cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1282440.v1
title: 2011 data on NTC in Sheffield with readmission rates

description: Data collected from NHS Sheffield (PCT as was) and also children's hospital - an overlapping series of non therapeutic child circumcisions with readmission rates of c10-12% (depending on series/calculation as episodes/patients). Note 'admission' can mean being held for treatment in a specialist area of A&E - these cases are grouped with visits to ward I believe because the resource implications are similar: for purposes of assessing NTC complications they are assumed to be more serious on an individual and financial level.
DOI: 10.6084/m9.figshare.1282402
title: NHS Leeds Contract with provider of plastibel NTC of infants

description: This is an example of an NHS contract for an external provider of religious or cultural circumcision of babies. Similar contracts exist with GPs in Tower Hamlets and Birmingham. My data shows the degree to which the contract is enforced varies. This has particularly been a problem in Birmingham where I have evidence suggestive that the contractor may have lied.
DOI: 10.6084/m9.figshare.1282402.v1
title: NHS Leeds Contract with provider of plastibel NTC of infants

description: This is an example of an NHS contract for an external provider of religious or cultural circumcision of babies. Similar contracts exist with GPs in Tower Hamlets and Birmingham. My data shows the degree to which the contract is enforced varies. This has particularly been a problem in Birmingham where I have evidence suggestive that the contractor may have lied.
DOI: 10.6084/m9.figshare.1282370
title: LTSTM data from August 2004

description: This is low temperature STM data from August 2004.
DOI: 10.6084/m9.figshare.1282370.v1
title: LTSTM data from August 2004

description: This is low temperature STM data from August 2004.
DOI: 10.6084/m9.figshare.1282334
title: Supplementary data and code to Keil, Storch & Jetz (2015) On the decline of biodiversity due to area loss. Nature Communications 6: 8837

description: R code, distributional data, phylogenies, functional dendrograms and shapefiles used for the analyses and simulations. See the readme.txt file in the .zip archive for more details.
DOI: 10.6084/m9.figshare.1282321
title: 5 year data on Leeds NHS NTCs with serious issues

description: This is data from 2008 to 2013 (5 financial years) on the non therapeutic circumcisions (NTCs) of children funded by NHS Leeds, with data also on those cases which resulted in a hospital stay of 1 d or more and/or a follow up urological surgery.Note the data on surgeries is by F/Y and complications by calendar year so not a perfect match. However it suggests that more serious complications may occur at a rate of &gt;2% on infants - contradicting NTC complications data controlled by US sources - eg CDC, AAP and also the WHO advice. Note tab 2 shows the cost of the 1d admissions allowing a calculation of the cost of treating more serious plastibell complications (tab 1). Note also the doc contains my annotations/calculations which should be clear. An original is also available. The questions I asked to get this response are below: Email 27.01.2013 to NHS Leeds Dear David<br>We had a conversation last week and you said you couldn't answer my<br>specific questions from your databases. I hope you might be able to<br>answer this instead, which is simpler and covers a shorter time period. 1. please advise how many religious/cultural male circumcisions (OPCS<br>code N303, diagnosis Z41.2) have been funded since 1st January 2005 on<br>boys aged &lt;18, with details of how many were undertaken on age 0 and<br>how many on age 1-17. Please provide the total cost to the PCT of all<br>these surgeries if possible. 2. please advise how many boys from the group above were admitted to<br>hospital within 30 days of religious circumcision for a length of stay<br>which was 1 day or more. For those cases, please advise the age of<br>child, the time gap between circumcision and admission, the primary<br>and secondary diagnosis code and text, the primary and secondary OPCS<br>code and text, and the cost of the episode. 3. I am also interested in knowing how many recircumcisions (OPCS<br>N303) followed the original circumcisions in Q1 in the period to date,<br>and how many children have subsequently returned (in the period to<br>date) with a diagnosis beginning with N - if you can extract this it<br>would tell me how many boys have subsequently been treated for issues<br>such as urethral fistula, and meatal stenosis. If you can't do question 3, I hope you will be able to answer questions<br>1 & 2.<br>Perhaps you could also provide me with a copy of the report into male<br>circumcision issues that preceeded the PCT funding, and a copy of the<br>service level agreement with those who do the circumcisions, if one<br>exists. I'm very grateful for all your help<br>With kind regards Laura
DOI: 10.6084/m9.figshare.1282334.v1
title: Supplementary data and code to Keil, Storch & Jetz (2015) On the decline of biodiversity due to area loss. Nature Communications 6: 8837

