dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular findings Exome sequencing has been performed in Family 2, in three individuals: the proband (F2-IV. 3) and her two unaffected parents (F2-III. 1 and F2-III. 2) (Figure  2 ). Considering the recessive inheritance of the disease in the pedigree and consanguinity (F = 1/16), we assumed identity by Descent  [8]. Using an in-house bioinformatics tool, we realized identity by descent filtering of exome data and identified 1037 homozygous variants in the proband, which were also heterozygous in both parents. Of these 1037 variants, 916 were exonic and/or splice site mutations, of which 434 were either non-synonymous and nonsense single nucleotide variants, or small insertions/deletions leading to a shift in the reading frame. In order to further refine the list of candidate nucleotide variations, additional filtering was performed on what we called the ''dbSNP13700'' database (i.
e. dbSNP137, from which we have removed mutations that are reported as pathogenic alleles, as well as all referenced variants with frequencies lower than 1%, or without any frequency information). Additional filtering was also performed using our in-house exome database that includes all homozygous variants detected by exome sequencing of 14 Lebanese unaffected individuals. We ended up with a list of 16 candidate homozygous by descent variants in the proband F2-IV. 3. In family 1, exome sequencing has been performed only in the proband (F1-IV. 3, Figure  2 ). Using the same analysis pipeline and after all filtering steps, we were able to identify 59 homozygous variants in the genes coding regions of this patient. In total, patients F1-IV. 3 and F2-IV. 3 shared 13872 homozygous variants, of which only 3 exonic variations were both homozygous by descent in the proband from family 2 (F2-IV.
3), and homozygous in the proband from family 1 (F1-IV. 3), after applying the different filters (Table  S1 ). Of those three variants, only one missense mutation (NM_016069: c. 226A. G; p. As-n76Asp) in the PAM16 gene (presequence translocase-associated motor 16), that is more commonly referred to as MAGMAS (Mitochondria-associated granulocyte macrophage CSF-signaling molecule), was predicted to have pathogenic effects using different bioinformatics prediction softwares, such as: Mutation Taster (disease causing variation with a probability value of 0. 99999957), SIFT (damaging effect, score 0. 006)  [9] , PROVEAN (deleterious effect, score 24. 021)  [10]  and PolyPhen-2 (possibly damaging effect, score 0. 728 HumDiv). By Sanger sequencing, we confirmed the segregation of the c. 226A. G transition in MAGMAS with the disease in both families (Figure  3A ): the mutation was homozygous in the patients, heterozygous in the parents and in the unaffected sibs in both families.
Gene expression analysis A naturally occurring read-through transcription between the neighboring CORO7 (coronin 7) and MAGMAS genes on chromosome 16 is stated in the Genome UCSC browser (NM_001201479). To determine if the fusion protein is involved in the pathogenesis of the severe skeletal manifestations observed in the affected cases, we checked the expression of CORO7, MAGMAS and CORO7-MAGMAS fusion transcript in human cultured control cells (fetal chondrocytes, osteoblasts and skin fibroblasts) by Reverse Transcriptase PCR. CORO7, MAGMAS.
DNA extraction and exome sequencing Genomic DNA was extracted from peripheral blood samples by standard salt-precipitation methods  [34]. Exome sequencing was carried-out on 3 individuals from family 2 (F2-III. 1, F2-III. 2 and F2-IV. 3) and the proband from family 1 (individual F1-IV. 3) (Figure  2 ). Targeted exome sequencing, library preparation, capture and sequencing were performed by the French National Genotyping Center (CNG). Exomes were captured and enriched using the in solution Agilent SureSelect Human All Exon kit v3. 0  [35]  and then sequenced on an Illumina HiSeq2000, using a paired-end 100-bp read sequencing protocol. Image analysis and base calling were performed using the Illumina Data Analysis Pipeline Software 1. 5 with default parameters. Raw data were mapped to the current built of the human genome (hg19) by using BWA 0.
