Gazing into space: Systematic biases in determining another's fixation distance from gaze vergence in upright and inverted faces

Reference method for simultaneous calibration of the three and more measurement standards for vertical angle measurement is developed. This method can to use for obtaining the systematic biases of the vertical angles measurements for each of the measuring standards relative of the horizontal plain was averaged from measurement results in time their calibration or comparison. For realization of the reference method was developed the autocollimationel electronic measurement standard for the automatization measurement of the vertical angles SeaLineZero_Standard™ (SLZ_S™). Summary standard deviation (k=1) of the vertical angle measurement relative the horizontal plane, from the results of their calibration by reference method, is not more 0,07ʺ…0,15ʺ. This result was obtained without the use the systematic biases, for each measurement standards, as measurements corrections (with opposite sign). The measuring standards, that were developed and researched, are necessary for obtaining the systematic biases of the vertical angle measurement for total stations and theodolites, that have the normed standard error 0,5ʺ and 1ʺ, when these instruments are calibrating.

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SAUTE: sequence assembly using target enrichment

BMC Bioinformatics ◽

10.1186/s12859-021-04174-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Alexandre Souvorov ◽

Richa Agarwala

Keyword(s):

De Bruijn Graph ◽

Challenging Problem ◽

Target Enrichment ◽

Rna Seq ◽

Sequencing Technology ◽

Insert Size ◽

Systematic Biases ◽

Target Sequences ◽

Genomic Regions ◽

Higher Sensitivity

Abstract Background Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions. Results To facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose SAUTE and SAUTE_PROT assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for SAUTE and SAUTE_PROT, respectively. Conclusions For RNA-seq, comparisons with Trinity, rnaSPAdes, SPAligner, and SPAdes assembly of reads aligned to target proteins by DIAMOND show that SAUTE_PROT finds more coding sequences that translate to benchmark proteins. Using AMRFinderPlus calls, we find SAUTE has higher sensitivity and precision than SPAdes, plasmidSPAdes, SPAligner, and SPAdes assembly of reads aligned to target regions by HISAT2. It also has better sensitivity than SKESA but worse precision.

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Evaluation of four different HPLC devices for hemoglobinopathy screening

Turkish Journal of Biochemistry ◽

10.1515/tjb-2019-0484 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Müjgan Ercan Karadağ ◽

Emiş Deniz Akbulut ◽

Esin Avcı ◽

Esra Fırat Oğuz ◽

Saadet Kader ◽

...

Keyword(s):

Gold Standard ◽

High Performance ◽

Public Health Problem ◽

Reference Value ◽

Comparison Study ◽

Gold Standard Method ◽

Blood Samples ◽

Systematic Biases ◽

Hemoglobin Variants ◽

Thalassemia Screening

AbstractObjectiveHemoglobinopathies are a common public health problem in Turkey. In the screening of these disorders in population, cation-exchange high performance liquid chromatography (HPLC) is accepted as the gold standard method. In this study, the aim was to assess four different HPLC devices used in hemoglobinopathy screening.Materials and methodsA total of 58 blood samples were analyzed with four different HPLC methods (Bio-Rad variant II, Agilent 1100, Tosoh G8 and Trinity Ultra2 trademarks).ResultsThe comparison study demonstrated a good correlation between the results of each HPLC analyzer and the reference value obtained by averaging all the HbA2 results belonging to the methods tested in the study [ (Tosoh G8 (r=0.988), Bio-Rad variant II (r=0.993), Agilent 1100 (r=0.98) and Trinity Ultra2 (r=0.992) ]. HbA2 determination in the presence of HbE was interfered in both Bio-Rad variant II and Tosoh G8.ConclusionThe analyzers were found to have compatible HbA2 results but with accompanying different degrees of proportional and systematic biases. HPLC analyzers may be affected by different hemoglobin variants at different HbA2 concentrations, which is an important point to take into consideration during the evaluation of HbA2 results in thalassemia screening.

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Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Database ◽

10.1093/database/baz085 ◽

2019 ◽

Vol 2019 ◽

Author(s):

Peter Brown ◽

Aik-Choon Tan ◽

Mohamed A El-Esawi ◽

Thomas Liehr ◽

Oliver Blanck ◽

...

Keyword(s):

Literature Search ◽

Relevant Literature ◽

Biomedical Literature ◽

Medical Subject Headings ◽

Document Similarity ◽

Inverse Document Frequency ◽

Research Fields ◽

Experience Levels ◽

Document Frequency ◽

Systematic Biases

Abstract Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

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Systematic biases in large-scale estimates of wetland methane emissions arising from water table formulations

Geophysical Research Letters ◽

10.1029/2010gl045450 ◽

2010 ◽

Vol 37 (22) ◽

pp. n/a-n/a ◽

Cited By ~ 25

Author(s):

Theodore J. Bohn ◽

Dennis P. Lettenmaier

Keyword(s):

Water Table ◽

Large Scale ◽

Methane Emissions ◽

Systematic Biases

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Evolution, lies, and foresight biases

Behavioral and Brain Sciences ◽

10.1017/s0140525x10002128 ◽

2011 ◽

Vol 34 (1) ◽

pp. 38-39 ◽

Cited By ~ 6

Author(s):

Thomas Suddendorf

Keyword(s):

Arms Race ◽

Hominin Evolution ◽

Systematic Biases

AbstractHumans are not the only animals to deceive, though we might be the only ones that lie. The arms race von Hippel & Trivers (VH&T) propose may have only started during hominin evolution. VH&T offer a powerful theory, and I suggest it can be expanded to explain why there are systematic biases in human foresight.

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