description: R code, distributional data, phylogenies, functional dendrograms and shapefiles used for the analyses and simulations. See the readme.txt file in the .zip archive for more details.
DOI: 10.6084/m9.figshare.1282321.v1
title: 5 year data on Leeds NHS NTCs with serious issues

description: This is data from 2008 to 2013 (5 financial years) on the non therapeutic circumcisions (NTCs) of children funded by NHS Leeds, with data also on those cases which resulted in a hospital stay of 1 d or more and/or a follow up urological surgery.Note the data on surgeries is by F/Y and complications by calendar year so not a perfect match. However it suggests that more serious complications may occur at a rate of &gt;2% on infants - contradicting NTC complications data controlled by US sources - eg CDC, AAP and also the WHO advice. Note tab 2 shows the cost of the 1d admissions allowing a calculation of the cost of treating more serious plastibell complications (tab 1). Note also the doc contains my annotations/calculations which should be clear. An original is also available. The questions I asked to get this response are below: Email 27.01.2013 to NHS Leeds Dear David<br>We had a conversation last week and you said you couldn't answer my<br>specific questions from your databases. I hope you might be able to<br>answer this instead, which is simpler and covers a shorter time period. 1. please advise how many religious/cultural male circumcisions (OPCS<br>code N303, diagnosis Z41.2) have been funded since 1st January 2005 on<br>boys aged &lt;18, with details of how many were undertaken on age 0 and<br>how many on age 1-17. Please provide the total cost to the PCT of all<br>these surgeries if possible. 2. please advise how many boys from the group above were admitted to<br>hospital within 30 days of religious circumcision for a length of stay<br>which was 1 day or more. For those cases, please advise the age of<br>child, the time gap between circumcision and admission, the primary<br>and secondary diagnosis code and text, the primary and secondary OPCS<br>code and text, and the cost of the episode. 3. I am also interested in knowing how many recircumcisions (OPCS<br>N303) followed the original circumcisions in Q1 in the period to date,<br>and how many children have subsequently returned (in the period to<br>date) with a diagnosis beginning with N - if you can extract this it<br>would tell me how many boys have subsequently been treated for issues<br>such as urethral fistula, and meatal stenosis. If you can't do question 3, I hope you will be able to answer questions<br>1 & 2.<br>Perhaps you could also provide me with a copy of the report into male<br>circumcision issues that preceeded the PCT funding, and a copy of the<br>service level agreement with those who do the circumcisions, if one<br>exists. I'm very grateful for all your help<br>With kind regards Laura
DOI: 10.6084/m9.figshare.1282281
title: Quantitative PCR analysis

description: Statistical analysis and data graphing on results from shearing knockdown and control cells
DOI: 10.6084/m9.figshare.1282279
title: Raw data qPCR

description: Raw data from qPCR analysis of endothelial cells treated with ctl or Notch1 siRNA that were sheared for 1 hour.
DOI: 10.6084/m9.figshare.1282280
title: qPCR Analysis

description: Statistical Analysis of qPCR and graphing
DOI: 10.6084/m9.figshare.1282279.v1
title: Raw data qPCR

description: Raw data from qPCR analysis of endothelial cells treated with ctl or Notch1 siRNA that were sheared for 1 hour.
DOI: 10.6084/m9.figshare.1282280.v1
title: Raw data from all qPCR runs

description: Raw data from qPCR on cells with either ctl or Notch1 siRNA that were sheared for 1h.
DOI: 10.6084/m9.figshare.1281451
title: Red or blue pill?

description: English translation will be added soon to this fig<strong>share</strong> article.
DOI: 10.6084/m9.figshare.1281450
title: LTSTM data from July 2004

description: This is low temperature STM data from July 2004.
DOI: 10.6084/m9.figshare.1281451.v1
title: Red or blue pill?

