciation to existing geochronological data and changes in a variety of potential forcing factors constrained through proxy records and numerical models to determine what deglaciation age is most consistent with existing evidence.
, 2000; Dowdeswell et al. , 2014; Svendsen et al. , 2015). Of the Pleistocene ice sheets, the British-Irish Ice Sheet (BIIS) provides a useful analogue. Its western margin was marine terminating while its position next to a major surficial artery of the Atlantic Meridionial Overturning Circulation (AMOC) rendered it potentially sensitive to small climatic perturbations  (Knutz et al. , 2007). This sensitivity is captured in proxy data  (Scourse et al. , 2009; Hibbert et al. , 2010)  and numerical modelling experiments  (Hubbard et al. , 2009). Past reconstructions of the BIIS relied heavily on onshore mapping of landforms that can be inferred to represent former ice limits including terminal, lateral and recessional moraines  (Sissons et al. , 1973; Ballantyne, 1989, Bennett and Boulton, 1993; Clark et al.
In northwest Scotland a regional scale readvance, the Wester Ross readvance has been delimited from a suite of onshore moraines and dated with 10 Be exposure ages to ~ 16 ka  (Robinson and Ballantyne, 1979; Bradwell et al. , 2008; Ballantyne et al. , 2009). However to date, this readvance has not been identified south of Skye. In this contribution we present bathymetric data from inshore waters near Skye, which highlights ice dynamics following ice stream retreat. Cosmogenic 36 Cl cosmic ray exposure (CRE) ages from moraine boulders provide geochronological constraints on the timing of this deglaciation.
Bathymetry To constrain deglaciation of the BDIS we confirmed the presence of ice margin positions in southern Skye from onshore fieldwork in Glen Brittle and a bathymetric survey of Loch Scavaig. This study used a SEA SwathPlus High Frequency System with a central frequency of 468 kHz and a ping rate of up to 30 pings per second giving a potential footprint of less than 5 cm at standard survey speed. Data were acquired with a TSSDMS205 motion reference unit and positioning provided by a Topcon Hiper RTK dGPS. The RTK dGPS base system was established on the loch shore and tied to the BNG datum using Rinex corrections from the OS. An Applied Microsystems MicroSV sound velocity probe was mounted at the sonar head in order to record changes in velocity due to mixing of different waters (and thus potential salinity changes) in the relatively enclosed waters of the loch.
Deglaciation of the BDIS The deposition age of the Glen Brittle moraine provides a constraint on final deglaciation of the BDIS as its morphology and lithology demonstrates deposition by valley glaciers fed from the locally nourished SID. As such, it would not be possible to form moraines in Glen Brittle until BDIS deglaciation was complete. Taken at face value, the 36 Cl CRE ages from Glen Brittle presented here suggest deglaciation of the northern sector of the BDIS had occurred by 17. 6 ± 1. 3 ka (SA scaling). Use of the Lm scaling makes deglaciation considerably earlier (19. 9 ± 1. 1 ka) although the ages do overlap at  Ireland and Jura (McCabe and Clark, 2003; Clark et al. , 2009; Ballantyne et al. , 2014)  (Figure  1 ), our data suggest that the entire marine portion of the former BDIS was deglaciated by 17.
Acknowledgements We thank  Joe Licciardi  for laboratory access at the  University of New Hampshire, USA  and preparation of 36 Cl targets. The French national  AMS facility ASTER (CEREGE, Aix en Provence)  is supported by the  INSU/CNRS , the  ANR  through the  "Projets thématiques d'excellence" program for the "Equipements d'excellence" ASTER-CEREGE action ,  IRD  and  CEA. We would like to thank  Shasta Marrero  for helpful and informative discussion on the CRONUScalc online calculator. DS was supported by a  SAGES  studentship and fieldwork by funds from the  QRA and BSG. Detailed comments from two anonymous reviewers have improved the quality and clarity of this manuscript.
We also applied single spectrum analysis (SSA), which applies an empirical orthogonal function (EOF) analysis to the autovariance matrix on the chronologies. Here we undertook a Monte Carlo significance test (95 % significance), using a window of 9, a Burg covariance, and eight components. Both analyses used the software kSpectra version 3. 4. 3 (3. 4. 5). Wavelet analysis and coherence was undertaken on the 30-year averaged data using the wt() and wtc() functions respectively in the R package "Biwavelet"  (Gouhier, 2013). The Morlet continuous wavelet transform was applied, and the data were padded with zeros at each end to reduce wraparound effects  (Torrence and Webster, 1999). To test the robustness of the obtained periodicities, the Lomb-Scargle algorithm was employed, a spectral decomposition method that computes the spectral properties of time series with irregular sampling intervals (Ruf, 1999) -in this instance, the "raw" charcoal values.
