dataesr/scientific-paragraphs-categorization huggingface dataset:
9 We will address the associations between multiple metal exposures and risk of diabetes and other health effects in future studies with the platform of the Jinchang Cohort Study. What are the main strengths and weaknesses? The Jinchang Cohort Study has several strengths. The main strengths are the unique exposure of the cohort population and the scheduled follow-up of each participant every 2 years with a repeated medical examination to update exposure and outcome information. Second, the location of the workers of the cohort is stable, and this will minimize loss to follow-up. Third, the large dataset the comprehensive epidemiological survey and medical examinations will permit extensive evaluation of the relationships between multiple metal exposures, gene, epigenetics and risk of human diseases.
UV-monitored thermal denaturation studies Absorbance versus temperature curves of duplexes Ld-sRNA24, 9a, 9b and 10 were measured at 1 M strand concentration in 10 mM phosphate buffer (pH 7. 0) containing 1 mM EDTA. In the case of duplexes LdsRNA29, 2a and 2b, 10 mM phosphate, 5 mM EDTA buffer (pH 7. 0) was used. Experiments were performed in Teflon-stoppered 1 cm path length quartz cells on a Varian-Cary-100 spectrophotometer equipped with thermoprogrammer. The samples were heated to 100 • C, allowed to slowly cool to 20 • C, and then warmed during the denaturation experiments at a rate of 0. 5 • C/min to 100 • C, monitoring absorbance at 260 nm. The data were analyzed by the denaturation curve processing program, MeltWin v. 3. 0. Melting temperatures (T m ) were determined by computerfit of the first derivative of absorbance with respect to 1/T.
Molecular dynamics simulations We simulated four systems, BC2-, BC6-and BC8-dumbbells (2a, 2b and 2c, respectively), as well as the linear dsRNA duplex analogue (LdsRNA29), used as a control system. The approach was similar to that used in previous study  (27). Linker structures were first geometrically optimized using Gaussian09 (33) package from which were calculated point charges using RESP calculation  (34). Simulations were done using AMBER14 package  (35). We used the latest DNA force-field, parmbsc1  (36)  with new RNA parameters developed recently in the lab. RNA structures were created using generic NAB module from AMBER14 package. The structures were solvated with TIP3P water molecules  (37) , neutralized with Na + ions  (38)  with an additional 0. 15 M of Na + Cl -added to the system, in order to approximate experimental conditions.
Systems were minimized, annealed and equilibrated following the standard AMBER simulation protocol, with 1 ns of equilibration time. Data were analyzed using Curves+ program  (39). Molecular Dynamics (MD) simulations of the double-stranded RNA containing 3 -terminal 1,2-di(5methylcytidin-N 4 -yl)ethane units (1; Figure  1 ) were performed using the same approach.
The most promising dumbbell design, (29 bp stem and a BC6 loop), was used to synthesize a dumbbell targeting the 1019-1037 site of the GRB7 mRNA (GenBank code: BC006535. 2), using a previously described sequence (dumbbell 14, Figure  1  and Figures  S3  and S7 )  (49). For comparison purposes, the corresponding 7 nt-loop ana- logue  (15)  was also prepared [according to the literature (28); Supplementary Figure  S3 ]. Transfection with the nontargeting control siRNA I (anti-Renilla luciferase siRNA) served as a negative control. Levels of GRB7 protein after treating the HER2+ breast cancer cell line SKBR3 with anti-GRB7 BC6-and 7 nt-loop dumbbells 14 and 15 and with a known anti-GRB7 siRNA as positive control (siRNA III; Figure  1 ) are shown in Figure  7A. In the three cases (siRNA III and dumbbells 14 and 15), the inhibition of GRB7 protein expression was very small on day 1, whereas after 48 h, the GRB7 expression was reduced by 95%, 92% and 78% in the cases of siRNA III and dumbbells 14 and 15, respectively.
