kdercksen/pragtag_sentence_classification · Datasets at Hugging Face

sentence stringlengths 2 660	label stringclasses 6 values
1) Abstract:	Structure
- It is always important to also having focus on more rare etiologies of IE.	Other
In the abstract it is stated that the mortality rate is high.	Recap
This is suggested to be modified to: Initial descriptions of collections of IE cases with A. urinae demonstrated a high morbidity and mortality rate, whereas a recent Swedish epidemiological study could not retrieve this.	Todo
2) Introduction:	Structure
- Dukes criteria should be mentioned.	Todo
- There is not a species named Streptococcus viridans.	Weakness
- Recent diagnostic improvements should be included, especially MALDI-TOF mass spectrometry.	Todo
- a gram-positive, catalase-negative	Other
3) Case description:	Structure
- Specific description of PM electrode findings should be given.	Todo
- A more detailed disease timespan is desirable.	Todo
- Microbiological data are very scarce.	Weakness
Blood-culture system and number of positive bottles should be given.	Todo
Likewise identification criteria and susceptibility methods and results, including MIC values of relevant antibiotics should be given.	Todo
- A thorough microbiological examination of the manuscript seems indicated	Todo
- Aerococcus urinae should only be fully written the first time	Todo
4) Discussion	Structure
- 16S is slang: it should be partial 16S rRNA gene sequencing analysis	Todo
Reviewer response for version 1	Structure
Concerning a case report of awake craniotomy in patient with cyanotic congenital heart disease (CHD).	Recap
The authors describe an unusual case of a rather complicated and rare pathology that needs an emergency surgical intervention during a night.	Recap
I have no specific scientific remarks concerning the content nor the design, but I think that for several reasons this case should be known by large anaesthesia community.	Other
First, the number of patients with CHD that can be scheduled for surgery is growing so our responsibility is to know how they should be handled, why spontaneous ventilation is preferable than mechanical, for which kind of complications we should be prepared etc.	Other
Second, we can always discuss which drugs should be used in a case of awake craniotomy, is dexmedetomidine better than other drugs?	Other
Personal experience and a local policy should be respected in such case.	Other
What is notable is that the authors were capable to establish, in this short time and during a night, an interdisciplinary consensus involving all disciplines, which was probably crucial to handle this case in this remarkable way.	Strength
Reviewer response for version 1	Structure
This paper describes the protocol for a clinical trial releasing Wolbachia bacterium infected male and female Aedes aegypti mosquitoes in Medellín and Bello, Colombia, with the primary endpoint objective of demonstrating reduction of human dengue infections in the population living in the treated areas.	Recap
Wolbachia infected female release over time results in replacement of the uninfected Aedes aegypti population with Wolbachia infected mosquitoes that have reduced ability to transmit arboviruses.	Other
The study design has two components, an interrupted time series (ITS) approach using passive arboviral disease surveillance data from Bello and a large area of Medellín, and a prospective case-control in a smaller area of northeast Medellin using arbovirus laboratory test negative acute febrile illness controls in 6 early release and late release zones.	Recap
The studies begin approximately one year after mosquito releases (in 2018 for the early release zone and 2019 for the releases outside the case-control area) to allow for mosquito population replacement.	Recap
This study employs a novel Aedes aegypti vector control approach to address the major and growing tropical public health problem of Aedes transmitted arboviruses including dengue, Zika, and chikungunya viruses.	Recap
The authors point out that such studies are badly needed as conventional Aedes aegypti vector control approaches have failed or been shown to be non-sustainable, and the only currently licensed dengue vaccine is partially effective and requires a laboratory test prior to immunization.	Recap
This study protocol builds on laboratory and fieldwork in Australia and elsewhere, and is well designed and well written with considerable detail (design, statistical power and analysis, laboratory testing, data management, etc) to address the question of human arboviral disease impact of Wolbachia replacement in a highly endemic tropical urban setting in Latin America.	Strength
The protocol is intentionally “pragmatic” to roll out the intervention at large scale under operational conditions in a timely and cost effective manner acceptable to the study community.	Recap