description: English translation will be added soon to this fig<strong>share</strong> article.
DOI: 10.6084/m9.figshare.1281450.v1
title: LTSTM data from July 2004

description: This is low temperature STM data from July 2004.
DOI: 10.6084/m9.figshare.1281423
title: 2011 data on NHS NTC in Leeds original return w/out annotation

description: This is the full response to my questions of July 2012 from NHS Leeds to a series of questions about urology operations on children and NTC and its follow ups. A simpler annotated version - which produces complication rates is found in the same regional file. A blog post explaining it is found at www.ukcircumcisionreport.org
DOI: 10.6084/m9.figshare.1281435
title: Chronic pelvic pain - pain drawings

description: Pain drawings provoked from intra-pelvic structures in women with and without chronic pelvic pain.
DOI: 10.6084/m9.figshare.1281449
title: aio

description: some code
DOI: 10.6084/m9.figshare.1281423.v1
title: 2011 data on NHS NTC in Leeds original return w/out annotation

description: This is the full response to my questions of July 2012 from NHS Leeds to a series of questions about urology operations on children and NTC and its follow ups. A simpler annotated version - which produces complication rates is found in the same regional file. A blog post explaining it is found at www.ukcircumcisionreport.org
DOI: 10.6084/m9.figshare.1281418
title: YORKSHIRE CIRCUMCISION REPORTS & SUMMARIES

description: Responses from hospitals and NHS commissioners in Yorkshire to questions about circumcision practice and complications 2009-2011
DOI: 10.6084/m9.figshare.1281449.v1
title: aio

description: some code
DOI: 10.6084/m9.figshare.1281414
title: 2009 data on NHS NTC in Leeds and its follow ups

description: This is a letter providing responses to questions I asked in 2011 about child NTC funded by the NHS in Leeds and its follow ups. Note this was an early piece of research which mistakenly did not ask for clarification about diagnosis of follow up issues - we therefore cannot be sure which subsequent presentations and admissions were likely or definately related to the prior circumcision. However the data is suggestive of significant rates of complications, particularly the 5/89 child NTC subjects who required follow up urological surgeries. See 2011 Leeds return for more clear information on the rate of complications. More information on religious cutting and its complications in Leeds can be found here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954356/
DOI: 10.6084/m9.figshare.1281417
title: 2011 data on NHS NTC in Leeds and its complications

description: This is an MS excel file from NHS Leeds Airedale and Bradford, provided in Aug 2012 and covering non therapeutic circumcisions funded in 2011 with detailed information on the subsequent A&E presentations and hospitalisations. The file is annotated by me (LM) to explain what it reveals. The original and covering letter are available on request (the original provides an additional breakdown of the NTCs performed in hospital - age 0-12 and other urology procedures fund coded 'L' - including treatments for meatal stenosis).
DOI: 10.6084/m9.figshare.1281414.v1
title: 2009 data on NHS NTC in Leeds and its follow ups

description: This is a letter providing responses to questions I asked in 2011 about child NTC funded by the NHS in Leeds and its follow ups. Note this was an early piece of research which mistakenly did not ask for clarification about diagnosis of follow up issues - we therefore cannot be sure which subsequent presentations and admissions were likely or definately related to the prior circumcision. However the data is suggestive of significant rates of complications, particularly the 5/89 child NTC subjects who required follow up urological surgeries. See 2011 Leeds return for more clear information on the rate of complications. More information on religious cutting and its complications in Leeds can be found here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954356/
DOI: 10.6084/m9.figshare.1281395
title: 2nd LTSTM data set from June 2004

description: This is the second low temperature data set from June 2004.
DOI: 10.6084/m9.figshare.1281395.v1
title: 2nd LTSTM data set from June 2004

description: This is the second low temperature data set from June 2004.
DOI: 10.6084/m9.figshare.1281417.v2
title: 2011 data on NHS NTC in Leeds and its complications

description: This is an MS excel file from NHS Leeds Airedale and Bradford, provided in Aug 2012 and covering non therapeutic circumcisions funded in 2011 with detailed information on the subsequent A&E presentations and hospitalisations. The file is annotated by me (LM) to explain what it reveals. The original and covering letter are available on request (the original provides an additional breakdown of the NTCs performed in hospital - age 0-12 and other urology procedures fund coded 'L' - including treatments for meatal stenosis).
DOI: 10.6084/m9.figshare.1281418.v1
title: Yorkshire circumcision and complication reports

description: Responses from hospitals and NHS commissioners in Yorkshire to questions about circumcision practice and complications 2009-2011
DOI: 10.6084/m9.figshare.1281376
title: PubMed Central literature composition and analysis

description: Compressed MySQL data dump of literature composition analyses including total token, sentence and syllable counts, Flesch readability scores, nouns, verbs and adjectives for the complete full-text open-access subset of PubMed Central. This is one of the research contributions of my PhD.
DOI: 10.6084/m9.figshare.1281391
title: LTSTM data from June 2004 part 1

