ライフサイエンスコーパス: read

1 n a specific cognitive/linguistic task (e.g. reading).

2 speed and accuracy of lexical and sublexical reading).

3 ut of epigenetic modifications from a single read.

4 ith real cells from those binding background reads.

5 errors from both simulated data and the raw reads.

6 mplate and demanding consensus over multiple reads.

7 em of assembling centromeres from translated reads.

8 ification of plasmid sequences from Illumina reads.

9 netic variants detected within the scRNA-seq reads.

10 embled from short Illumina 150 bp paired-end reads.

11 rated long accurate Pacific Biosciences HiFi reads.

12 A), which otherwise dominates transcriptomic reads.

13 appa = 0.48 +/- 0.14 SEM) with the consensus reading.

14 se of cancers detected at radiologist double reading.

15 st, further illustrating its crucial role in reading.

16 al code potentially contributes to efficient reading.

17 gnizing the lack of emotion in body language reading.

18 al locations while the participants silently read a boring text in front of them.

19 Each scenario was then repeated while reading a 2-minute script, simulating a talking patient.

20 ven proper time conditioned on another clock reading a different proper time is derived.

21 nsidered a text mining problem that requires reading a lot of academic documents for identifying a sm

22 The probability that one clock reads a given proper time conditioned on another clock r

23 contrast, classical behavioral predictors of reading abilities and the ability to benefit from visual

24 pability of LVAs to successfully restore the reading ability in patients with corneal diseases, which

25 very timely and will be a refreshing take on reading about opioids and disease.

26 pore with two constrictions improved single-read accuracy by 25 to 70% in homopolymers up to 9 nucle

27 ibility and the need to fill data gaps using read-across approaches.

28 reads with high confidence for multiple long-read aligners including Minimap2 (74.3-90.6%) and BLASR

29 Read alignment is central to many aspects of modern geno

30 nomic HPV genotyping algorithms use a simple read-alignment and filtering strategy that has difficult

31 aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable

32 cific fluorescence signals which were easily read and analysed by our programmed smartphone.

33 es as a mechanical band-pass filter, able to read and interpret frequency-dependent mechanical inform

34 incorporation of information both from short-read and long-read DNA sequencing technologies.

35 High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) r

36 thout regional perfusion defects on clinical read and no known macrovascular coronary artery disease

37 829 patients aged 18 years or older, able to read and write Italian and hospitalized for at least 3 d

38 iding the missing link between body language reading and limbic pathways.

39 increasing non-native language proficiency, reading and speech comprehension displayed substantial c

40 cs of cancers detected at radiologist double reading and those detected through quality assurance ses

41 d assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single indivi

42 from discordant paired-end alignments, split-reads and read depth information to improve upon existin

43 ize-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a

44 iphages contributed up to 12% of all viromic reads annotated in the analysed viromes.

45 y as well as those deposited in the Sequence Read Archive (SRA) database.

46 ister interactions based on the strands that reads are mapped to.

47 On average, 0.5-1 million unique mapped reads are obtained for each single cell.

48 These long reads are used to construct an assembly (i.e. the subjec

49 trical stimulation of this region results in reading arrest, further illustrating its crucial role in

50 rasounds at 1 year were equally likely to be read as normal (85.7% in TT vs 85.1% in pCND, P = 1.00).

51 By CryptoPS, 52 samples were read as positive, with 88% sensitivity (50/57; 95% CI, 0

52 In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic da

53 ss and contiguity than state-of-the-art long-read assemblers.

54 scientists, and students in performing long-read assembly of bacterial and bacteriophage genomes and

55 tanding the power and limitations of various read assembly programs in practice is important for rese

56 The resulting accumulation of reads at the start site may be especially useful for det

57 these variables, information is continuously read back into the active membrane state for processing.

58 ctivation in response to OW expectancy or OW reading between groups (CW as baseline).

59 with dual-energy CT and MRI, and images were read by four readers who were blinded to clinical inform

60 se shape into a cortical pattern that can be read by the spindle, which then guides the axis of cell

61 brain dialysate fluid sample and demonstrate reading by comparing with a gold-standard spectrometry t

62 232 patients were included, and a consensus reading by three specialized pathologists was used.

63 lies, and increased the proportion of mapped reads by up to 13.3% compared to standard references.