Very interestingly, the inhibitory effect of the BC6-loop dumbbell 14 was marked at 72 h and persisted up to 6 days, whereas unmodified siRNA III, starts losing efficiency after 72 h. Although the activity of the 7 nt-loop dumbbell 15 was also marked at 72 h (100% GRB7 suppression), it also started to decrease at this point, although significantly slower than unmodified siRNA III. On day 6, the suppression activity of the BC6-loop dumbbell 14 was 1. 6-fold and 3. 8-fold more potent than those of RNAs 15 (7 nt loop) and siRNA III, respectively, with cells treated with dumbbell 14 showing a marginal 5% expression of GRB7. These results were further confirmed using a different siRNA sequence that had as target the 943-961 site of the same mRNA (GRB7) (GenBank code: BC006535. 2)  (45). The BC6-loop dumbbell directed against this second region (18; Figure  1 ; synthesized by double ligation of BC6-loop hairpins 16 and 17; Supplementary Figure  S7 ) induced changes in gene expression profiles over the timecourse similar to the ones observed for anti-GRB7 BC6loop dumbbell used in our first series of studies (14, see panels A and B in Figure  7 ).
ACKNOWLEDGEMENTS The HeLa H/P cell line was kindly provided by  Dr A. Alagia  ( IQAC, CSIC, Barcelona, Spain ). We thank  Dr M. Soler-L ópez ,  Dr. M. Royo ,  Prof. Dr R. Eritja ,  Prof. Dr E. Pedroso ,  Prof. Dr A. Grandas ,  Dr A. Avi  ñ ó,  A. Fàbregas  and  Dr I. Faustino  for their help and valuable comments. IRB Barcelona is the recipient of a  Severo Ochoa Award of Excellence  from  MINECO (Government of Spain). All the experimental work was performed in the EBL laboratory.
Participants were assessed at the Lausanne University Hospital, Switzerland. Of the proband carriers,. 87% were referred to the study by the clinical geneticist who had initially established the genetic diagnosis in the context of a neurodevelopmental disorder. Seven probands (four duplication carriers and three deletion carriers) were identified in the population biobank of Estonia as previously described (  16 ), and one duplication carrier was referred for psychiatric problems. All but four participants (n = 2 Asian descent and n = 2 African descent) were of European descent. Simons Variation in Individuals Project Cohort. For replication analyses on language, we used data from the Simons Variation in Individuals Project (VIP) cohort (http://sfari. org/resources/simons-vip), which aims at phenotyping carriers with a 16p11.
Cognitive Assessment Trained neuropsychologists performed all cognitive assessments. Participants underwent age-appropriate and developmentally appropriate neuropsychological tests assessing overall cognitive functioning, fine motor skills, language, memory, and executive functions. All Z scores were derived from standardized scores based on population norms provided by the testing manuals. When normative data were unavailable, we used raw scores that were adjusted for age and sex when appropriate. We specified the tasks where the latter procedure was applied. We used the following psychometric tests.
Statistical Analyses Neuropsychological Data Analyses. Variables derived from normative data were converted into Z scores for each participant (mean = 0; SD = 1) (Supplemental Methods and Materials). Raw scores of variables without available normative data were systematically adjusted for age and sex where appropriate. We performed either linear or generalized regression analyses depending on data distribution. Cognitive measures were the dependent variables. To investigate the effect of CNV on cognition, we used linear models including the following ordinal variables: deletion = 1, control = 2, duplication = 3. For contrasts between groups, we used post hoc t tests. Appropriate linear mixed models or generalized linear mixed models were performed taking the variable "family" as a random factor to account for correlated measures within family.
