SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: This study was approved by the Institutional Review Board of the Emory University School of Medicine.

Consent: IRB of Emory University School of Medicine gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Inclusion and Exclusion Criteria

not detected.

Attrition

The first case was identified in September of 2006 , 13 cases were detected in 2007 , and 16 cases in 2008 across these two hospitals ( total of 30 with 120 matched controls) .

Sex as a biological variable

Mean Median 60 62 ( range from 27 to 90 ) Sex Female Male 25 ( 52 ) 23 ( 48 ) Site of isolation Urine

Subject Demographics

Age: not detected. Weight: not detected.

Randomization

Controls, patients without CRKP were randomly selected from a computerized list of inpatients who matched the case age (+/- 5 years), sex, and facility and whose admission date was within 48 hours of the date of the initial, positive culture.

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Availability: The comparison of clinical characteristics between cases and controls was made using Chi-Square (or It is made available under a CC-BY-NC-ND 4.0 International license .

Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2022.02.08.22269570; this version posted February 9 , 2022 . https://doi.org/10.1101/2022.02.08.22269570

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: The ethics committee approval of the research protocol was made by the Ankara City Hospital Consent: Informed consent was obtained from the patients to participate in the study.

Inclusion and Exclusion Criteria

not detected.

Attrition

Two publications are evaluating the association with Netrin-1 in bleomycin-induced lung fibrosis in mice and SSc lung cell culture in humans.

Sex as a biological variable

A total of 56 SSc patients (mean age: 48.08±13.59) consisting of 53 females and 3 males, who were followed up in the rheumatology department of Ankara city hospital, diagnosed according to the 2013 ACR (American College of Rheumatology)/EULAR (European League Against Rheumatism) SSc classification criteria were included in the study.

Subject Demographics

Age: For the control group, 58 healthy volunteers (mean age: 48.01±11.59 years) consisting of 54 females and 4 males were included in the study.

Randomization

not detected.

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Availability: It is made available under a CC-BY-NC-ND 4.0 International license .

Identifiers: preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in medRxiv preprint doi: https:// doi.org/10.1101/2022.02.05.22270510; this version posted February 10, 2022. https://doi.org/10.1101/2022.02.05.22270510

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Field Sample Permit: The research has been conducted using the UK Biobank Resource and has been approved by the UK Biobank under Application no. 36226.

Consent: I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Inclusion and Exclusion Criteria

Similarly , individuals where a large proportion of SNPs could not be measured were excluded.

Attrition

not detected.

Sex as a biological variable

not detected.

Subject Demographics

Age: not detected.

Weight: not detected.

Randomization

Mendelian randomization ( MR ) is a robust and accessible tool to examine the causal relationship between an exposure variable and an outcome from GWAS summary statistics. [ 19 ] We employed two-sample summary data Mendelian randomization to further validate causal effects of neutrophil cell count genes on the outcome of critical illness due to COVID-19

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2021.05.18.21256584; this version posted February 14 , 2022 . https://doi.org/10.1101/2021.05.18.21256584

Identifiers: Manhattan plot of neutrophil cell count showing that we reproduce the reported CDK6 signal ( rs445 ) on chromosome 7 . rs445

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: 234 Ethical clearance was obtained from the regional Ethical Review Board of Amhara

Consent: The general aim and purpose of the study was described to each 239 eligible patient and all voluntary participants gave verbal informed consent prior to 240 enrolment.

Inclusion and Exclusion Criteria

Those 135 patients who were critically ill and unable to respond and those not voluntary to 136 participate were excluded.

Attrition

Those 135 patients who were critically ill and unable to respond and those not voluntary to 136 participate were excluded .

Sex as a biological variable

Sex Male Female Age group 18-24 25-44 ≥45

Subject Demographics

Age: 130 All adult patients ( aged ≥18 years ) who were using clinical laboratory services at 131 public health facilities of east Amhara , northeast Ethiopia were source population.

Randomization

132 Study population and eligibility criteria 133 Adult patients who received general laboratory services at the randomly selected 134 government health facilities during the study period were study population .

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Availability: It is made available under a CC-BY-NC-ND 4.0 International license .

Identifiers: preprint doi: https:// doi.org/10.1101/2022.01.25.22269238; this version posted January 25 , 2022 . https://doi.org/10.1101/2022.01.25.22269238

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

Field Sample Permit: Our findings indicate a paucity of 217 research focusing on field trials and implementation studies related to CHIKV RDTs .

