Reporting Checklist for Nature Neuroscience

Transcription

1 Correponding Author: Manucript Number: Manucript Type: Jeremy Elman NNBC48172A Brief Communication Reporting Checklit for Nature Neurocience # Figure: 2 # Figure: 5 # Table: 6 # Video: 0 Thi checklit i ued to enure good reporting tandard and to improve the reproducibility of publihed reult. For more information, pleae read Reporting Life Science Reearch. Pleae note that in the event of publication, it i mandatory that author include all relevant methodological and tatitical information in the manucript. Statitic reporting, by figure example example Pleae pecify the following information for each panel reporting quantitative data, and where each item i reported (ection, e.g., & paragraph number). Each figure legend hould ideally contain an exact ample ize (n) for each experimental group/condition, where n i an exact number and not a range, a clear definition of how n i defined (for example x cell from x lice from x animal from x litter, collected over x day), a decription of the tatitical tet ued, the reult of the tet, any decriptive tatitic and clearly defined error bar if applicable. For any experiment uing cutom tatitic, pleae indicate the tet ued and tat obtained for each experiment. Each figure legend hould include a tatement of how many time the experiment hown wa replicated in the lab; the detail of ample collection hould be ufficiently clear o that the replicability of the experiment i obviou to the reader. For experiment reported in the but not in the figure, pleae ue the paragraph number intead of the figure number. Note: Mean and tandard deviation are not appropriate on mall ample, and plotting independent data point i uually more informative. When technical replicate are reported, error and ignificance meaure reflect the experimental variability and not the variability of the biological proce; it i mileading not to tate thi clearly. FIGURE NUMBER 1a reult, TEST USED WHICH TEST? oneway ANOVA unpaired t tet legend EXACT VALUE 9, 9, 10, 15 n DEFINED? mice from at leat 3 litter/group 15 lice from 10 mice para 8 DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? error bar are mean / SEM error bar are mean / SEM legend P VALUE EXACT VALUE p = p = legend DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(3, 36) = 2.97 t(28) = legend 1

2 FIGURE NUMBER 1a, 1b 2a, 2b, 2c 2d, 2e, 2f 2a, 2b, 2c 2d, 2e, 2f 3 4 TEST USED WHICH TEST? para 4, para 5,, para 5, para 5, para 5 para 7 EXACT VALUE 33, 16, 22 33, 22 33, 16 33, 22 33, 16 33, 16, 22 n DEFINED? ubject, PIB older ubject, young control ubject ubject, young control ubject ubject, PIB older ubject ubject, young control ubject ubject, PIB older ubject ubject, young control ubject 49 all older ubject : t : t : t : t : t : t : t DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? Subjectlevel line are diplayed a well a group etimate fit. Thee plot are purely decriptive viualization to uppnt the voxelwie analye. Subjectlevel line are diplayed a well a group etimate fit. Thee plot are purely decriptive viualization to uppnt the voxelwie analye. Error bar are mean / SEM Error bar are mean / SEM P VALUE EXACT VALUE para 3, : para 5, : para 6, : : : : : DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE Mulltiple zvalue each tatitical Mulltiple zvalue each tatitical Mulltiple zvalue each tatitical Mulltiple zvalue each tatitical Mulltiple zvalue each tatitical lem e Table 3 & 4 lem e Table 6 lem e Table 6 lem e Table 5 lem e Table 5 2

3 5 para 7, le menta ry 5 captio n Repreentative figure 16 PIB older ubject : t 1. Are any repreentative image hown (including Wetern blot and immunohitochemitry/taining) in the paper? If o, what figure()? 2. For each repreentative image, i there a clear tatement of how many time thi experiment wa uccefully repeated and a dicuion of any limitation in repeatability? If o, where i thi reported (ection, paragraph #)? Statitic and general method 1. I there a jutification of the ample ize? If o, how wa it jutified? Where (ection, paragraph #)? Even if no ample ize calculation wa performed, author hould report why the ample ize i adequate to meaure their effect ize. 2. Are tatitical tet jutified a appropriate for every figure? Where (ection, paragraph #)? a. If there i a ection ummarizing the tatitical method in the method, i the tatitical tet for each experiment clearly defined? b. Do the data meet the aumption of the pecific tatitical tet you choe (e.g. normality for a parametric tet)? Where i thi decribed (ection, paragraph #)? Regreion line of PIB group diplayed. Box plot of PIB group preented for comparion purpoe. c. I there any etimate of variance within each group of data? I the variance imilar between group that are being tatitically compared? Where i thi decribed (ection, paragraph #)? No l ement ary 5 captio n p=0.034 lem e 5 caption B= 1.89, t(11)= lem e 5 caption The ample ize i conitent with previou tudie which employ and amyloid imaging (e.g., PIBPET). We attempted to collect enough data uch that the ize of the mallet group (older PIB individual, who make up roughly 25% of our larger cohort) wa in line with previou tudie employing and PIBPET imaging. Our young control and PIB group are alo conitent or even larger than thoe ued in many other takbaed tudie. Ye. :, paragraph 2. Thi ection decribe the tet ued in all analye. Ye. :, paragraph 2 Ye. :, paragraph 2 The tet incorporate an etimate of variance in generating t/z core. The amount of variance in each group i not decribed. However, a mixed effect model i employed uch that ubject are treated a random effect and variance within group i taken into account. d. Are tet pecified a one or twoided? Ye, twoided. :, paragraph 2 3