16p. 11. 2 Locus Modulates Phonology, Written Language, and Vocabulary The number of genomic copies positively correlated with phonology measures such as nonword repetition (p = 9. 9e-05), oromotor sequences (p = 8e-05), and sentence repetition (p =. 0001) as well as a closely related task, reading fluency (p =. 0009). This effect was mainly driven by the deletion carriers, who performed worse than control subjects and duplication carriers; these two latter groups did not significantly differ (Figure  1A-C ). Word definition showed a similar trend (p =. 0047) (Table  2 ). Except for trends, none of the measures assessing spelling, verbal fluencies, verbal comprehension, and verbal reasoning were significantly affected by the 16p11. 2 locus (Supplemental Table  S5 ). Results from the VIP data set confirmed that the number of genomic copies correlated with performance in the nonword repetition task adjusted for NVIQ (p = 9e-6).
We present Z scores when normative data are available in the testing manual. Otherwise, we present raw scores adjusted for age and sex when appropriate. All scores are adjusted for IQ except for panel (I). (42). Both mammalian target of rapamycin signaling and MAPK3 signaling regulate local synaptic protein synthesis, which modulates memory performances in murine models  (43, 44). The expression levels of MAPK3, which maps within the BP4-BP5 interval, and of mammalian target of rapamycin pathway members are significantly altered in 16p11. 2 CNV carriers  (45). These are good candidate genes underlying or mediating the  Deletion and duplication are strongly and equally associated with ASD, but our study shows that their cognitive profiles seem to be distinct, highlighting the heterogeneity of ASD.
Circles are outliers. Copy number variation effect (one, two, or three copies) and group contrasts are estimated using a linear mixed model to account for correlated measures withinfamilies (A, B, D, G, H, I) and a linear model when only one family member is included in the analysis (E, F). A nonlinear model was required for panels (C, G, H). We present Z scores when normative data are available in the testing manual. Otherwise, we present raw scores adjusted for age and sex when appropriate. All scores are adjusted for IQ except for panel (I). Significant post hoc group comparisons (p-corrected threshold =. 001) are represented by solid lines with exact p values above, and trends are represented by dashed lines with exact p values above. CTRL, intrafamilial control subjects; DEL, deletion carriers; DUP, duplication carriers.
ACKNOWLEDGMENTS AND DISCLOSURES This work was supported by the  Leenaards Foundation Prize (SJ, ARey, NH) ,  Swiss National Science Foundation (SNSF)  Sinergia Grant No. CRIS FN CRSII33-133044  (ARey, SJ),  National Center of Competence in Research Synapsy  Project Grant Nos. 320030_135679  and Special Program University Medicin 33CM30_140332/1 (BD),  Simons Foundation Autism Research Initiative (SFARI)  Grant No. SFARI274424  (ARey),  Foundation Parkinson Switzerland (BD), Foundation Synapsis (BD) ,  Human Brain Project , a  European Union initiative (BD) ,  SNSF  Grant No. PP00P3_144902/ 2  (SJ), a  Canada Research Chair (SJ) ,  Jeanne and Jean Louis Lévesque Foundation (SJ) ,  Center of Excellence in Genomics (Estonian Genome Center , the  University of Tartu [EGCUT] [AMe, ARei, AK, KM]) ,  University of Tartu  Grant No.
5 * interquartile range). Circles are outliers. Copy number variation effect (one, two, or three copies) and group contrasts are estimated using a linear mixed model to account for correlated measures withinfamilies (A, B, D, G, H, I) and a linear model when only one family member is included in the analysis (E, F). A nonlinear model was required for panels (C, G, H). We present Z scores when normative data are available in the testing manual. Otherwise, we present raw scores adjusted for age and sex when appropriate. All scores are adjusted for IQ except for panel (I). Significant post hoc group comparisons (p-corrected threshold =. 001) are represented by solid lines with exact p values above, and trends are represented by dashed lines with exact p values above. CTRL, intrafamilial control subjects; DEL, deletion carriers; DUP, duplication carriers.
ACKNOWLEDGEMENTS This work was primarily funded by  GAČR   16-05649S ,  AZV 16-27790A  and  LH15170  (TS). Other support includes AZV  15-27757A (PK ), AZV  16-31586A  (VP) and GAUK-202715 (ND). Institutional support includes  UNCE 204021 ,  PRVOUK P24 ,  LQ1604   NPU II  and  CZ. 1. 05/1. 1. 00/02. 0109.