description: This is the first part of the June 2004 data set of low temperature STM data.
DOI: 10.6084/m9.figshare.1281417.v1
title: 2011 data on NTC in Leeds and its complications

description: This is an MS excel file from NHS Leeds Airedale and Bradford, provided in Aug 2012 and covering non therapeutic circumcisions funded in 2011 with detailed information on the subsequent A&E presentations and hospitalisations. The file is annotated by me (LM) to explain what it reveals. The original and covering letter are available on request (the original provides an additional breakdown of the NTCs performed in hospital - age 0-12 and other urology procedures fund coded 'L' - including treatments for meatal stenosis).
DOI: 10.6084/m9.figshare.1281418.v2
title: Yorkshire circumcision and complication reports

description: Responses from hospitals and NHS commissioners in Yorkshire to questions about circumcision practice and complications 2009-2011
DOI: 10.6084/m9.figshare.1281376.v1
title: PubMed Central literature composition and analysis

description: Compressed MySQL data dump of literature composition analyses including total token, sentence and syllable counts, Flesch readability scores, nouns, verbs and adjectives for the complete full-text open-access subset of PubMed Central. This is one of the research contributions of my PhD.
DOI: 10.6084/m9.figshare.1281372
title: Inferring gene function from evolutionary change in signatures of translation efficiency

description: <strong>Krisko, Copic, Gabaldon, Lehner and Supek. Genome Biol 2014.</strong> doi:10.1186/gb-2014-15-3-r44<br><strong>"Inferring gene function from evolutionary change in signatures of translation efficiency"</strong> Additional file 18. All COG gene families found to be significantly enriched/depleted for<br>highly expressed (HE) genes across 911 microbial genomes in any of the 24 examined<br>phenotypes or environments. The HE genes were determined by quantifying the use of<br>optimal codons, which was compared against the composition of intergenic DNA<br>using a randomization test. <strong>(Table A)</strong> All 200 shown expression-phenotype links have (i) Fisher's exact test<br>for enrichment P&lt;0.01, (ii) magnitude of enrichment &gt;2x or &lt;0.5x, and<br>(iii) Random Forest (RF) randomization test for confounding<br>phenotypes/environments/phylogeny P&lt;0.01. A total of 187 unique COGs are<br>represented in the list. The "numOrgs" column shows a number of organisms positive for the given trait,<br>and the total number of organisms where that trait is defined. For instance,<br>traits named "Mammalian pathogen: (tissue or organ)" are positive for pathogens<br>infecting that organ, negative for all other mammalian pathogens,<br>and undefined for the rest of examined Bacteria and Archaea. In some cases<br>(e.g. halophiles), many microbes have undefined values due to missing annotations. In every COG, column "a" is the number of HE genes in microbes positive for the given trait,<br>"b" is the count of non-HE genes in the same microbes, "c" is HE genes in microbes where<br>the trait is negative and "d" is the count of non-HE genes in the negative organisms.<br>"Enrich" is the enrichment = a/(a+b) / ( c/(c+d) ). <strong>(Table B)</strong> Same as table A, but with the threshold for the RF test for counfounders<br>slightly relaxed to P&lt;0.05, yielding 167 additional COG-phenotype links (total: 367). <strong>(Table C)</strong> A set of 2386 inferred COG-phenotype links with broader coverage due to relaxed<br>criteria for magnitude of enrichment (1.5x or 0.66x, instead of 2x or 0.5x); the criteria<br>for significance of the enrichment remained the same (P&lt;0.01 in Fisher's exact test).<br>Additionally, the COG-phenotype links in this table did not have to pass the<br>RF randomization test for confounders (meaning there is no control for phylogeny,<br>genome size/GC content, or the inter-correlation of phenotypes).
DOI: 10.6084/m9.figshare.1281374
title: 2009 data on NHS NTC in Oldam and complications + details of other life threatening incidents

description: Data from NHS Oldham in 2009 showing that in 2009 254 non therapeutic circumcisions were performed on under 16s. The Commissioner estimates based on A&E attendance data that 17 presented in A&E with a complication within 30 days and that within 3 months, four children suffered a complication requiring hospital re-admission. The overlap between these two sets is not known but we can assume that complication rates within 3 months were at least 6.7% (N=17) and that the most serious complications affected 1.57% (N=4). In addition, NHS Oldham notes that it has funded the treatment of 9 babies for post circumcision haemorrhage and shock in the period April 2006 - March 2011 (5 years).
DOI: 10.6084/m9.figshare.1281375
title: NORTH WEST CIRCUMCISION REPORTS & SUMMARIES