4 e. Are there adjutment for comparion? Ye, clutercorrection i performed. 3. Are criteria for excluding data point reported? Wa thi criterion etablihed prior to data collection? Where i thi decribed (ection, paragraph #)? 4. Define the method of randomization ued to aign ubject (or ample) to the experimental group and to collect and proce data. If no randomization wa ued, tate o. Where doe thi appear (ection, paragraph #)? 5. I a tatement of the extent to which invetigator knew the group allocation during the experiment and in aeing outcome included? If no blinding wa done, tate o. Where (ection, paragraph #)? 6. For experiment in live vertebrate, i a tatement of compliance with ethical guideline/regulation included? Where (ection, paragraph #)? 7. I the pecie of the animal ued reported? Where (ection, paragraph #)? 8. I the train of the animal (including background train of KO/ trangenic animal ued) reported? Where (ection, paragraph #)? 9. I the ex of the animal/ubject ued reported? Where (ection, paragraph #)? 10. I the age of the animal/ubject reported? Where (ection, paragraph #)? 11. For animal houed in a vivarium, i the light/dark cycle reported? Where (ection, paragraph #)? 12. For animal houed in a vivarium, i the houing group (i.e. number of animal per cage) reported? Where (ection, paragraph #)? Ye, criteria are reported. Ye, criteria wa etablihed prior to data collection. : t paragraph 1 No randomization wa ued. Subject were grouped baed on age and PIB tatu. paragraph 3. : t, paragraph 1 Experimenter were blinded to older ubject' PIB tatu during data collection. : PIBPET Proceing paragraph 2. Ye, main paragraph 3. : t, paragraph For behavioral experiment, i the time of day reported (e.g. light or dark cycle)? Where (ection, paragraph #)? 4

5 14. I the previou hitory of the animal/ubject (e.g. prior drug adminitration, urgery, behavioral teting) reported? Where (ection, paragraph #)? a. If behavioral tet were conducted in the ame group of animal, i thi reported? Where (ection, paragraph #)? 15. If any animal/ubject were excluded from analyi, i thi reported? Where (ection, paragraph #)? Reagent a. How were the criteria for excluion defined? Where i thi decribed (ection, paragraph #)? b. Specify reaon for any dicrepancy between the number of animal at the beginning and end of the tudy. Where i thi decribed (ection, paragraph #)? 1. Have antibodie been validated for ue in the ytem under tudy (aay and pecie)? a. I antibody catalog number given? Where doe thi appear (ection, paragraph #)? b. Where were the validation data reported (citation, upp information, Antibodypedia)? Where doe thi appear (ection, paragraph #)? 2. If cell line were ued to reflect the propertie of a particular tiue or dieae tate, i their ource identified? Where (ection, paragraph #)? a. Were they recently authenticated? Where i thi information reported (ection, paragraph #)? Ye. : t, paragraph 1 Ye. : t, paragraph 1 The criteria were baed on poor tak performance, exceive motion, and problem with data collection. : t, paragraph 1 5

6 Data depoition Data depoition in a public repoitory i mandatory for: a. Protein, DNA and RNA equence b. Macromolecular tructure c. Crytallographic data for mall molecule d. Microarray data Depoition i trongly recommended for many other dataet for which tructured public repoitorie exit; more detail on our data policy are available here. We encourage the proviion of other ource data in upp information or in untructured repoitorie uch a Fighare and Dryad. 1. Are acceion code for depoit date provided? Where (ection, paragraph #)? Computer code/oftware Any cutom algorithm/oftware that i central to the method mut be upplied by the author in a uable and readable form for reader at the time of publication. However, referee may ak for thi information at any time during the review proce. 1. Identify all cutom oftware or cript that were required to conduct the tudy and where in the procedure each wa ued. 2. I computer ource code/oftware provided with the paper or depoited in a public repoitory? Indicate in what form thi i provided or how it can be obtained. Human ubject 1. Which IRB approved the protocol? Where i thi tated (ection, paragraph #)? 2. I demographic information on all ubject provided? Where (ection, paragraph #)? 3. I the number of human ubject, their age and ex clearly defined? Where (ection, paragraph #)? 4. Are the incluion and excluion criteria (if any) clearly pecified? Where (ection, paragraph #)? No Intitutional Review Board of the Univerity of California, Berkeley, and the Lawrence Berkeley National Laboratory approved thi tudy. : t, paragraph 1 Ye. : t. Table 1, Table 1 & 2 Ye. : t. Table 1 Ye. : t, paragraph 1 6