The authors thus effectively answer potential criticisms of the study design not being a cluster randomized clinical trial as recommended by the WHO Vector Control Advisory Group.	Strength
The case control study design also importantly accounts for the extent of replacement with Wolbachia infected mosquitoes in the treated area and human mobility out of the treatment area with a calculated Wolbachia exposure index calculated for each acute febrile illness patient.	Strength
The test negative case control study design obviates the need for expensive clinical cohort follow up to monitor disease incidence and treated and untreated areas.	Strength
The authors correctly point out that the risk estimate from the test negative case control approach is likely to be unbiased and can be used to calculate efficacy confidence limits.	Strength
The ITS approach is a less rigorous experimental design in that the vast majority of passively reported cases are not virologically confirmed, and surveillance may not be always be done in a consistent manner, but is another practical approach using available data from the Ministry of Health that allows for monitoring of reductions in arboviral case reports over a long time period (5 years) after the Wolbachia replacement treatment during which arbovirus outbreak cycles would be expected to occur.	Other
The discussion appropriately comments on the potential generalizability of the findings to other settings and that cost effectiveness analysis of this approach is underway.	Strength
The following are suggestions to clarify aspects of the protocol:	Structure
Background:	Structure
- While Medellín is clearly highly endemic for dengue, including the historical annual average incidence of dengue would be of interest, as the case-control study will be just be done over a one year time period.	Todo
Dengue transmission dropped to unusually low levels throughout most of South America after the Zika epidemic, and is on the increase in the region as of mid-2019.	Other
Methods:	Structure
- The entomologic details regarding the mosquito releases and strain(s) of Wolbachia could be expanded upon.	Todo
What is being done differently in 2018 and 2019 compared to the 2017 releases that achieved temporary high Wolbachia prevalence?	Todo
- More details on the Wolbachia sampling and monitoring strategy would be helpful.	Todo
What is the extent of the monitoring area?	Todo
All comuna outside the case-control area?	Todo
Checking BG traps once a week does not ensure that the mosquito specimens will be identified correctly because of damage from the trap fans to captured mosquitoes.	Weakness
Many samples will be lost because of loss of power, ants, etc.	Other
BG traps should be checked daily.	Other
- For the ITS component and the secondary endpoint of severe dengue incidence, how does the Ministry of Health define severe dengue, and has severe dengue been consistently defined over time?	Todo
- Regarding the case control study participant recruitment, what is the possibility that patients with acute febrile illness in the study areas will seek care in clinics outside the network?	Todo
- With regard to the laboratory testing algorithm to exclude potential dengue serologic positives from being control patients, the authors could more explicitly state that PanBio IgG ELISA test is designed with cutoffs to only detect high IgG titers consistent with acute secondary infections, and not past infections.	Todo
Excluding all patients with IgG antibody due to past dengue infection in this setting would eliminate a large percentage of the potential control patients.	Weakness
- Consider observing changes in the vector-bacteria-virus interaction through time.	Todo
Coevolution is likely.	Other
Whether virus blocking ability changes over time (e.g., lowered bacteria concentration in the mosquito cells) is not clear.	Weakness
Reviewer response for version 1	Structure
The paper describes protocols for assessing the efficacy of Wolbachia releases on reducing dengue incidence based on data from release trials conducted in municipalities in Columbia.	Recap
The Wolbachia has been released into 6 adjacent zones covering a sub-area, where 3 of the zones have early releases and the other 3 have later releases – the zones which receive late releases are regarded as non-intervention arms for the purposes of the trial analysis.	Recap
It is always difficult to measure the efficacy of vector control interventions using randomized trials because of community level effects such as herd immunity, so that the intervention has impacts on both treatments and controls, and the estimated effect of the intervention is diluted – an effect known as contamination.	Other
In the case of Wolbachia releases, the effect is particularly difficult to quantify because the Wolbachia may spread to mosquito populations in the control arms, or Wolbachia may only have an intermediate (and variable) prevalence in the intervention arms.	Other