Capillary sequencing Genomic and cDNA sequences of MAGMAS (also known as PAM16) were obtained from UCSC Genomic Browser on Human February 2009 (NM_016069). Primers used for PCR amplification were designed using Primer3 software (http://frodo. wi. mit. edu) to amplify the region surrounding the mutation detected by exome sequencing in exon 4. PCR products were purified by exonuclease I/Shrimp Alakaline Phosphatase treatment (ExoSAP-IT; Fisher Scientific SAS, Illkirch, France) according to the manufacturer's instructions and both strands were sequenced using the Big Dye The non-processed Hsp60 precursor accumulated in the mutant strain after induction of the phenotype. Only the mature form of Hsp60 was detected in wild-type yPAM16 and MAGMAS expressing yeast cells. PGK was used as a loading control and Porin as a mitochondrial loading control.
p: precursor form of Hsp60, m: mature form of Hsp60. (B) Immunoblotting using Human anti-MAGMAS antibodies detected a lower level of MAGMAS protein in the mutant strain when shifted at non-permissive temperature, compared to the amount in MAGMAS WT expressing strains. doi:10. 1371/journal. pgen. 1004311. g007 Terminator v1. 1 Cycle Sequencing Kit (Applied Biosystems). Sequence reactions were purified on Sephadex G50 (Amersham Pharmacia Biotech, Foster City, CA) and capillary electrophoresis was performed on Genetic Analyser 3100 (Applied Biosystems). Electropherograms were analyzed on the Sequence Analysis Software version 5. 2 (Applied Biosystems) and aligned with the WT MAGMAS gene sequence using ChromasPro version 1. 22 (Technelysium, Queensland, Australia).
Quantitative Real-Time RT-PCR Reactions were conducted in a 96-well plate with the ABI 7500 Sequence Detection System (Applied Biosystems). Primers against MAGMAS, CORO7 and CORO7-MAGMAS were designed using Primer Express software (Applied Biosystems) (Figure  S3 ). PCR was performed in a 20-ml reaction volume containing 10 ml Power SYBR-GreenPCR Master Mix of SYBR Green PCR Master Mix buffer (Applied Biosystems, Foster City, CA, USA), 10 pmol forward and reverse primers and 5 ng of RNAse H-treated (Invitrogen Life Technologies) cDNAs obtained from reverse transcription of DNAse I-treated total RNA extracted from control fibroblasts and chondrocytes cDNA. The reaction cycling conditions were 95uC for 10 min, followed by 40 cycles of 95uC for 15 s and at 60uC for 1 min. Sequence Detection Software was used for exporting the threshold cycle data and further analyzing differences in threshold cycle values (DCt) between the test locus and the control locus.
15uK) in minimal medium, were shifted to 37uC (310. 15uK), for 6 hours then harvested, washed and transferred to slides for visualization. The slides were examined with a DMIRE2 microscope (Leica, Deerfield, IL). For GFP fluorescence, filters used were 450/ 490 nm for excitation and 500/550 nm for emission whereas for Ds. Red fluorescence, filters were 542/582 nm for excitation and 604/644 nm for emission. Images were captured using a CCD camera (Roper Scientific, Tucson, AZ) and Metamorph software (Universal Imaging, WestChester, PA) was used to deconvolute Zseries and treat the images.
Acknowledgments We express our deepest gratitude and sympathy to the families for their full cooperation throughout the study. We are grateful to  Mark Lathrop  and to the  Centre National de Genotypage (CNG)  for exome sequencing. We are grateful to  D'Silva , P. , Guiard B. , Winzeler E. A. , Dujardin G. and Westermann B. for their generous gifts of plasmids, antibodies and yeast strains. We thank  Le Goff C. for her guidance and assistance in the directed mutagenesis experiment.
Data Due to the very small number of goats and sheep in the area we focused this study on the cattle population. A first serological survey was conducted in 2009 in 984 animals of 43 villages of the study area. A seroprevalence rate of 28% (95% CI: 25-31%) was observed, that varied between 0% and 71. 4% according to the village  [22]. A census of the cattle population was performed in each village: the number of cattle and cows belonging to each breeder was recorded. In 2010, a second serosurvey conducted in 484 animals of 39 villages showed a seroconversion rate of 7% (95% CI: 5-10%)  [23]. This seroconversion rate ranged from 0% to 20% according to the village  [23]. Movements of cattle in the study area were also documented: renewal practices of each breeder (usual trade, barter) and number of animals sold, bought or bartered in the.
Captures were carried out on a monthly basis: more than 56,000 adult mosquitoes of 35 different species were collected. Aedes mosquitoes were rare. The most abundant captured mosquitoes were Culex pipiens, Culex antennatus, Culex univittatus, Anopheles squamosus and Anopheles coustani. Rice field are the larval habitat of the above mentioned mosquito species and their population dynamics in the area were similar  [24]. We thus considered a single biotype for vectors. We also considered rice fields as a homogeneous biotope that represents the potential sources of exposure to mosquito bites. Using aerial pictures (300*300 ppp) obtained from the National land plan (PNF) of Madagascar (June 2011), rice fields of the study area were digitized using ArcGIS 10 software. The villages of the area were geolocated using Global Positionning System (GPS).