While the data set from Palm2 does not have the resolution of the other records, a similar trend with pervasive lower salinities (stronger westerly winds) is recorded between 2000 and 1000 cal. years BP (Fig. 7e ). Whilst the change in the trend may be interpreted as reflecting either a change in the latitude and/or strength of the winds, the parallel peaks and troughs in Nothofagus and charcoal from Canopus Hill (in contrast to constant Nothofagus levels at Laguna Guanaco -  Moreno et al. , 2009)  imply that the core latitude of the westerly winds has not changed and instead was particularly strong between 2000 and 1000 cal. years BP, resulting in increased fire frequency in Patagonia  (Holz and Veblen, 2012). This is supported by a study on Patagonian Fitzroya cupressoides from 40-42 S  (Roig et al.
Existing studies have revealed contradictory results, highlighting either normative functioning  [3] [4] [5] [6] [7] [8] [9] [10] [11]  or a high proportion of psychiatric comorbidity  [12] [13] [14] [15] [16]. These discrepancies may the result of the following methodological differences. First, the studies included heterogeneous populations and often examined mixed clinical groups that included both transsexuals and other gender-nonconforming individuals, as well as individuals in different phases of the gender transition process. Second, psychological characteristics were established using varying psychometric measures, including different tests and structured psychiatric interviews. Although psychological distress may result from multiple stressors associated with sex reassignment, including frequent familial and social rejection, employment problems, and economic and legal difficulties  10, 17  , few data are available.
Data collection The following data were collected. 1. Sociodemographic information: medical files and interviews were used to report gender identity (male-to-female MtF/female-to-male FtM), age (younger: < median age; older: ≥ median age), hormonal therapy (the patients were categorized into the hormonal therapy group if they had received physician-prescribed cross-sex hormones for a minimum of 3 months' as a part of the sex reassignment procedure, corresponding to a minimal delay for expected physical changes 2 ), onset age (early vs. late onset age, i. e. , beginning before vs. after puberty  21  ), and sexual orientation (same biological sex exclusively vs. others). 2. Personality test scores: personality was assessed using the Minnesota Multiphasic Personality Inventory 2 (MMPI-2), administered by a psychologist as part of a more extensive psychological evaluation.
Statistical analysis. The MMPI-2 data were analysed using both means and standard deviations (T-scores) and the proportions of individuals with a score higher than 65 according to the MMPI-2 manual. Comparisons between sex reassignment surgery eligible and non-eligible patients were performed for biological sex, age, hormonal therapy status, and MMPI-2 scales. For each biological sex, the MMPI-2 scores were compared according to four variables of interest: age group (younger vs. older), hormonal therapy status (yes vs. no), onset age (early vs. late onset age), and sexual orientation (same biological sex vs. others), using the two-tailed Mann-Whitney t-test for independent samples. The proportions of individuals with scores ≥ 65 were compared among the subgroups using chi-squared or Fisher's exact tests.
For each individual, the number of scales (excluding the Masculinity/Femininity scale which reflects gender dysphoria) on which he or she scored in the clinical range was calculated. To determine potential variables of interest linked to the MMPI-2 scores (biological sex, age group, hormonal therapy status, onset age, and sexual orientation), logistic regression models were performed using a forward stepwise approach. The final models expressed the odds ratios (OR) and 95% confidence intervals (CI). All of the tests were two-sided. Statistical significance was defined as p < 0. 05. Statistical analysis was performed using the SPSS version 15. 0 software package (SPSS, Inc. , Chicago, IL, USA).
Some authors have suggested that the MMPI scores of transsexual individuals should be interpreted using the normative data for the subject's gender identity  5, 28, 36. The Masculinity/Femininity scale scored for the biological sex is frequently abnormal but becomes normal when it is scored for the desired sex. The Masculinity/Femininity scale may be considered a reflection of the gender role dysphoria of these individuals. It is also often viewed as a nonclinical dimension of the MMPI  7. MtFs scored in the clinical range more often than FtMs on the Hypochondriasis and Depression scales. The literature shows contradictory results. Whereas similar studies did not find significant differences in the MMPI-2 profile according to sex  4, 5, 10  , other authors have tended to indicate that MtF individuals are more psychologically distressed than FtMs  3, 25, 26, 37, 38.
It is now well established that, by inducing external physical modifications, regular hormone treatments produce a change in the gender role, greater self-confidence, greater comfort with others, and better social skills, and they reinforce gender affirmation through social recognition  44, 49, 50. This finding is in line with recent studies suggesting the positive role of hormonal therapy in the quality of life of transsexuals  51, 52. There were several strengths and limitations of this study: 1. This study compared psychological test data obtained from individuals approved for gender reassignment procedure with test data obtained from individuals who were rejected. This comparison showed higher scores among the non-eligible individuals for two clinical scales: Hysteria and Schizophrenia.
Author Summary Schools, offices, hospitals play an important role in the spreading of epidemics. Information about interactions between individuals in such contexts can help understand the patterns of transmission and design ad hoc immunization strategies. Data about contacts can be collected through various techniques such as diaries or proximity sensors. Here, we first ask if the corresponding datasets give similar predictions of the epidemic risk when they are used to build a network of contacts among individuals. Not surprisingly, the answer is negative: indeed, if we consider data from sensors as the ground truth, diaries are affected by low participation rate, underreporting and overestimation of durations. Is it however.