The trial described in this paper has additional complications which the authors describe in the manuscript, including the non-random allocation of intervention clusters and the small size of the study area with intervention arms adjacent to control arms and no buffer between them.	Recap
The authors explain that these limitations mean that a pragmatic approach to analysis of Wolbachia efficacy is required.	Recap
I think the paper would benefit from a more rigorous quantitative protocol for how intervention efficacy can be quantified in the presence of contamination (see Silkey et al .	Todo
2016, Trials 1 ).	Other
The power calculation that the authors provide doesn’t explore impacts of contamination, or impacts of incomplete spread of Wolbachia in the intervention arm.	Weakness
In addition the issue of herd immunity should be pointed out in the paper.	Todo
It seems that given the configuration of the release zones, an effective Wolbachia intervention could greatly interrupt dengue transmission in the non-intervention (later release zones) as well, thus making efficacy very difficult to evaluate.	Weakness
I find the Wolbachia Exposure Index proposed for individual participants (to account for their movements outside/into release zones) to be problematic.	Weakness
Aedes aegypti have a very heterogeneous local distribution, and I don’t think variations in exposure can be calculated using travel histories – these estimates are likely to be misleading at best.	Weakness
Regarding the interrupted time series approach, I think a more detailed and formal mathematical description of the method is needed, detailing the sampling distribution of the infection data with respect to the location of Wolbachia interventions, and the statistical model for handling spatiotemporal autocorrelation.	Todo
It does not seem straightforward to distinguish the effect of Wolbachia from non-related fluctuations in disease incidence caused by environmental factors.	Weakness
More explanation of how this will be achieved is required.	Todo
Please put a scale on the map in Figure 1.	Todo
Reviewer response for version 1	Structure
In this article, the authors Perraudeau, Risso, Street, Purdom and Dudoit present a nice workflow for normalization, dimensionality reduction, clustering, and lineage inference of single-cell RNA-seq data (scRNA-seq) using R packages from the open-source Bioconductor project.	Strength
I enthusiastically agree with the authors on an “increasing need for workflows that integrate these tools to yield a seamless scRNA-seq data analysis pipeline” and this workflow is a great step in the right direction.	Strength
However, I have some constructive suggestions that will better integrate other previously developed work and improve this workflow.	Other
- In this workflow, the authors start with a count table.	Recap
However, the majority of researchers will start with raw reads (e.g. a FASTQ file).	Other
It would be great if the author discussed current best practices for the quantification step of scRNA-seq data.	Todo
Alternatively, the authors could point to other references that have already been developed.	Todo
- I would like to see the authors take advantage of the rich functionality and data exploration tools for cell- and gene-specific quality control (QC) introduced in low-level analysis workflows such as the one from Lun et al. (2016) 1 .	Todo
Also, in this workflow, the authors create multiple SummarizedExperiment objects (e.g. one with only the top 1000 highly variable genes (HVGs), one with all genes, etc).	Recap
This doesn’t seem efficient, especially with large single cell data sets such as the 1.3 million cells from embryonic mouse brains.	Weakness
I think both of these concerns can now be addressed with efforts such as the recently developed SingleCellExperiment Bioconductor object ( https://github.com/drisso/SingleCellExperiment ).	Other
For example, the authors could add a “USE” column in the gene- or cell-specific meta table to represent whether or not a particular gene in a particular cell met the filtering criteria applied.	Todo
The authors could store W in the reduceDim assay of the SingleCellExperiment object.	Todo
- In ZINB-WaVE, the authors specify the number of dimensions for the low-dimensional space (K) to be K=50.	Recap
Could the authors add more details for the reader explaining why they picked K=50 and describe situations in which a user would want to specify a higher or lower K?	Todo
In particular, it would be useful to discuss computational time in terms of number of genes and cells.	Todo
Also, it would be useful to note that if you only wanted to use ZINB-WaVE to remove known covariates for normalization, you can use K=0.	Todo
Minor comments:	Structure
- When selecting the top 1000 HVGs, why do the authors not take into account the overall mean-variance relationship and only select genes based on the variance?	Todo