64 prone third-generation sequencing (TGS) long reads can be corrected by the high-quality second-genera

65 of written health information must match the reading capacities of the target audience.

66 tively from existing anonymized Doheny Image Reading Center datasets.

67 Two masked reading center graders (N.S., J.S.) independently and bl

68 ken at baseline and annually, were graded by reading center graders masked to clinical data.

69 .0 mg and were treated according to the same reading center-guided T&E regimen after 3 initial monthl

70 luated in a masked fashion at an independent reading center.

71 ingle-molecule, real-time shotgun sequencing reads collinear with an optical map.

72 studies of microbial communities, the short reads come from mixtures of genomes.

73 ment gap will decrease, given the stagnating reading competencies in most countries.

74 A challenge of next generation sequencing is read contamination.

75 We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal

76 biome analysis workflows often normalize the read counts prior to downstream analysis.

77 ular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a

78 Samples underwent small RNA sequencing, and read counts were normalized and filtered by depth and co

79 , it is inaccurate because of relatively low read counts.

80 ble, VALERIE displays PSI values, in lieu of read coverage, which is more suitable for representing a

81 Encoding the reference genome and aligned reads covering sites of genetic variation as numeric ten

82 bilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites.

83 not designed to incorporate long- and short-read data from mother-father-child trios, and therefore

84 ing have made HLA typing from standard short-read data practical.

85 ire relatively high coverages of costly long-read data to produce high-quality assemblies.

86 713 additional variants supported by linked-read data were identified.

87 Incorporating seven linked-read de novo assemblies and three existing assemblies, t

88 igh RNA background (n = 1), insufficient RNA read depth (n = 3), or quality control (QC) failure with

89 Analysis of read depth finds mixed evidence that up to 4% of the sha

90 ool that utilizes next-generation sequencing read depth information and variant allele frequency patt

91 rdant paired-end alignments, split-reads and read depth information to improve upon existing methods.

92 e ability of nanopore sequencing to directly read DNA modifications.

93 Third-generation long-read DNA sequencing technologies are increasingly used,

94 of information both from short-read and long-read DNA sequencing technologies.

95 Single-molecule long-read DNA sequencing with biological nanopores is fast an

96 med scores from the emotional, mobility, and reading domains of the Impact of Visual Impairment (IVI)

97 and refined analysis of metagenomic data to read error correction and reference-free haplotype recon

98 both temporal and occipital lobes predicted reading errors.

99 We also report high accuracy for long reads even at relatively low coverage (25x-30x).

100 ools: Quality Control, Read Subsampling, and Read Filtering.

101 , and clinicians were trained to effectively read fluorescent margins with a short guided instruction

102 d RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification

103 ines two organisms and (ii) separate sets of reads for several reference genomes of known origins.

104 workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the unde

105 ranslated from nonannotated Alternative Open reading frame (AltORFs) were discovered using customized

106 s during virus replication, although an open reading frame (ORF) is retained among an unknown percent

107 To address this, we replaced the NSP3 open reading frame (ORF) of the segment 7 (pT7/NSP3) transcri

108 NA1 dsRNA is 1,683 bp in length with an open reading frame (ORF) that encodes 539 amino acids (molecu

109 tional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human disea

110 in encoded in part by a +1 frameshifted open reading frame (X-ORF) in segment 3.

111 o2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be

112 ls), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing sho

113 s that contained mutations in the viral open reading frame 5 (ORF5) protein.

114 ted expression of CXorf67 (chromosome X open reading frame 67), which frequently occurs in PFA ependy

115 f a pathogenic mutation in chromosome 9 open reading frame 72 (C9orf72), progranulin (GRN) or microtu

116 e of Pfn2 or overexpression of the Pfn2 open reading frame alone in otherwise wild-type cells largely

117 eye mutant strain had an intact transposase reading frame and terminal sequences consistent with fun

118 an immunogenic peptide derived from an open reading frame downstream of the melanoma stem cell marke

119 Mutations that shift the reading frame generally cause gene inactivation and in e

120 s mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N (6)-erA

121 analysis demonstrated that KSHV latent open reading frame K12 (ORFK12) gene (kaposin A)-mediated dec

122 a library of fragments derived from an open reading frame of interest and enriching for the interact

123 the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the

124 PrEP), we performed KSHV typing with K1 open reading frame Sanger and KSHV whole-genome sequencing.

125 Both are encoded by a single 870-bp open reading frame that exhibits genetic polymorphisms in hum

126 region was found to contain an upstream open reading frame that is required for Pi-responsive express

127 s a consensus 3' splice site that shifts the reading frame, and creates a premature stop codon downst

128 icistronic viruses but contain a single open reading frame, thus likely representing a recent example

129 smid DNA encoding the 3.9 kb human NPC1 open reading frame, under the influence of a 1.5 kb platelet

130 o embryos with non-mosaic restoration of the reading frame.

