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When can I use "Only do ..." vs. when must I use "Only ..." without the "do"?

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Which is better ? 'Only When can I use "Only do males have .. '" vs 'Only males have. when must I use "Only.'." without the "do"?

I'm writing a scientific paper and my supervisor (who is non-native speaker, whereas I am a native speaker) asked me to change this construct:

Only do males have a y chromosome.

to

Only males have a y chromosome.

with no do. Is the former construct ungrammatical, or barring that, awkward?

I know that there are some situations where we need to use the do-structure, e.g.:

Only afterwards does she apologise.

So does this pattern apply to my sentence? Why or why not?

For context, the broader passage I'm writing begins with:

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis (GSEA). Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

Which sets up a context describing different types of sets; then, the passage where the sentence in question appears is:

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand ...

Which is better ? 'Only do males have .. ' vs 'Only males have..'

I'm writing a scientific paper and my supervisor (who is non-native speaker, whereas I am a native speaker) asked me to change this construct:

Only do males have a y chromosome.

to

Only males have a y chromosome.

with no do. Is the former construct ungrammatical, or barring that, awkward?

I know that there are some situations where we need to use the do-structure, e.g.:

Only afterwards does she apologise.

So does this pattern apply to my sentence? Why or why not?

For context, the broader passage I'm writing begins with:

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis (GSEA). Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

Which sets up a context describing different types of sets; then, the passage where the sentence in question appears is:

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand ...

When can I use "Only do .." vs. when must I use "Only.." without the "do"?

I'm writing a scientific paper and my supervisor (who is non-native speaker, whereas I am a native speaker) asked me to change this construct:

Only do males have a y chromosome.

to

Only males have a y chromosome.

with no do. Is the former construct ungrammatical, or barring that, awkward?

I know that there are some situations where we need to use the do-structure, e.g.:

Only afterwards does she apologise.

So does this pattern apply to my sentence? Why or why not?

For context, the broader passage I'm writing begins with:

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis (GSEA). Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

Which sets up a context describing different types of sets; then, the passage where the sentence in question appears is:

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand ...

5 deleted 665 characters in body
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Which sentence is better?I'm writing a scientific paper and my supervisor (who is non-native speaker, whereas I am a native speaker) asked me to change this construct:

  1. Only do males have a y chromosome.

Only do males have a y chromosome.

Or:to

  1. Only males have a y chromosome.

Only males have a y chromosome.

What iswith no do. Is the reason for thisformer construct ungrammatical, or barring that, awkward?

====added by another user=====

I know that there are some situations where we need to use the same structure as in (1)do-structure, e.g.:

  1. Only afterwards does she apologise.

Only afterwards does she apologise.

IsSo does this pattern apply to my sentence the same? Why or different - why not?

====end other users input=====

I am actually writing a scientific paper and my supervisor (non native speaker ) asked me to change this construct. But for some reasonFor context, the flow felt betterbroader passage I'm writing begins with 'do' to me. I think because it is referring back to a previous paragraph. Full context:  

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis (GSEA). Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis(GSEA) \citep{subramanian_gene_2005}. Here the set of identified genes are compared with predefined sets of genes. The predefinedWhich sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection inup a gene regulatory network.

=======In the above I mentionedcontext describing different types of sets =======

In contrast to having two stages for analysissets; then, analysis can be performed in one stage. Past ILP research \citep{gamberger_induction_2004} has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignorepassage where the detailed relations between entitiessentence in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand these often create crude clusters of genes, and do not follow biological intuition of information flow through the pathway. e.g. by using an inappropriate network abstraction or failing to adapt the clustering method to work on an appropriate network abstraction. When considering biological pathways simple directed networks of genes and proteins are not appropriate. Thisquestion appears is because this formalism does not adequately model the dependencies of biochemical reactions i.e. bipartite graphs or hypergraphs are required. See \citep{whelan2011representation} for more details on this.:

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand ...

Which sentence is better?

  1. Only do males have a y chromosome.

Or:

  1. Only males have a y chromosome.

What is the reason for this?

====added by another user=====

I know that there are some situations where we need to use the same structure as in (1):

  1. Only afterwards does she apologise.

Is my sentence the same or different - why?

====end other users input=====

I am actually writing a scientific paper and my supervisor (non native speaker ) asked me to change this construct. But for some reason the flow felt better with 'do' to me. I think because it is referring back to a previous paragraph. Full context:  

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis(GSEA) \citep{subramanian_gene_2005}. Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

=======In the above I mentioned different types of sets =======

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research \citep{gamberger_induction_2004} has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand these often create crude clusters of genes, and do not follow biological intuition of information flow through the pathway. e.g. by using an inappropriate network abstraction or failing to adapt the clustering method to work on an appropriate network abstraction. When considering biological pathways simple directed networks of genes and proteins are not appropriate. This is because this formalism does not adequately model the dependencies of biochemical reactions i.e. bipartite graphs or hypergraphs are required. See \citep{whelan2011representation} for more details on this.

I'm writing a scientific paper and my supervisor (who is non-native speaker, whereas I am a native speaker) asked me to change this construct:

Only do males have a y chromosome.

to

Only males have a y chromosome.

with no do. Is the former construct ungrammatical, or barring that, awkward?

I know that there are some situations where we need to use the do-structure, e.g.:

Only afterwards does she apologise.

So does this pattern apply to my sentence? Why or why not?

For context, the broader passage I'm writing begins with:

In stage 3 researchers look for connections between these genes, for example by performing Gene Set Enrichment Analysis (GSEA). Here the set of identified genes are compared with predefined sets of genes. The predefined sets of genes indicate a known relation. For example having a related function, existing in the same location in the cell or taking part in the same pathway. A further way a set could be defined is a topological set, which takes into account finer grained internal relations to define a set. For example a topological set could be identified by community detection in a gene regulatory network.

Which sets up a context describing different types of sets; then, the passage where the sentence in question appears is:

In contrast to having two stages for analysis, analysis can be performed in one stage. Past ILP research has integrated the two stages of finding differently expressed genes and GSEA by using relational subgroup discovery. These have used the hierarchical Gene Ontology to relate genes and has the advantage of being able to construct novel sets by sharing variables across predicates that define the sets. For example a set could be defined as the genes that have been annotated with two GO terms. Other ways researchers have tried to integrate the use of known relations is by adapting the classification approach. New features are built by aggregating across a predefined set of genes - for example by taking an average expression value for a pathway, see ~\citep{holec_comparative_2012} for a review of these methods.

In most of these methods it is common to ignore the detailed relations between entities in a pathway, the pathway is treated as an unstructured set of genes. Only do topologically defined sets take advantage of any known internal relations. On the other hand ...

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