1) Abstract:

Structure

- It is always important to also having focus on more rare etiologies of IE.

Other

In the abstract it is stated that the mortality rate is high.

Recap

This is suggested to be modified to: Initial descriptions of collections of IE cases with A. urinae demonstrated a high morbidity and mortality rate, whereas a recent Swedish epidemiological study could not retrieve this.

Todo

2) Introduction:

Structure

- Dukes criteria should be mentioned.

Todo

- There is not a species named Streptococcus viridans.

Weakness

- Recent diagnostic improvements should be included, especially MALDI-TOF mass spectrometry.

Todo

- a gram-positive, catalase-negative

Other

3) Case description:

Structure

- Specific description of PM electrode findings should be given.

Todo

- A more detailed disease timespan is desirable.

Todo

- Microbiological data are very scarce.

Weakness

Blood-culture system and number of positive bottles should be given.

Todo

Likewise identification criteria and susceptibility methods and results, including MIC values of relevant antibiotics should be given.

Todo

- A thorough microbiological examination of the manuscript seems indicated

Todo

- Aerococcus urinae should only be fully written the first time

Todo

4) Discussion

Structure

- 16S is slang: it should be partial 16S rRNA gene sequencing analysis

Todo

Reviewer response for version 1

Structure

Concerning a case report of awake craniotomy in patient with cyanotic congenital heart disease (CHD).

Recap

The authors describe an unusual case of a rather complicated and rare pathology that needs an emergency surgical intervention during a night.

Recap

I have no specific scientific remarks concerning the content nor the design, but I think that for several reasons this case should be known by large anaesthesia community.

Other

First, the number of patients with CHD that can be scheduled for surgery is growing so our responsibility is to know how they should be handled, why spontaneous ventilation is preferable than mechanical, for which kind of complications we should be prepared etc.

Other

Second, we can always discuss which drugs should be used in a case of awake craniotomy, is dexmedetomidine better than other drugs?

Other

Personal experience and a local policy should be respected in such case.

Other

What is notable is that the authors were capable to establish, in this short time and during a night, an interdisciplinary consensus involving all disciplines, which was probably crucial to handle this case in this remarkable way.

Strength

Reviewer response for version 1

Structure

This paper describes the protocol for a clinical trial releasing Wolbachia bacterium infected male and female Aedes aegypti mosquitoes in Medellín and Bello, Colombia, with the primary endpoint objective of demonstrating reduction of human dengue infections in the population living in the treated areas.

Recap

Wolbachia infected female release over time results in replacement of the uninfected Aedes aegypti population with Wolbachia infected mosquitoes that have reduced ability to transmit arboviruses.

Other

The study design has two components, an interrupted time series (ITS) approach using passive arboviral disease surveillance data from Bello and a large area of Medellín, and a prospective case-control in a smaller area of northeast Medellin using arbovirus laboratory test negative acute febrile illness controls in 6 early release and late release zones.

Recap

The studies begin approximately one year after mosquito releases (in 2018 for the early release zone and 2019 for the releases outside the case-control area) to allow for mosquito population replacement.

Recap

This study employs a novel Aedes aegypti vector control approach to address the major and growing tropical public health problem of Aedes transmitted arboviruses including dengue, Zika, and chikungunya viruses.

Recap

The authors point out that such studies are badly needed as conventional Aedes aegypti vector control approaches have failed or been shown to be non-sustainable, and the only currently licensed dengue vaccine is partially effective and requires a laboratory test prior to immunization.

Recap

This study protocol builds on laboratory and fieldwork in Australia and elsewhere, and is well designed and well written with considerable detail (design, statistical power and analysis, laboratory testing, data management, etc) to address the question of human arboviral disease impact of Wolbachia replacement in a highly endemic tropical urban setting in Latin America.

Strength

The protocol is intentionally “pragmatic” to roll out the intervention at large scale under operational conditions in a timely and cost effective manner acceptable to the study community.