5 mmol/L MgCl 2 , 1 U Taq polymerase (Abgene), and 3 lL of DNA (1:25 dilution); PCR cycling included an initial denaturing step at 94°C for 3 min, followed by 35 cycles at 94°C for 45 sec, 50°C for 60 sec, and 72°C for 90 sec with a final elongation step of 72°C for 7 min. The same thermocycler conditions were used for both loci. Finally, PCR products were purified and sequenced by LGC genomics (Berlin, Germany). The sequences were edited and aligned using Codoncode Aligner v. 3. 7 (www. codoncode. com).
Diversity Partial rbcL and cox1 sequences were obtained for 521 Polysiphonia morrowii individuals including 353 individuals from introduced populations and 168 from its native range. Molecular diversity indices, haplotype diversity (H, the probability that two randomly chosen chlorotypes or mitotypes are different) and nucleotide diversity (p, the probability that two randomly chosen homologous nucleotide sites are different), were calculated for each sampled location and for each region using Arlequin v 3. 11  (Excoffier et al. 2005). To compare haplotype richness (rh) across regions, rarefaction was used to correct for unequal sample sizes using FSTAT 2. 9. 3 software  (Goudet 1995) , with n = 56 for the chloroplastic and mitochondrial data. Each region was thus considered as a set of 56 individuals.
We extrapolated rarefaction curves with a factor of 1. 5 to the sample set. Phylogenetic relationships among chlorotypes and mitotypes were reconstructed using median-joining networks using Network software version 4. 2. 0. 1  (Bandelt et al. 1999). To test for genetic divergence among three regions, populations were grouped according to their geographic location. A hierarchical analysis of molecular variance (AMOVA) was implemented in Arlequin v 3. 11  (Excoffier et al. 2005)  to analyze the partitioning of genetic variance among and within the three geographic regions. Φ-statistics were calculated as pairwise differences among locations and their significance was evaluated using a nonparametric permutation test with 10,000 permutations. Moreover, the genetic structure between sampled areas was implemented in GENEPOP web version 4.
Chloroplast diversity After editing rbcL sequences, an alignment of 1225 bp was built on 521 individuals. Ten polymorphic chlorotypes and nine polymorphic sites (0. 73%) were observed (GenBank accession number: KP729448-KP729457, Supporting information). Chlorotypes differed by 1-4 bp (Fig. 2 ). The distribution of these chlorotypes is given in Figure  2. Over the whole dataset, three chlorotypes (C1, C2, and C4) were found at high frequency (>20%) compared with the others that showed a frequency lower than 7% (C3: 6. 9%, C5: 0. 8%, C6: 0. 4%, C7: 0. 2%, C8: 0. 2%, C9: 1. 2%, and C10: 1%). The most frequent chlorotype C1 was observed in 250 individuals (48%) and corresponded to the central chlorotype in the network. The C2 was observed in 110 individuals (21%), and C4 was observed in 106 individuals (20%).
Mitochondrial diversity After editing cox1 sequences, an alignment of 559 bp was built on 521 individuals. Ten polymorphic sites (1. 8%) defining 10 mitotypes were observed (GenBank accession number: KP729458-KP729467, Supporting information). Pairs of mitotypes were separated by 1-7 bp (Fig. 3 ). The cox1 network revealed four frequent mitotypes (Fig. 3 ). The most frequent haplotype M2 (32%) was found at the center of the network. The mitotypes M3, M6, and M4 were found at frequencies of 27%, 20%, and 18. 5%, respectively. Six mitotypes M1, M5, M7, M8, M9, and M10 were infrequent (between 0. 2% and 0. 6%). Two mitotypes (M3 and M4) were common to all three regions (South Atlantic, North Atlantic, and North Pacific), and two other mitotypes (M2 and M6) were shared only between the North Atlantic and the North Pacific (Fig.