Measuring directly such networks represents an important challenge  [20]. Many studies have relied on contact diaries or surveys  [10, 12, [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] , while technological advances have led to a strong increase in the use of wearable sensors in the recent years  [9, 13-15, 17-20, 33-35]. Quantitative comparisons between datasets obtained from sensors and self-reported diaries, in terms of the numbers and durations of contacts between individuals and of the contact network statistics, are however scarce, mainly because very few studies have combined these two data collection means  [21, 36]. These investigations have shown that diaries suffer from small participation rates, under-reporting of contacts, and over-estimation of the contact durations. Under-reporting is particularly strong for short contacts, while long ones are better reported, and some studies have put forward methods to estimate its magnitude and to correct for it  [29, 37].
Interestingly, and despite the much lower number of nodes and links in contact networks inferred from contact diaries, the overall structure of these networks is very similar to the one obtained from wearable sensors. Moreover, the links with largest weights (as measured by sensors), which might play a major role in propagation processes, are reported with high probability in the contact diaries. In this paper, we go beyond the comparison of the contact networks obtained by these methodologies and explore the impact of their differences on the evaluation of the epidemic risk when such datasets are used in numerical simulations of infectious disease propagation. Our goal is to understand to what extent and how the information gathered from contact diaries can be used in such simulations in order to yield an accurate description of the epidemic risk, despite the biases mentioned above.
We first compare the outcomes of spreading simulations performed using data coming from wearable sensors and from contact diaries that describe the contacts between students in the same context (a high school) and on the same day. Although the two networks are supposed to describe the same reality, we observe important differences in the simulations, due to the low participation rate in the diaries and to a stronger community structure in the contact diaries network than in the contact sensors network. We then design and evaluate a set of methods to use the information contained in the contact diaries to build surrogate versions of the contacts that yield, when used in the simulations, a better estimation of the real epidemic risk as quantified by the distribution of epidemic sizes (considering as ground truth the dataset from the sensors).
Data description We use two datasets collected in a French high-school in 2013 and made publicly available in  [21]. The data describe face-to-face contacts between students of 9 classes as collected by (i) the SocioPatterns infrastructure  [38]  based on wearable sensors, during one week and (ii) selfreported contact diaries filled on a specific day of the same week (Dec. 5 th , 2013). In the diaries, contact was explicitly defined as close (less than 2 m) face-to-face proximity, in order to match as much as possible this definition to the contacts detected by sensors. Using these data, we build two distinct contact networks for the day in which the diaries were collected: the Contact Sensors Network (CSN) and the Contact Diaries Network (CDN). In each network, nodes represent students and a link is drawn between a pair of nodes (i, j) if at least one contact between students i and j is present in the corresponding dataset during the considered day.
e. , of the fraction of individuals in the Recovered category at the end of the process), obtained by repeating the simulations with randomly chosen seeds. Note that, since we consider static networks, only the ratio β/μ is relevant, and multiplying both by a certain factor only changes the timescale on which the epidemic unfolds. The shape of the distribution of epidemic sizes depends on the features of the underlying network structure in terms of possible patterns of contagion. The comparison of these distributions gives hints about similarities and discrepancies of various datasets for the evaluation of the epidemic risk. We first compare in Fig  1  the outcome of simulations of the SIR model performed on the CSN and on the two versions of the CDN described above (CDN D with weights reported by students and CDN S with weights registered by sensors assigned randomly to the links), for one specific value of β/μ = 30.
In the same spirit as  [40] , we start from the available dataset and extend it by adding the missing nodes to the contact network, as well as surrogate links. We build these surrogate networks using only information known in the CDN m. We note that we do not try to infer the true missing links but to build a "plausible" version of these links, such that the simulations of epidemic spread on the resulting network yield an accurate estimation of the epidemic risk. The rationale behind the procedures we propose comes from (i) the observed similarity between the overall structure of the contact networks measured by sensors and by diaries, as quantified by the contact matrices of the densities of links between classes  [21]  shown in Fig  3,  and ( ii) the results of  [44]  that show how such contact matrices, together with information on the heterogeneity of contact durations, play a crucial role in determining propagation patterns in a structured population.
In order to build CDN s nz;S , we have used in step (iii) the distribution of aggregate contact durations measured by the sensors. We however need to consider the possibility that only diaries have been collected in a given setting, so that such a distribution is not available. To this aim, we take advantage of the robustness of such distributions, as discussed for instance in  [9]. We investigate this issue in some more details here, to understand if distributions of contact durations are similar enough in different contexts: our aim is to use publicly available data on contact duration distributions in a context-independent way in the step (iii) of our procedure. We consider five publicly available datasets, corresponding to contacts measured by wearable sensors in: a French and an American primary school  [35, 45] , an office building  [5]  a hospital  [22]  and a conference  [39].