Ethics statement For cultural reasons, no ethical body was involved in the study protocol. However, data collections, blood samples and protocol were done in collaboration with the Malagasy Veterinary Services and according to Malagasy regulations about animal welfare. Serological products were treated according to international regulations. Meetings were organized with breeders of the study area to explain the goals of the study and the decision to participate was taken individually according to the breeders' willingness and at the village level (all villages were visited). Breeders gave the permission to use their animals for the whole study and could stop at any time. Informed consent was given orally and documented in questionnaires. Written consent could not be obtained for the same cultural reason.
Fixed parameters. Observational data collected in 2009 were used to set the number of cattle and cows per village and per group of breeders (defined based on renewal practices), and the average number of cattle moved from one village to another, either by usual trade or by barter. The monthly follow-up performed in 2011 allowed estimating daily per-capita calving (n) and death rates (m). Neither calving nor mortality was seasonal in the study area. The duration of incubation (y) and viraemic (r) periods were set according to literature (Table  1 ). The mosquito species observed in the area are active at dusk and during the night. Field observations performed during the 2011 follow-up showed that breeders wanting to barter some of their animals did it after the working day, at dusk. Afterwards, they came back to their village.
The initial value of the parous rate (0. 56 for October, 1) and the slope of the linear increase (0. 002) were computed from field data collected during the 2009-2010 entomological survey. The parous rate was assumed to show a plateau once having reached a maximal value, denoted g max. This maximal value was set to 0. 90, the maximal value observed during the entomological survey. The duration of the gonotrophic cycle (c) and that of the extrinsic incubation period (w) were set according to literature to 3 and 7 days, respectively (Table  1 ). Estimated parameters. Three parameters were estimated using seroprevalence data (n = 81 village-level seroprevalence data: the date, the number of positive and of tested animals) and seroconversion data (n = 109 village-level seroconversion data: two dates, the number of animals initially seronegative and, among them, the number of observed seroconversions) collected in the study area between 2009 and 2011: the vector-host ratio (H v ), the relative abundance of vectors during the cold and dry season (a min ), and the direct transmission parameter (b).
Field data showed that cattle purchase from distant markets mainly occurred after the rice harvest (when breeders have money available), during the dry and cold season (May to September). Eight dates were thus considered for virus introduction (T 0 ): the first day of each month between June 2007 and January 2008. Because RVFV circulation cannot start during the dry and cold season for M0, only 4 dates were considered for that model: 2007-10-01, 2007-11-01, 2007-12-01 and 2008-01-01. Parameter estimation was thus performed for 28 models (M0 for 4 introduction dates; M1, M2 and M3 for 8 introduction dates). These 28 models were ranked according to the Akaike Information Criterion, corrected for small samples (because the number of parameters k was small compared to size of the dataset n: n=kv40): AICc~{2LLz2kz 2k kz1 ð Þ n{k{1 where LL is the minimal log-likelihood, n is the number of observations (81 seroprevalence data and 109 seroconversion data), and k is the number of parameters of the model (1 for M0, 2 for M1 and M2 and 3 for M3).
Multimodel inference methods were then used to combine the 28 models  [27, 28]. A weight was first computed for each of them: The core of the model was programmed using the Java language. It was embedded in the R environment with which statistical analyses were performed  [29]. The source code is available upon request. w i ~exp {D i =2 ð Þ P 28 j~1 exp {D j =2 À Á , with D i ~AICc i {AICc min ,.
Discussion In the temperate and mountainous ecosystem of Madagascar highlands, the high altitude and low temperature, especially during the dry and cold season, make climatic conditions unfavourable to a yearlong mosquito proliferation, and thus to a permanent RVFV circulation. Nevertheless, successive serological surveys conducted in a pilot area after the 2008 epidemic peak showed a recurrent circulation of RVFV. A model was elaborated to mimic RVFV transmission between cattle and mosquito populations in villages and rice fields of the study area. Data collected during field investigations were used to parameterize this model. The model was then used to investigate possible mechanisms explaining the recurrent circulation of RVFV in the study area. Two mechanisms were considered: RVFV circulation during the dry and cold season thanks to an active residual mosquito population, and direct transmission of RVFV between cattle when viraemic cows calve.