Recap

The authors thus effectively answer potential criticisms of the study design not being a cluster randomized clinical trial as recommended by the WHO Vector Control Advisory Group.

Strength

The case control study design also importantly accounts for the extent of replacement with Wolbachia infected mosquitoes in the treated area and human mobility out of the treatment area with a calculated Wolbachia exposure index calculated for each acute febrile illness patient.

Strength

The test negative case control study design obviates the need for expensive clinical cohort follow up to monitor disease incidence and treated and untreated areas.

Strength

The authors correctly point out that the risk estimate from the test negative case control approach is likely to be unbiased and can be used to calculate efficacy confidence limits.

Strength

The ITS approach is a less rigorous experimental design in that the vast majority of passively reported cases are not virologically confirmed, and surveillance may not be always be done in a consistent manner, but is another practical approach using available data from the Ministry of Health that allows for monitoring of reductions in arboviral case reports over a long time period (5 years) after the Wolbachia replacement treatment during which arbovirus outbreak cycles would be expected to occur.

Other

The discussion appropriately comments on the potential generalizability of the findings to other settings and that cost effectiveness analysis of this approach is underway.

Strength

The following are suggestions to clarify aspects of the protocol:

Structure

Background:

Structure

- While Medellín is clearly highly endemic for dengue, including the historical annual average incidence of dengue would be of interest, as the case-control study will be just be done over a one year time period.

Todo

Dengue transmission dropped to unusually low levels throughout most of South America after the Zika epidemic, and is on the increase in the region as of mid-2019.

Other

Methods:

Structure

- The entomologic details regarding the mosquito releases and strain(s) of Wolbachia could be expanded upon.

Todo

What is being done differently in 2018 and 2019 compared to the 2017 releases that achieved temporary high Wolbachia prevalence?

Todo

- More details on the Wolbachia sampling and monitoring strategy would be helpful.

Todo

What is the extent of the monitoring area?

Todo

All comuna outside the case-control area?

Todo

Checking BG traps once a week does not ensure that the mosquito specimens will be identified correctly because of damage from the trap fans to captured mosquitoes.

Weakness

Many samples will be lost because of loss of power, ants, etc.

Other

BG traps should be checked daily.

Other

- For the ITS component and the secondary endpoint of severe dengue incidence, how does the Ministry of Health define severe dengue, and has severe dengue been consistently defined over time?

Todo

- Regarding the case control study participant recruitment, what is the possibility that patients with acute febrile illness in the study areas will seek care in clinics outside the network?

Todo

- With regard to the laboratory testing algorithm to exclude potential dengue serologic positives from being control patients, the authors could more explicitly state that PanBio IgG ELISA test is designed with cutoffs to only detect high IgG titers consistent with acute secondary infections, and not past infections.

Todo

Excluding all patients with IgG antibody due to past dengue infection in this setting would eliminate a large percentage of the potential control patients.

Weakness

- Consider observing changes in the vector-bacteria-virus interaction through time.

Todo

Coevolution is likely.

Other

Whether virus blocking ability changes over time (e.g., lowered bacteria concentration in the mosquito cells) is not clear.

Weakness

Reviewer response for version 1

Structure

The paper describes protocols for assessing the efficacy of Wolbachia releases on reducing dengue incidence based on data from release trials conducted in municipalities in Columbia.

Recap

The Wolbachia has been released into 6 adjacent zones covering a sub-area, where 3 of the zones have early releases and the other 3 have later releases – the zones which receive late releases are regarded as non-intervention arms for the purposes of the trial analysis.

Recap

It is always difficult to measure the efficacy of vector control interventions using randomized trials because of community level effects such as herd immunity, so that the intervention has impacts on both treatments and controls, and the estimated effect of the intervention is diluted – an effect known as contamination.

Other

In the case of Wolbachia releases, the effect is particularly difficult to quantify because the Wolbachia may spread to mosquito populations in the control arms, or Wolbachia may only have an intermediate (and variable) prevalence in the intervention arms.