131 at induces exon skipping to restore the open reading frame.

132 indings demonstrate the utility of ASO-based reading-frame correction as an approach to treat CLN3 Ba

133 Novel open reading frames (nORFs) with coding potential may arise f

134 have revealed abundant expressed short open reading frames (ORFs) in bacteria.

135 s of HIV-RNA transcripts with competent open reading frames (ORFs), and can be found in the periphera

136 ncoding distinct repeat epitopes in two open reading frames (ORFs), one translated from the 5' cap, a

137 In addition to canonical open reading frames (ORFs), thousands of translated small ORF

138 , identification of actively translated open reading frames (ORFs), to the quantification of translat

139 d analysis of the remaining alleles for open reading frames (ORFs).

140 Upstream open reading frames (uORFs) are known to control the translat

141 Upstream open reading frames (uORFs) are tissue-specific cis-regulator

142 ved thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to t

143 Also, SSP-coding small open reading frames are often expressed at low levels or only

144 o saturation of inserts adjacent to all open reading frames as well as conventional inactivation.

145 o (SD) sequences positioned upstream of open reading frames facilitate translation initiation.

146 ludes those lncRNA gene loci with small open reading frames from being regarded as protein-coding.

147 Two open reading frames predicted from the genomic islands coded

148 generate multiple proteins from overlapping reading frames within its RNA genome.

149 We identified 220 OR open reading frames, 20 of which are full length, intact OR g

150 Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in

151 tation pipelines generally ignore small open reading frames, which are those most likely to encode SS

152 tiple microproteins encoded in upstream open reading frames, which form stable complexes with the mai

153 GR), and the biosynthetic trpB and trpA open-reading frames.

154 lutionary record of variation and divergence read from sequence comparisons.

155 algorithms can only polish an assembly using reads from either a certain sequencing technology or a s

156 ng reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, c

157 rk the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from kno

158 guity and accuracy of the assembly using the reads from the known genomes.

159 he challenge of translating long error-prone reads from the nucleotide alphabet into the alphabet of

160 The inputs are (i) the set of mixed reads generated from a sample that combines two organism

161 The mean consensus reading grade level was similar between academic (11.73

162 ology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%).

163 e PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respect

164 Sustained gazing, such as in silent reading, has a measurable negative impact on visual perf

165 A effectively reduces highly abundant hgbRNA reads; however, it does not result in a statistically si

166 ess in the distribution of inter-chromosomal reads in the scHi-C contact matrix to measure the level

167 icult problem of assembling centromeres from reads (in the nucleotide alphabet) into a more tractable

168 The accurate translation of reads into the monomer alphabet turns the notoriously di

169 Lip-reading is known to improve auditory speech understandin

170 hat population-level resequencing using long reads is likely to provide novel insight into the evolut

171 Rapid Electro-Analytical Device (READ) is a point-of-care device that uses impedance chan

172 We read jubmled wrods effortlessly, but the neural correlat

173 esulted in 44% of the genome covered by >= 5 reads), leading to an average 14-fold increase in genome

174 ing' technologies produce a relatively short read length and demand a reverse-transcription step, pre

175 was to determine how library size selection, read length and format, protein database, e-value thresh

176 d by the loss of native modifications, short read length, high input requirements, low yield or long

177 d Nanopore Technology (ONT) with exceptional read length.

178 ation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and it

179 ral variant (SV) analyses are limited by NGS read lengths.

180 genome bisulfite sequencing datasets reveals read-level signatures associated with cell type and cell

181 We assessed read loss during mapping and designed a graph-based clas

182 ion (defined as peripheral oxygen saturation reading < 80% during intubation).