It can use both simple and complex carbohydrates such as cellulose, cellobiose, xylose, glucose, and mannose to carry out mixed-product fermentation, producing acetate, formate, ethanol, H 2 , and CO 2 in amounts comparable to those of other cellulolytic Clostridia  [18] [19] [20] [21]. In addition, experiments conducted recently in our laboratory suggest growth ability on xylan polymers (Figure  2 ). This makes Clostridium termitidis potentially suitable for biofuel production through consolidated bioprocessing. The C. termitidis genome has recently been sequenced (GenBank accession number AORV00000000)  [22] , though investigation of its CAZyme content relative to other cellulolytic Clostridia has not yet been reported. CAZymes have a variety of functions within a cell, but are also involved in the biosynthesis and degradation of cellulose and other polysaccharides.
The CAZy database (http://www. cazy. org/) [23] , organizes CAZymes into 6 main classes: i) Glycoside hydrolases (GH), are a large group of enzymes that hydrolyze the glycosidic linkages between two or more carbohydrates or between a carbohydrate and a noncarbohydrate molecule; ii) Carbohydrate esterases (CE), are involved in the hydrolysis of ester bonds; iii) Glycosyl transferases (GTs) catalyze the formation of glycosidic bonds to form a glycoside; iv) Polysaccharide lyases (PLs), cleave glycosidic linkages present in acidic polysaccharides by a beta-elimination mechanism; v) Auxillary activities  [24] , are redox enzymes that act in conjunction with other CAZymes to breakdown lignocellulose; and vi) Carbohydrate binding modules (CBMs) are non-catalytic protein domains which function in binding polysaccharides, thus bringing the biocatalyst into close and prolonged proximity with its substrate, allowing carbohydrate hydrolysis  [25].
Phylogenetic placement Phylogenetic analyses were carried out to determine the relatedness of C. termitidis with other members of the Clostridia family based on chaperonin 60 (cpn60) universal target sequences (549-567 bp region of cpn60 gene), which were collected from the Cpn60 database  [28]. The phylogenetic tree was obtained using neighbor-joining  [29]  in MEGA version 4  [30]. Bootstrap tests with 1000 replications were conducted to examine the reliability of the interior branches.
CAZyme annotation Translated protein sequences of C. termitidis were analyzed de novo for identification and annotation of its CAZymes and assigned to carbohydrate active enzyme (CAZy) families using the CAZy pipeline  [23] , as described in  Floudas et al. (2012)   [31]. CAZymes of all other Clostridium species analyzed, were directly accessed through the CAZy database  [23] , and manually compared. Homologous sequences were obtained by screening the CAZyme sequences of the Clostridia and applying BLASTP search tools using the IMG-ER. Unless specified, highest percentage identity and coverage were reported, based on hits with lowest expect (e)-value (threshold 0. 01). Sequence coverage was manually assessed by considering the amino acid (AA) sequence length of the query and the data base target.
In addition C. termitidis had the greatest number of sequences belonging to GH2  (15) , GH3  (11) , GH4  (10) , GH8 (4), GH18 (8), GH23 (3) GH29 (5), GH30 (5), GH31 (6), GH35 (2), GH38  (14) , GH43 (12) GH51 (  6 ), GH78 (4), GH94(11), GH95 (5), GT2 (20), GT28 (4), CBM12 (8), CBM32  (14) , and CBM35  (24). There were, notably a number of CAZyme genes which were only found in C. termitidis: GH50 (1), GH64 (1), GH76 (1), GH93 (1), GH97 (2), GH 110 (1), PL8 (3) and CBM66 (8) (Table  S1  in File S1, Table  S2  in File S1, Table  S3  in File S1 and Table  S5  in File S1). Interestingly, of the 133 families of GHs currently identified in the CAZy database, the lowest numbers were seen in C. thermocellum, with 27 GH families. C. thermocellum is known to be a comparatively efficient biomass degrader, which identifies it as an attractive candidate organism for CBP  [2].
Two extracellular genes in family GH8, with dockerin I domains, were identified in C. termitidis (Table  3 ). As with members of the GH5 family, members of the GH8 family have a variety of functions and can cleave b-1,4 linkages of cellulose, xylan, chitosans, and lichenans. Cter_0523 shows high AA sequence identity (74%) with the cloned and characterized endoglucanase C Ccel_0730 from C. cellulolyticum  [51] , and 54% AA sequence identity with the characterized C. thermocellum Cthe_0269, also an endoglucanase  [52]. C. termitidis encodes 11 GH3 genes, highest amongst the other Clostridium species examined (Table  S1  in File S1), of which only 2 are extracellular (Table  3 ), and are annotated as b-glucosidases on IMG database. This suggests that C. termitidis is able to hydrolyze complex sugars to glucose monomers extracellularly before assimilation.