IRB: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Consent: I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Inclusion and Exclusion Criteria

98 Articles were excluded if (i) the studies were reviews, case reports, or opinion articles; (ii) 99 the studies evaluated the performance of reverse transcription loop-mediated isothermal 100 amplification (RT-LAMP) assays; (iii) the studies were related to an outbreak investigation 101 without the evaluation of the accuracy of CHIKV RDTs; (iv) the studies used an inappropriate 102 study population (asymptomatic individuals); (v) the studies described inappropriate It is made available under a CC-BY-NC-ND 4.0 International license.

Attrition

Based on the tile and the abstract , 96 were excluded , with 89 full-text 158 articles retrieved and assessed for eligibility .

Sex as a biological variable

not detected.

Subject Demographics

Age: not detected. Weight: not detected.

Randomization

Similarly , there was a high risk of bias in 210 the patient selection domain because only three studies enrolled a consecutive or random 211 sample of eligible patients with suspicion of CHIKV infection to reduce the bias in the 212 diagnostic accuracy of the index test .

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Availability: The 90 Prisma-ScR checklist is available in the Supplementary material.

Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2022.01.28.22270018; this version posted January 30 , 2022 . https://doi.org/10.1101/2022.01.28.22270018

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: Institutional Review Board and all participants gave their signed informed consent.

Consent: Institutional Review Board and all participants gave their signed informed consent.

Inclusion and Exclusion Criteria

83 years; 34 males; 57 righthanded , see Table 1 ) met the inclusion criteria: All patients were older than 18 years , presented with first-ever ischemic ( 83 % ) or haemorrhagic ( 17 % ) stroke and behavioural deficits as assessed by a neurological examination.

Attrition

Patients who had a history of neurological or psychiatric presentations ( e.g. transient ischemic attack) , multifocal or bilateral strokes , or had MRI contraindications ( e.g. claustrophobia , ferromagnetic objects ) were excluded from the analysis ( n = 131 patients , see the enrollment flowchart in the supplementary materials from Corbetta et al. 2015).

Sex as a biological variable

Handedness ( % right-handed ) 91.94 Sex ( % female ) 45.16 Abbreviations: SD = standard deviation It is made available under a CC-BY-NC 4.0 International license.

Subject Demographics

Age: 83 years; 34 males; 57 righthanded , see Table 1 ) met the inclusion criteria: All patients were older than 18 years , presented with first-ever ischemic ( 83 % ) or haemorrhagic ( 17 % ) stroke and behavioural deficits as assessed by a neurological examinatio .

Randomization

The task instructions require patients to place and remove the nine pegs one at a time and in random order as quickly as possible ( Mathiowetz et al. 1985; Oxford Grice et al. 2003).

Blinding

Two boardcertified neurologists ( Drs Corbetta and Carter ) reviewed all segmentations blinded to the individual behavioural data .

Power Analysis

We believe that adding other factors ( e.g. demographic , clinical , socioeconomic variables ) that likely interact with the recovery of patients can help us increase the model’s predictive power.

Replication

not required.

Cell Line Authentication

Authentication: However , most of the studies fall into one of the pitfalls that were described above ( i.e. overfitting , generalisability , and diaschisis ) as the models are not validated in an independent dataset.

Code Information

Identifiers: This procedure is available as supplementary code with the manuscript ( see https://github.com/lidulyan/Hierarchical-Linear- Regression-R- ).

https://github.com/lidulyan/Hierarchical-Linear- Regression-R-

Data Information

Availability: Handedness ( % right-handed ) 91.94 Sex ( % female ) 45.16 Abbreviations: SD = standard deviation It is made available under a CC-BY-NC 4.0 International license .

Identifiers: preprint doi: https:// doi.org/10.1101/2021.12.01.21267129; this version posted December 2 , 2021.

https://doi.org/10.1101/2021.12.01.21267129

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

Field Sample Permit: Collection of data for detecting cellular spatiotemporal condition supporting circularization For this purpose, online database and web server were used by taking specific queries like , RBP-types or lncRNAs to search out their special location inside cellular spaces

Inclusion and Exclusion Criteria

not required.

Attrition

not required.

Sex as a biological variable

not required.

Subject Demographics

Age: not required.

Weight: not required.

Randomization

To reduce computational complexity in dealing with very large database where number of data is greater than 1000 , sample datasets were used through random selection of data from the original database .

Blinding

not detected.

Power Analysis

not detected.