Other

The trial described in this paper has additional complications which the authors describe in the manuscript, including the non-random allocation of intervention clusters and the small size of the study area with intervention arms adjacent to control arms and no buffer between them.

Recap

The authors explain that these limitations mean that a pragmatic approach to analysis of Wolbachia efficacy is required.

Recap

I think the paper would benefit from a more rigorous quantitative protocol for how intervention efficacy can be quantified in the presence of contamination (see Silkey et al .

Todo

2016, Trials 1 ).

Other

The power calculation that the authors provide doesn’t explore impacts of contamination, or impacts of incomplete spread of Wolbachia in the intervention arm.

Weakness

In addition the issue of herd immunity should be pointed out in the paper.

Todo

It seems that given the configuration of the release zones, an effective Wolbachia intervention could greatly interrupt dengue transmission in the non-intervention (later release zones) as well, thus making efficacy very difficult to evaluate.

Weakness

I find the Wolbachia Exposure Index proposed for individual participants (to account for their movements outside/into release zones) to be problematic.

Weakness

Aedes aegypti have a very heterogeneous local distribution, and I don’t think variations in exposure can be calculated using travel histories – these estimates are likely to be misleading at best.

Weakness

Regarding the interrupted time series approach, I think a more detailed and formal mathematical description of the method is needed, detailing the sampling distribution of the infection data with respect to the location of Wolbachia interventions, and the statistical model for handling spatiotemporal autocorrelation.

Todo

It does not seem straightforward to distinguish the effect of Wolbachia from non-related fluctuations in disease incidence caused by environmental factors.

Weakness

More explanation of how this will be achieved is required.

Todo

Please put a scale on the map in Figure 1.

Todo

Reviewer response for version 1

Structure

In this article, the authors Perraudeau, Risso, Street, Purdom and Dudoit present a nice workflow for normalization, dimensionality reduction, clustering, and lineage inference of single-cell RNA-seq data (scRNA-seq) using R packages from the open-source Bioconductor project.

Strength

I enthusiastically agree with the authors on an “increasing need for workflows that integrate these tools to yield a seamless scRNA-seq data analysis pipeline” and this workflow is a great step in the right direction.

Strength

However, I have some constructive suggestions that will better integrate other previously developed work and improve this workflow.

Other

- In this workflow, the authors start with a count table.

Recap

However, the majority of researchers will start with raw reads (e.g. a FASTQ file).

Other

It would be great if the author discussed current best practices for the quantification step of scRNA-seq data.

Todo

Alternatively, the authors could point to other references that have already been developed.

Todo

- I would like to see the authors take advantage of the rich functionality and data exploration tools for cell- and gene-specific quality control (QC) introduced in low-level analysis workflows such as the one from Lun et al. (2016) 1 .

Todo

Also, in this workflow, the authors create multiple SummarizedExperiment objects (e.g. one with only the top 1000 highly variable genes (HVGs), one with all genes, etc).

Recap

This doesn’t seem efficient, especially with large single cell data sets such as the 1.3 million cells from embryonic mouse brains.

Weakness

I think both of these concerns can now be addressed with efforts such as the recently developed SingleCellExperiment Bioconductor object ( https://github.com/drisso/SingleCellExperiment ).

Other

For example, the authors could add a “USE” column in the gene- or cell-specific meta table to represent whether or not a particular gene in a particular cell met the filtering criteria applied.

Todo

The authors could store W in the reduceDim assay of the SingleCellExperiment object.

Todo

- In ZINB-WaVE, the authors specify the number of dimensions for the low-dimensional space (K) to be K=50.

Recap

Could the authors add more details for the reader explaining why they picked K=50 and describe situations in which a user would want to specify a higher or lower K?

Todo

In particular, it would be useful to discuss computational time in terms of number of genes and cells.

Todo

Also, it would be useful to note that if you only wanted to use ZINB-WaVE to remove known covariates for normalization, you can use K=0.

Todo

Minor comments:

Structure

- When selecting the top 1000 HVGs, why do the authors not take into account the overall mean-variance relationship and only select genes based on the variance?

Todo