Population structure Over the whole dataset, the number of chlorotypes was similar to that of mitotypes, regardless of the region: 5, 5, and 5 chlorotypes versus 6, 8, and 2 mitotypes, for the North Pacific, North Atlantic, and South Atlantic regions, respectively (Table  2 ). The sequence divergences estimated by haplotype diversity (H) and nucleotide diversity (p) for the chloroplastic and the mitochondrial markers are given in Table  2. The estimates of genetic diversity (H) were similar for rbcL and cox1, regardless of the region considered (Table  2 ). The values of chloroplast and mitochondrial haplotype richness were not significantly different among regions (nonparametric permutation test, P-value = 0. 92). The genetic diversity of the native populations (North Pacific) varied widely among locations.
Acknowledgments This study was partially supported by grants from the  French Ministry for the Economy, Industry and Employment and the Brittany Regional Council  through the project  AQUACTIFS "Convention de soutien de l' etat a des actions de recherche et d'innovation par voie de subvention -Fonds de comp etitivit e des entreprises ". Sequencing was carried out by Genoscope through the  "Biblioth eque du Vivant" network  funded by the  CNRS , the  French National Natural History Museum ,  INRA , and the  CEA (Centre National de S equenc ßage). Warm thanks to  J. Moreau  for her help in sampling, to  I. Barbara  and  M. Verlaque  for providing samples from the  Mediterranean Sea.
Results and Discussion Identification of OBP3 in M. viciae and N. ribisnigri. To identify genes encoding OBP3 in M. viciae and N. ribisnigri, which do not have genome sequences available, we used primers designed to match the ApisOBP3 mature protein (GenBank accession: FM242529), a strategy likely to work because of the high similarity between OBPs of different aphid species  6. This allowed the successful cloning of the genes encoding mature MvicOBP3 and NribOBP3 (GenBank accessions: KT750882 and KR139668), which like ApisOBP3, can be classified as "classic" OBPs, with the usual conserved spacing between the six conversed cysteines  2. The mature proteins have 118 and 114 amino acids with theoretical pIs of 5. 20 and 5. 18, and molecular weights of 13. 7 and 13. 4 kDa, respectively. In contrast to the high diversity amongst OBPs from the same species  6  , the OBP3 sequences are very similar between aphid species with ApisOBP3 and MvicOBP3 having only three amino acid differences, and NribOBP3 having two amino acid differences plus four fewer residues at the C-terminus (Supplementary Figure  1 ).
X-ray structure of MvicOBP3 and NribOBP3. Experimentally-determined 3D structures of eighteen different classic and two plus-C insect OBPs are available in the Protein Data Bank (http://www. rcsb. org/pdb/ home/home. do) and many of these have different structures dependent on their crystal form, pH or ligand. There are a further 8 salivary, haemolymph or venom protein structures that share the Interpro domain motif (IPR006170) with OBPs, but differ in length and other structural features. In total there are 104 PDB files of IPR006170 proteins containing 171 chains (August 2015 search). The OBP structures are from Diptera (mosquitos and fruitflies), Hymenoptra (honey bee), Lepidoptera (moths), Orthoptera (locust) and Dictyoptera (cockroach), but to date there are no such structures for aphid OBPs.
Indeed there are no reports of an OBP 3D structure for any Hemipteran, which comprise around 50,000-80,000 species of aphids, planthoppers, leafhoppers, shield bugs, and other crop pests despite there being more than 300 Hemipteran OBPs reported in NCBI GenBank. Thus, we present the first 3D structures of OBPs from aphids, M. viciae (MvicOBP3) (PDB: 4Z39) and N. ribisnigri (NribOBP3) (PDB: 4Z45), by X-ray diffraction (Supplementary Table  1 ). The OBP3s from both aphid species have a similar structure to other classical OBPs i. e. six α -helices connected by extended loops, with three disulphide bridges formed by the six conserved cysteine residues between Cys17-Cys44; Cys40-Cys101 and Cys86-Cys110 (Fig. 1 ). The 5 chains in the two structures are reasonably similar (Calpha RMSD less than 1.