JDR-2 with similar modular structure, and 604 AA that are identical with the Ccel_2320 of C. cellulolyticum. CBM22 and CBM9 modules are both considered to have xylan-binding capabilities  [23]. To further degrade xylo-oligomers into simple sugars, five GH43 genes coding for secreted xylosidases were identified in C. termitidis. Two of these (Cter_0945 and Cter_4060) contain three C-terminal SLH domains for cell attachment. Cter_4060 has a multi-domain structure with domains GH43-CBM35-CBM35-CBM35-CBM35-CBM13-SLH-SLH-SLH. CBM35 and CBM13 are known to primarily bind with both xylan and mannans  [55] [56] [57]. BLAST analysis shows 61% AA identity to the multi-domain C. cellulolyticum b-xylosidase Ccel_3240, which also has a similar modular structure, suggesting that Cter_4060 may have putative xylan hydrolyzing properties.
Arabinofuranosidases hydrolyze arabinose side chains in xylan degradation and are members of GH51 family. C. termitidis encodes genes for two extracellular putative arabinofuranosidases (Table  3 ). Interestingly, only C. cellulovorans appears to have extracellular homologs among the Clostridium species considered (Table  S6  in File S1). Four putatively secreted members of the GH30 family annotated as O-glycosyl hydrolases on the IMG database were identified in C. termitidis (Table  3 ). The GH30 family has members with activities ranging from glucosylceramidase, b-1,6glucanase, b-xylosidase, b-fucosidase, b-glucosidase and endo-b-1,6-galactanase  [23]. Cter_0267 and Cter_2867 are putatively cellulosomal due to the presence of a C-terminal dockerin 1 domain. BLAST analysis shows 80% homology with C.
cellulolyticum Ccel_0649, which is putatively involved in xylan degradation with high activity towards feruloylated arabinoxylans. Members of GH30 have not been functionally characterized in Clostridia. The 3192 AA sequence of Cter_2817, a multidomain GH5 protein, has a modular structure CBM66-CBM66-CBM66-GH5_distGH43-CBM35-CBM66-GH43-SLH-SLH-SLH and putatively bound to the cell via the SLH domains. This enzyme seems to be unique to C. termitidis, because BLAST searches did not give hits in other bacteria in the data base. In addition to the GH43 catalytic domain, there is an additional GH5 domain of subfamily 43 (GH5_43). GH5_43 has not been functionally assigned as of yet  [49]. However, Cter_2817 has been annotated as a b-xylosidase on IMG database, perhaps due to the presence of the putative GH43 domain.
According to the CAZy database, GH43 has members that have xylosidase, arabinofuranosidase, arabinose, xylanase, and galactosidase activities  [23]. The presence of multiple CBM66 domains and a CBM35 domain indicates its ability to target both fructans  [58]  and xylans  [54]  respectively. Endoxylanase Cter_2829, belongs to GH8 family and has a dockerin I domain. BLAST analysis shows 77% AA sequence identity with the Ccel_1298. Hydrolysis of mannans is mainly carried out by the action of bmannanases found in the GH26 family. Our results show that the genome of C. termitidis contains a single GH26 gene annotated as b-mannanase (Cter_4544), which may putatively be involved in the breakdown of the mannan backbone. Even though Cter_4544 has a dockerin domain, PSORTb 3. 0 analysis was unable to predict its location.
cellulolyticum. However, none of these have a multi-domain structure. Carbohydrate esterases (CEs) catalyze de-acylation of saccharides. The C. termitidis genome encodes a total of 15 CEs belonging to five different families, following C. cellulovorans, which has 21 CEs. (Table  2 , Table  S4  in File S1). The C. termitidis CE15 and one CE4 (Cter_5018) gene products both carry a dockerin 1 domain, suggesting their putative association with the cellulosome. CE4 enzymes, of which C. termitidis has 9 members, are annotated as either acetyl xylan esterases or chitin deacetylases, indicating their putative ability to have activity against both xylans and chitins. All the members of the CE7 family are annotated on the IMG database as acetyl xylan esterases. The C. termitidis family CE9 gene product, annotated as N-acetylglucosamine 6-phosphate deacetylase (EC 3.