183 We also provide a method to count reads mapping to peaks across samples, which can be used

184 to conventional RNA-Seq, hsRNA-Seq increased reads mapping to the Bacteroides fragilis genome by 48-

185 arily include similar basic functionality to read mass spectral data from standard file formats, proc

186 lenge of assembling viral genomes from short-read metagenomes.

187 The annotation of short-reads metagenomes is an essential process to understand

188 bromo-associated BAF factor), which involves reading of acetylated histone tails by the bromodomain-c

189 ference standard for fracture was a combined reading of MRI and dual-energy CT scans.

190 sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 u

191 ome was mean change in VA (number of letters read on a logarithm of the minimum angle of resolution c

192 es strain-mediated magnetoelectric write and read operations simultaneously in Co(60)Fe(20)B(20)/Pb(M

193 strand sequencing(1,2) with continuous long-read or high-fidelity(3) sequencing data.

194 of inherent sampling bias and unidentifiable read origins.

195 e molecular junction, and the information is read out by monitoring the electrical conductance of eac

196 ing tissue development could be harnessed to read out lineage relationships after a single step of cl

197 e of hierarchical processing as higher areas read out locations in chromatic space from progressive i

198 nsitions with an optical frequency comb, and read out the final state nondestructively, leaving the m

199 We have developed a micro-pixel read-out anode technique that significantly saves power

200 y reversible, thus representing a principled read-out for the neurophysiological assessment of stroke

201 oosted on average a 30 fold chemiluminescent read-out of the biosensor.

202 e and to enhance the optical interferometric read-out signal.

203 um technologies are qubit initialization and read-out.

204 cteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which requir

205 tion is to sequence at a depth of around one read per cell per gene.

206 mor RNA-seq data with a few hundred thousand reads per sample provide sufficient information for outc

207 e syllabic content of SiN account for global reading performance (i.e., speed and accuracy of lexical

208 gies there remains a trade-off between short-read platforms, having limited ability to sequence homop

209 or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or

210 d signal, while separation of subnucleosomal reads post-sequencing did not improve signal or peak cal

211 ich the AI system participated in the double-reading process that is used in the UK, and found that t

212 antum computer able to manipulate, store and read quantum information with a high degree of fidelity.

213 low modulation flicker fusion threshold and reading rate for the two subgroups were significantly di

214 Long nano-COP reads reveal that, in human and Drosophila cells, splici

215 sing chemical modifications with direct long-read RNA sequencing and machine learning to detect secon

216 fication of full-length transcripts in short-read RNA-Seq data, which encourages the development of m

217 NAs, parallel analysis of RNA ends/degradome reads, RNA sequencing, and even chromatin immunoprecipit

218 considering only the supine chest radiograph reading score 2 as positive for pneumonia.

219 s with amusia (N = 15) and controls (N = 15) read sentences where a comma indicated a grammatical phr

220 Using long-read sequence data we obtained complete sequences of two

221 f plasmid epidemiology based solely on short-read sequence data.

222 sembly of a human genome using nanopore long-read sequences has been reported, but it used more than

223 across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containing prot

224 Here we incorporated long-read sequencing and state-of-the-art scaffolding protoco

225 amples that are suitable for downstream long-read sequencing applications.

226 Long-read sequencing coupled with bioinformatics tools enable

227 , deletions, and translocations using linked-read sequencing data.

228 GEs and their insertion sites by using short-read sequencing data.

229 Although long-read sequencing improves this issue, it is not amenable

230 These findings highlight the need for long-read sequencing of cancer genomes for the precise analys

231 High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comp

232 Recent advances in long-read sequencing solve inaccuracies in alternative transc

233 h with an accuracy approaching that of short-read sequencing technologies, these platforms have prove

234 Using long-read sequencing technologies, we provide a high-quality

235 inducibility of meropenem resistance, short read sequencing was performed using an Illumina NextSeq5

236 We combine long-read sequencing with a Hi-C-based proximity guided assem

237 mic region and, using third generation, long-read sequencing, we identified a 120 kb insertion in the

238 With long-read sequencing, we obtained chromosome-level genome seq

239 r-related genes detectable only through long-read sequencing.

240 resent megabase inversions confirmed by long read sequencing.

241 of which are physically phased using linked-read sequencing.

242 l is to provide a single algorithm that uses read sets from all available sequencing technologies to

243 dings in an artificial intelligence-assisted reading setting.