description: Returns from NHS and other sources in north west England, regarding male circumcision morbidity and mortality. Many more datasets to follow...
DOI: 10.6084/m9.figshare.1281391.v1
title: LTSTM data from June 2004 part 1

description: This is the first part of the June 2004 data set of low temperature STM data.
DOI: 10.6084/m9.figshare.1281372.v1
title: Inferring gene function from evolutionary change in signatures of translation efficiency

description: <strong>Krisko, Copic, Gabaldon, Lehner and Supek. Genome Biol 2014.</strong> doi:10.1186/gb-2014-15-3-r44<br><strong>"Inferring gene function from evolutionary change in signatures of translation efficiency"</strong> Additional file 18. All COG gene families found to be significantly enriched/depleted for<br>highly expressed (HE) genes across 911 microbial genomes in any of the 24 examined<br>phenotypes or environments. The HE genes were determined by quantifying the use of<br>optimal codons, which was compared against the composition of intergenic DNA<br>using a randomization test. <strong>(Table A)</strong> All 200 shown expression-phenotype links have (i) Fisher's exact test<br>for enrichment P&lt;0.01, (ii) magnitude of enrichment &gt;2x or &lt;0.5x, and<br>(iii) Random Forest (RF) randomization test for confounding<br>phenotypes/environments/phylogeny P&lt;0.01. A total of 187 unique COGs are<br>represented in the list. The "numOrgs" column shows a number of organisms positive for the given trait,<br>and the total number of organisms where that trait is defined. For instance,<br>traits named "Mammalian pathogen: (tissue or organ)" are positive for pathogens<br>infecting that organ, negative for all other mammalian pathogens,<br>and undefined for the rest of examined Bacteria and Archaea. In some cases<br>(e.g. halophiles), many microbes have undefined values due to missing annotations. In every COG, column "a" is the number of HE genes in microbes positive for the given trait,<br>"b" is the count of non-HE genes in the same microbes, "c" is HE genes in microbes where<br>the trait is negative and "d" is the count of non-HE genes in the negative organisms.<br>"Enrich" is the enrichment = a/(a+b) / ( c/(c+d) ). <strong>(Table B)</strong> Same as table A, but with the threshold for the RF test for counfounders<br>slightly relaxed to P&lt;0.05, yielding 167 additional COG-phenotype links (total: 367). <strong>(Table C)</strong> A set of 2386 inferred COG-phenotype links with broader coverage due to relaxed<br>criteria for magnitude of enrichment (1.5x or 0.66x, instead of 2x or 0.5x); the criteria<br>for significance of the enrichment remained the same (P&lt;0.01 in Fisher's exact test).<br>Additionally, the COG-phenotype links in this table did not have to pass the<br>RF randomization test for confounders (meaning there is no control for phylogeny,<br>genome size/GC content, or the inter-correlation of phenotypes).
DOI: 10.6084/m9.figshare.1281418.v3
title: Yorkshire circumcision and complication reports

description: Responses from hospitals and NHS commissioners in Yorkshire to questions about circumcision practice and complications 2009-2011
DOI: 10.6084/m9.figshare.1281371
title: Software and database resource mentions across the whole of PubMed Central full-text articles

description: This is a compressed .sql.gz file of a MySQL database dump. The table contains the automatically extracted mentions of database and software resource names as extracted by bioNerDS across the full sub-set of open-access full-text PubMed Central articles. Each matched resource is identified by name, text offsets and "normalised" name, and also includes details of the rules from which the name was matched. This dataset is one of the primary research contributions of my PhD work, and a paper currently being finalised for submission to PLoS Computational Biology.
DOI: 10.6084/m9.figshare.1281368
title: Space use variation in co-occurring sister species: response to environmental variation or competition?

description: Data of Dufour et al 2015 Plos One Space use variation in co-occurring sister species: response to environmental variation or competition? Claire M.S Dufour1,2,+, Christine Meynard3, Johan Watson4, Camille Rioux1, Simon Benhamou5, Julie Perez1, Jurie J. du Plessis6, Nico Avenant6, Neville Pillay2,Guila Ganem1,2,+