Replication

not required.

Data Information

Identifiers: We analyzed the spread of this biomolecular entity outside and inside the sub- cellular space along with assimilating other reported pieces of information (e.g., about RBP molecules involved in circularization of such bioRxiv preprint doi: https:// doi.org/10.1101/2021.10.26.465935; this version posted October 26, 2021. https://doi.org/10.1101/2021.10.26.465935

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

Field Sample Permit: Seeds of sorghum (Sorghum bicolor) were obtained from the seed collection unit of the Office of the Agricultural Development Programme, Benin City, Edo State, Nigeria. Ferruginous (or iron elevated) soil used in this present study was obtained from around the Life Sciences Faculty environment and pooled to obtain composite sample.

Inclusion and Exclusion Criteria

not required.

Attrition

not required.

Sex as a biological variable

not required.

Subject Demographics

Age: not required.

Weight: not required.

Randomization

In order to confirm ferrugenicity, samples were collected from random areas and iron content was first confirmed in the area before more samples were collected and pooled.

Blinding

not detected.

Power Analysis

not detected.

Replication

The experiment was laid out incompletely randomized design in a factorial arrangement and replicated three times per treatment.

Number: The experiment was laid out incompletely randomized design in a factorial arrangement and replicated three times per treatment .

Data Information

Availability: It is made available under aCC-BY 4.0 International license.

Identifiers: preprint doi: https:// doi.org/10.1101/2021.11.22.469542; this version posted November 22 , 2021 .

https://doi.org/10.1101/2021.11.22.469542

SciScore rigor report

Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.

Not required = Field is not applicable to this study

Not detected = Field is applicable to this study, but not included.

Ethics

IRB: Samples and data collections were conducted according to the guidelines of the Declaration of Helsinki , and approved by the Ethics Committee Sciences et Santé Animale n°115 ( protocol code COVIFEL approved on 1 September 2020 , registered under SSA_2020_010 ) .

Euthanasia Agents: Cells were then incubated for 72 h at 37 °C with 5 % of CO2 .

Field Sample Permit: These experiments were approved by the Anses/ENVA/UPEC ethic committee and the French Ministry of Research ( Apafis n°24818-2020032710416319 ) .

Consent: All sera from the first cohort , and whole blood samples from the second cohort , were obtained from the Toulouse hospital , where all patients give , by default , their consent for any biological material left over to be used for research purposes after all the clinical tests requested by doctors have been duly completed.

Inclusion and Exclusion Criteria

not detected.

Attrition

One additional conclusion that can be drawn from the comparison of the results of the RBD-ELISA with those of the Jurkat-S&R-flow test is that, whilst the two methods show similar sensitivities, the ELISA signals tend to saturate very rapidly, and are thus much less dynamic that those obtained by flow cytometry.

Sex as a biological variable

Of note, we did not notice an increased frequency of allo-reactivity in samples from women compared to men, which suggests that allo-reactivity after pregnancy is not a major cause in the origin of those allo-reactions.

Subject Demographics

Age: Experiments on virally-infected hamsters Eight week-old female Syrian golden hamsters ( Mesocricetus auratus , strain RjHan:AURA ) from Janviers’s breeding Center ( Le Genest , St Isle , France ) were housed in an animal-biosafety level 3 ( A-BSL3) , with ad libidum access to water and food.

Randomization

The results of the second cohort, which comprised a few Covid patients, but also a large proportion of blood samples randomly picked among those from patients hospitalized for conditions unrelated to Covid-19, yielded a much less clear picture than the first one.

Blinding

On the other hand, the situation was much less clear-cut for the cohort comprising blood samples picked more or less randomly and blindly among those available as left-overs from the hematology department and was, therefore, more akin to a ‘real’ population.

Power Analysis

not detected.

Replication

not required.

Cell Line Authentication

Contamination: The Jurkat-S and Jurkat-R cell lines were both checked for the absence of mycoplasma contamination using the HEK blue hTLR2 kit ( Invivogen , Toulouse , France ).

Authentication: For the same reason , the blood samples for the experiment shown on Figure 3A were collected by one of the authors by simple finger-pricking.

Yang Yang: The Replicability of Scientific Findings Using Human and Machine Intelligence (Video). Metascience 2019 Symposium. https://www.metascience2019.org/presentations/yang-yang/

Great overview and commentary. However, I would have liked some more insight into the ethical ramifications and potential destructiveness of an ASI-system as demonstrated in the movie.