7 5. How well were the group matched? Where i thi information decribed (ection, paragraph #)? 6. I a tatement included confirming that informed conent wa obtained from all ubject? Where (ection, paragraph #)? 7. For publication of patient photo, i a tatement included confirming that conent to publih wa obtained? Where (ection, paragraph #)? tudie There were more older PIB ubject than either of the other two group. Collecting a large number of older ubject wa required in order to enure enough ubject in our PIB group a previou tudie report roughly 25% of cognitively older ubject are PIB. paragraph 1. : t. Table 1. Ye. : t, paragraph 1 For paper reporting functional imaging () reult pleae enure that thee minimal reporting guideline are met and that all thi information i clearly provided in the metho 1. Were any ubject canned but then rejected for the analyi after the data wa collected? a. If ye, i the number rejected and reaon for rejection decribed? Where (ection, paragraph #)? 2. I the number of block, trial or experimental unit per eion and/ or ubject pecified? Where (ection, paragraph #)? 3. I the length of each trial and interval between trial pecified? Ye. 4. I a blocked, eventrelated, or mixed deign being ued? If applicable, pleae pecify the block length or how the eventrelated or mixed deign wa optimized. 5. I the tak deign clearly decribed? Where (ection, paragraph #)? Ye. : t, paragraph 1. Table 2 (decribe performance between included and excluded ubject). Ye. paragraph 3. : Behavioral Procedure, paragraph 1 & 2. : Behavioral Procedure, paragraph 1 & 2. 1 An eventrelated deign wa ued. The trial order at encoding and retrieval wa randomized for each ubject. Repone were counterbalanced acro ubject. The timuli ued a old and new item were alo counterbalanced. In the detail tak, 24 detail were randomly elected to be true. Ye. paragraph 3. : Behavioral Procedure, paragraph 1 & 2. Figure How wa behavioral performance meaured? Hit rate, correct rejection rate and dprime core on the git recognition tak were aeed. The average number of correct detail per item wa alo aeed. 7

8 7. I an ANOVA or factorial deign being ued? No. 8. For data acquiition, i a whole brain can ued? If not, tate area of acquiition. a. How wa thi region determined? 9. I the field trength (in Tela) of the MRI ytem tated? Ye. : MRI Acquiition a. I the pule equence type (gradient/pin echo, EPI/piral) tated? b. Are the fieldofview, matrix ize, lice thickne, and TE/TR/ flip angle clearly tated? 10. Are the oftware and pecific parameter (model/function, moothing kernel ize if applicable, etc.) ued for data proceing and preproceing clearly tated? 11. I the coordinate pace for the anatomical/functional imaging data clearly defined a ubject/native pace or tandardized tereotaxic pace, e.g., original Talairach, MNI305, ICBM152, etc? Where (ection, paragraph #)? 12. If there wa data normalization/tandardization to a pecific pace template, are the type of tranformation (linear v. nonlinear) ued and image type being tranformed clearly decribed? Where (ection, paragraph #)? 13. How were anatomical location determined, e.g., via an automated labeling algorithm (AAL), tandardized coordinate databae (Talairach daemon), probabilitic atlae, etc.? 14. Were any additional regreor (behavioral covariate, motion etc) ued? Ye Ye. : MRI Acquiition Ye. : MRI Acquiition Ye. : PIBPET Proceing, Proceing,. Ye, MNI152. : Proceing, paragraph 1. Ye, : Proceing, paragraph 1. From the HarvardOxford Cortical Atla. Ye. Motion parameter and outlier volume were included a nuiance regreor at the firt level. Hit rate and gray matter were included in all group level analye, age wa included in comparion of PIB and PIB group. 15. I the contrat contruction clearly defined? Ye, main paragraph 3 and :, paragraph I a mixed/random effect or fixed inference ued? Mixed effect inference wa ued. a. If fixed effect inference ued, i thi jutified? 17. Were repeated meaure ued ( meaurement per ubject)? Ye. a. If o, are the method to account for within ubject correlation and the aumption made about variance clearly tated? Ye. : 8

9 18. If the threhold ued for inference and viualization in figure varie, i thi clearly tated? 19. Are tatitical inference for comparion? Ye, cluter. a. If not, i thi labeled a un? The threhold for all reult were the ame and thi i tated. 20. Are the reult baed on an ROI (region of interet) analyi? No. Plot of data extracted from reult cluter are preented but thi i for decriptive/viualization purpoe only. a. If o, i the rationale clearly decribed? b. How were the ROI defined (functional v anatomical localization)? 21. I there correction for comparion within each voxel? No. 22. For cluterwie ignificance, i the cluterdefining threhold and the ignificance level defined? Additional comment Additional Comment Ye. : and figure caption. (p<0.05 and cluterdefining threhold of p<0.05) 9