244 known taxonomic and gene abundances of short-read shotgun metagenomics sequencing data.

245 onstrate that the brain can use a silent lip-read signal to synthesize a coarse-grained auditory spee

246 alent, 20/800) and 70 or fewer ETDRS letters read (Snellen equivalent, 20/40) in the study eye.

247 ptome of C. elegans Taking advantage of long reads spanning the full length of mRNA transcripts, we p

248 ferent cognitive components recruited during reading, spatial judgments, and visual exploration.SIGNI

249 atients and control subjects with respect to reading speed (172 vs 180 wpm, respectively; P = 0.21) o

250 reading, the dry eye patients had decreased reading speed and increases in the length of time to rea

251 Black background enables fastest reading-speeds, probably due to less blinding.

252 ram containing three tools: Quality Control, Read Subsampling, and Read Filtering.

253 mbly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ran

254 A delayed word reading task was administered inside MEG to assess tDCS-

255 arch, and responses to jumbled words in word reading tasks.

256 n the compression of data generated by short-read technologies.

257 With the ability to generate reads tens to thousands of kilobases in length with an a

258 Importantly, the paired-end reads that are properly aligned to the bovine Y sequence

259 on sequencing technologies can sequence long reads that contain as many as 2 million base pairs.

260 wpm, respectively; P = 0.21) or the time to read the excerpt (33 vs 30 seconds, respectively; P = 0.

261 t is with great interest and sadness that we read the experience of Akalin et al. and Pereira et al.

262 NA sequencing, is required to simultaneously read the key and the data.

263 speed and increases in the length of time to read the passage compared to baseline (161 vs 172 wpm, r

264 We carefully read the recently published research letter "Is asthma p

265 NAs (tRNAs) are well known for their role in reading the codons on messenger RNAs and translating the

266 After silent reading, the dry eye patients had decreased reading spee

267 increase in the average size of the produced reads, the reduction in their cost and the portability o

268 ransgene robustly silenced transcription and read through its polyadenylation sequence.

269 corporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs.

270 Here, we demonstrate translational read-through across two evolutionarily conserved, in-fra

271 e experiments demonstrate that translational read-through drugs are able to suppress the Mecp2 p.R294

272 iple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing.

273 ligation gives a urea linkage with excellent read-through speed, or a squaramide linkage that is read

274 rough speed, or a squaramide linkage that is read-through under selective conditions.

275 MTCH2 read-through-deficient cells, generated using CRISPR-Cas

276 mum sequencing depth of 5 million merge-able reads to enable detection of specific target genes.

277 developed MRLR, a software using 10X linked reads to identify crossover events at a high resolution.

278 cess both uniquely aligned and multi-aligned reads to produce accurate abundance estimates.

279 After we filtered reads to remove sequences of mouse origin, the actual in

280 e sequence datasets can contain terabytes of reads, too many to be coassembled together on a single s

281 It recruits organelle-associated reads using a modified "baiting and iterative mapping" a

282 different alignment methodology, or aligning reads using different parameters, on quantification esti

283 ps with variants and adversely impacts short-read variant calling.

284 roteomic and osteological estimates when DNA reads were above 100,000 total sequences.

285 931,698 reads were annotated into 11,676 coding sequences (CDS),

286 Results from two independent reads were compared.

287 CMV reads were identified in 120 (5.4%) samples.

288 he sequence results indicated that 68.90% of reads were Y chromosome-related sequences as they are ho

289 It is important to read what the authors have written and to pay attention

290 ity second-generation sequencing (SGS) short reads, which is referred to as hybrid error correction.

291 Long-read whole genome sequencing was performed using Pacific

292 Short-read whole-genome sequencing data are often applied to l

293 ally, using a combination of short- and long-read whole-genome sequencing, we found no significant as

294 Access to deep and accurate long reads will facilitate prediction of key beneficial mutat

295 We read with interest the article by Baiges et al [1] which

296 increased the percentage of correctly mapped reads with high confidence for multiple long-read aligne

297 overlap detection algorithms, especially for reads with relatively short overlapping lengths.

298 e bit error rates as low as 0.11% for single reads, without library purification.

299 mantic impairments including difficulties in reading words with exceptional orthographic to phonologi

300 Here we discuss the range of read-write genome changes found in two well-studied kine