!batch
!echo
!limit=1000
!short=20
!constituents=1
!spell=0

% Test sentences taken from bio-medical, biochemistry journal articles.
% These tests sentences are originally from the biolg project.

% UNITS --------------------------------------------------------

% Some basic cases
The 50 kDa protein is examined
The protein ( 50 kDa ) is examined
The mass is 50 kDa
A protein of 50 kDa is examined
The rate is 10 nm per msec
The rate is 10 nm per one msec of time
The last 195 bp of the DNA are examined

% These should work also if the tokens are "merges" of number and unit
The 50-kDa protein is examined
The 50kDa protein is examined
The mass is 50kDa
A protein of 50kDa is examined
The rate is 10nm per msec
The rate is 10nm per 1msec of time
The last 195bp of the DNA are examined

% Number derived units are also recognized
The rate is 10 mg/sec
The rate is 10 mol/day
The rate is 10 micrograms/mouse/day

% Units previously in the dictionary have not been modified, and are
% not allowed all the necessary roles.
The 10 foot distance is examined

% The following dont work yet, and would require special ".p" definitions
% of the units, similar to, for example, feet.p and seconds.p.
% This would require an OD- connectors (see feet.p)
It fell 10 nm
% This would require an OT- connector (see seconds.p)
It lasted 10 msec
% This would require Yd+ (see feet.p)
It happened 10 nm away
% This would require Yt+ (see seconds.p)
It happened 10 msec later
% This would require EC+ to have the intended parse (compare feet.p)
The 10 bp longer sequence is examined

% This one doesn't work because of "leftmost"
The leftmost 195 bp of the DNA are examined

% NUMERIC RANGES ------------------------------------------------

The 50 to 100 kDa protein is examined
Exons 40 to 50 were examined
It was submitted in the period 1990 to 1995
The range is 0 to 1
The range is nine to twenty
% ambiguities are mainly due to the bracketed part
The production is low in rich media ( 50 to 300 LrpC molecules per cell )
The enzyme has a weight of 125,000 to 130,000
The domain ( residues 73 to 90 ) was shown
The analysis revealed a transcript after 6 to 7.5 h
CSF reached 50 to 100 nM
A shift from 37 to 20 degrees C resulted in an increase
An operon showed at 310 to 320 kb
The sequence shows 28.2 to 34.6 % identities
In the past 4 to 5 years results have advanced 
One is the region 1911 to 1917
% unnecessary (?) ambiguity with the range linking to "are"
The segment includes the pacL from which genes 1 to 7 are transcribed
The gene 1 to 7 mRNA synthesis was reduced
There are  deviations of 2 to 3 A 
% the range should link to the verb with MVp (~ "north"): to much ambiguous ?
These transcripts are located 5 to 3
These transcripts are located 5' to 3'

% Ranges with hyphens

The 50 - 100 kDa protein is examined
Exons 40 -- 50 were examined
It was submitted in the period 1990 --- 1995

% Cases with "from" (e.g. "from 10 to 20") (TODO):
% shifts
The number of repeats was increased from 7 to 11 .
Experiments revealed an increase from 0 to 5 min postinduction
The transfer of cells from 37 to 50 degrees C repressed synthesis .
The concentration increased from 125 to 325 microgram per assay .
% ranges
We inserted sequences from 5 to 21 bp in length
The start point ranged from 17 to 18 base pairs
The promoter contained a sequence near the region ( from 60 to 73 % )
A region extending from 183 to 118 base pairs was required

% Cases with "between"
Transcription sets in ( between 8 and 16 h of culture ) .
The pH optimum is between 5 and 7
concentrations were measured  between 0 and 3 h after the beginning
it shows activity at a temperature between 60 and 70 degrees C
The activity is stable between pH 6 and 12

% Numeric ranges with "merged" units (or "fold") also occur
An 80 to 100-fold increase was observed
Antigens ranged 82 to 90%

% FOLD-WORDS --------------------------------------------------------

This included an up to threefold increase
There were increases in proteins, including actin (twofold to threefold)
The association rate constant is also increased about 2-fold
The affinity is approximately 30-fold weaker
Leaves display a 2-fold accumulation
This was about 10-fold higher
% correct parse ranked second
sigmaF was some twofold higher than sigmaE
% does not parse
It was two to threefold more abundant
I found an at least twofold reduction
It showed a fivefold anaerobic induction
loci increased more than twofold
% correct parse ranked fourth
It corresponds to one- , two- and threefold phosphorilated proteins
The structure shows a fold consisting of a beta-sheet