Comparison of MvicOBP3 and NribOBP3 with other OBPs. To compare the aphid OBP3s with other OBPs in the PDB, searches on PDBefold and DALI were run with chain A of the two OBP3 structures. Using PDBefold MvicOBP3 gave 87 hits. Only the lowest hit by Z-score (PDB: 1M63) does not match IPR006170, this is also the 72 nd by Z-score and only non-match to IPR006170 of the 75 matches to NribOBP3. RMSD Calpha for these hits varies from 2. 1-3. 7 Å, number of aligned residues from 71 to 104 (out of 118 or 121) and sequence identity from 8-20% (Supplementary Table  2 ). A DALI server search with MvicOBP3 and NribOBP3 gave 167 and 160 hits respectively, before the first non-IPR006170 protein, with all 160 common to both hit lists. The RMSD of these fits ranges from 2. 7 to 5. 1 Å, with the number of aligned residues ranging from 80 to 111 and the sequence identity from 7-20%.
Molecular docking. A blind molecular docking approach was used with Eβ f, β -pinene, (-)-α -pinene and (+)-limonene using Autogrid in Autodock Tools software with a grid box big enough to cover the whole chain A protein area of MvicOBP3 and NribOBP3. This indicated that the four ligands were mainly docked in the region of Tyr30 and in the groove. To further investigate the ligand binding, directed-molecular docking was performed on the chain A of MvicOBP3 using Autodock Vina, which is more precise and faster than its predecessor Autodock 4. 0  39. The best conformation for the lowest free binding energy for Eβ f, β -pinene, (-)-α -pinene and (+)-limonene are given in Table  2  and shown in Fig. 6. The docking results indicate that there is no major difference in the binding energy of MvicOBP3 to (-)-α -pinene (-5.
Before cDNA synthesis, the RNA samples were treated with amplification grade DNase I (Life Technologies, Carlsbad, CA), according to the manufacturer's instructions. cDNA was prepared from 1 μg of total RNA by reverse transcription, using SuperScript ® III First-Strand Synthesis System for RT-PCR (Life Technologies, Carlsbad, CA), following the manufacturer's protocol. Cloning and subcloning of OBP3 genes. First strand cDNA (1 μL) was amplified in a G-STORM thermocycler in a total reaction solution (20 μL) containing 1 unit of Taq DNA polymerase (Life Technologies, Carlsbad, CA), 0. 1 mM of each dNTP, 1. 5 mM MgCl 2 , 0. 2 μM of each PCR primer in the Taq Buffer supplied with the polymerase. The PCR primers were designed to match the A. pisum OBP3 sequence (GenBank accession: FM242529) using the online tool Primer3 (http://wwwgenome.
3 (http://protcalc. sourceforge. net/). MvicOBP3 crystallised from a mother liquor of 0. 3 M AmSO4, 30% (w/v) PEG 4000, 7. 5% (v/v) Glycerol. NribOBP3 was crystallised from 20% PEG 6000, 0. 1 M Sodium Citrate pH 5 10 mM ZnCl2. All crystals were harvested in 2 μL of mother liquor with glycerol adjusted to 30% (v/v). Crystal data were collected at Diamond Synchrotron, Harwell beamlines I24 and I04-1. Data was processed automatically through xia2  49  to determine space groups and unit cell dimensions; in all cases the 3dii operation mode, which used XDS  50  and scala  51  and a wide scan of images for indexing, gave the best quality results. The structure of MvicOBP3 was solved with Phaser crystallographic software 52 using sequential searches for two copies of three separate helices taken from the structure of the Drosophila melanogaster PBP LUSH (α -helices 2, 3 and 5).