% EQUATIONS ETC. --------------------------------------------------

non-denaturing gradient gel electrophoresis (r = 0.859) was used
preparations of 5 x 10(8) cfu/ml are made
phosphorylation was observed (P = 0.06)
bacteria with low G + C DNA content contain genes
the strength was in the order of gerE > cotD > yfhP P2 > yfhP P1
delta binds RNAP with an affinity of 2.5 x 10(6) M-1

% "x" between numbers denoting multiplication
A single cell inside a pool of 5 x 10000 lymphocytes could be quantified
A single cell inside a pool of 5 x 10(4) could be quantified

% "Arrows"
We consider the MPO --> PAG pathway
Codon 311 (Cys --> Ser) polymorphism is associated with apolipoprotein E4

% GREEK LETTERS ----------------------------------------------------------
minicells revealed the expression of both lambda and SPP1 genes
We cloned a new gene encoding an alternative sigma factor
The sigma factor sigma 35 of B. thuringiensis is homologous
Each polymerase had a subunit composition analogous to beta beta2 alpha sigma delta omega 1 omega 2

% MISC ADVERB CASES ----------------------------------------------------
% compare
patients are treated, therefore, even if they are negative
patients are treated, however, even if they are negative
% related?
the results indicated, therefore, that it is required

they prefer studies that are, however, open
more importantly , they are open

% i.e., e.g. and related
they were not side-by-side (i.e., stacked)
antagonists (e.g. WEB-2086) were examined 
receptors, e.g. GluR5 and GluR, have been examined
there is genetic heterogeneity, i.e. there are several genes

% UPSTREAM, DOWNSTREAM, 3', 5'
The soil from the river banks is washed downstream.
He was making his way upstream.
The view is upstream and the discharge is about 5.0 m3/s.
It will require more information from upstream.
The inverted repeat is found upstream of the promoter.
The promoter is located immediately upstream of ftsY.
The cryIAb gene was located 3 kb upstream of its initiator codon.
mphR is located downstream from mrx.
These transcripts are oriented 5' to 3'

% MISCELLANIA (commented out not to confuse)
% the patient tested negative

% "MADE OF" VARIANTS
the protein films have a microstructure formed of woven sheaves
The sheaves are composed of well-defined whisker crystallites
Different conjugates, composed of a peptide carrier and a cytotoxic moiety, have been investigated
A study was made of the stability
a protein made of the luminal domain fused to the tail
the intracellular pool of enzyme is formed of newly synthesized molecules

% "DESIGNATED" ETC.
Mice that express epitope tagged SF-1 are being used
The method labelled FAXS is rapid

% ATTACH TO
Isolated eosinophils from healthy donors rapidly attach to ASMC
Dystrophin can attach to the cytoskeleton

% INVESTIGATED, EXAMINED WHETHER
this study examined whether AQP1 is present in HPMC


% from PASBio -------------------------------------------------------

% abolish.01
% MEDLINE No.1
This mutation abolishes splicing
% EMBO No.1 (passive)
Transcription is completely abolished

% alter.01
% MEDLINE No.1
Mutations alter splice sites
% EMBO No.3
Phosphorylation was not altered by treating the cells

% begin.01 ("start existing")
% EMBO No.1
The density begins between amino acids 136 and 140

% begin.02 ("start doing")
% EMBO No.1
The levels begin to return

% block.01
% MEDLINE No.1  ('the' was manually added to "step")
Mutations block the step II
% EMBO No.3 (passive)
Labeling is blocked by pre-incubation

% catalyse.01, ("catalyze") is unknown
% EMBO No.2 
enzymes catalyze the unwinding
% MEDLINE No.1 (passive)
The metabolism is most likely catalysed by P450

% confer.01
% MEDLINE No.2
The variant does not confer a risk
% EMBO No.1 (passive)
The phenotype can be conferred by replacing the C-terminus with Stat5

% decrease.01
% MEDLINE No.1
Treatment decreased synthesis
% EMBO No.2 (passive)
The protection is decreased

% delete.01
% MEDLINE No.1
Transcripts delete exons
% EMBO No.4 (passive)
the binding was deleted

% develop.01 
% MEDLINE No.1 ('a' was manually added to "deficiency")
The son developed a deficiency

% disrupt.01
% MEDLINE No.1
A mutation disrupted a sequence

% eliminate.01
% MEDLINE No.1 
Deletion would eliminate a residue within a domain
% EMBO No.4 (passive)
All three sites are eliminated

% encode.01
% MEDLINE No.1 
Supt4h2 encodes a protein
% EMBO No.1
SBP2 may be encoded by three transcripts

% express.01
% MEDLINE No.1  (passive) ('the' was manually added to "brain")
The enzyme was expressed exclusively in the brain
% MEDLINE No.7
Retroelements express Pol

% generate.01
% MEDLINE No.1
Prnd generates transcripts
% MEDLINE No.7
Molecules are generated by an alternative splicing

% inhibit.01 MEDLINE No.1
This peptide inhibited binding
% inhibit.01 MEDLINE No.2 (passive)
Isoforms are inhibited by rolipram

% initiate.01 MEDLINE No.1 (?)
Tumours had altered mRNAs , initiated within intron 1
% initiate.01 MEDLINE No.2
Cells initiate transcription at multiple sites
% initiate.01 MEDLINE No.3 (intransitive)
Translation initiates from an internal codon

% lead.01 MEDLINE No.1
A mutation leads to ligation
% lead.01 ? (passive)

% lose.01 MEDLINE No.1
A variant which lost a site has been characterized
% lose.01 EMBO No.3 (passive)
Anchoring ability was lost

% modify.01 MEDLINE No.1 (passive)
Genes were modified
% modify.01 EMBO No.2
Factors that can modify the binding may regulate binding

% mutate.01 MEDLINE No.1 (adj?)
% [there may be a problem here with "deficiency"]
The mutated allele resulted in deficiency
% mutate.01 MEDLINE No.2 (passive participle postmodifier)
The gene mutated in mice encodes a protein
% mutate.01 EMBO No.4
The fragments were mutated by the sequence
% mutate.01 ? (active)

% proliferate.01 MEDLINE No.1
Cells are characterized by an ability to proliferate
% proliferate.01 MEDLINE No.2
Cells proliferate
% proliferate.01 ? (passive)

% recognize.01 MEDLINE No.1 (passive participle postmodifier)
The protein would lack epitopes recognized by the serum
% recognize.01 MEDLINE No.3
A number recognized by cells have been isolated
% recognize.01 MEDLINE No.5
Antibodies recognize specifically a polypeptide

% result.01 MEDLINE No.1
We report the existence of isoforms which result from splicing
% result.01 MEDLINE No.2
Both mutations result in high proportions of mRNAs
% result.01 ? (passive)

% skip.01 MEDLINE No.1
sequencing revealed a mutation, which skipped exon 3
% skip.01 MEDLINE No.2
An exon can be skipped by splicing

% splice.01 MEDLINE No.1
exon 30 is spliced together with the intron
% splice.01 PNAS No.4
3I spliced 20% as efficiently as 3F
% splice.01 PNAS No.4 (oversimplified?)
3I spliced

% splice.02 MEDLINE No.1
CD1c has a form that is thought to be spliced out
% splice.02 MEDLINE No.2
One exon is spliced out of the transcript
% splice.02 MEDLINE No.9
Exon 16 can be spliced out

% transcribe.01 MEDLINE No.1
The gene is transcribed
% transcribe.01 MEDLINE No.2
KLK41 transcribes two alternative transcripts

% transform.01 MEDLINE No.1
FGF8b can transform the midbrain into a cerebellum fate
% transform.01 MEDLINE No.3
Phospholipase D is known to transform cells into tumorigenic forms

% transform.02 MEDLINE No.1
The DNA was used to transform E. coli

% translate.01 MEDLINE No.1
Splicing results in a transcript which would be translated into a protein
% translate.01 EMBO No.1
Stat1 was translated
% translate.01 EMBO No.2 (oversimplified? slightly modified)
Stat1 translated can become a dimer

% translate.02 MEDLINE No.1
This review examines technologies that can be used to translate information
% translate.02 MEDLINE No.3
Acj6 translates information into specificity

% translate.03 MEDLINE No.1
The functions translate into modulations

% truncate.01 MEDLINE No.1
Changes were predicted to truncate the protein
% truncate.01 MEDLINE No.2
The domains were truncated

% verbs taking particles
The recombinant plasmid was screened out
The adenine bulge is looped out
A monomer is built up of strands

% "in gel"
% should have been in-gel to be grammatical -- could a spell cheker guess this?
They were measured by in gel kinase assays


% IMPORTANT: CAPITALIZED-WORDS SHOULD ALLOW "that" ETC. (<noun-sub-s> missing)
it encodes a GPCR that is homologous to the chemokine
% compare
it encodes a gPCR that is homologous to the chemokine

% "ORDERED" as an adjective
The complex plays a role in the construction of ordered multicellular structures

% CONCENTRATED as an adjective
the genes were most concentrated in the cell
