Reference Bias Research Articles

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

SummaryLAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads.Availability and Implementationthe source code is freely available at http://last.cbrc.jp/Supplementary information Supplementary data are available at Bioinformatics online.

World Views and Reference BiasWorld Views and Reference Bias

World Views and Reference BiasWorld Views and Reference Bias

Risk Taking Dynamics in Tournaments: Evidence from Professional Golf

Analyzing strategies in tournaments can be difficult to analyze given data limitations. We analyze golfers’ risk taking strategies with a unique data-set from ten seasons of professional golf tournaments and present three major findings. First, as the value of taking on a risk rises, golfers become more likely to adopt risky strategies, a finding that aligns well with classic economic thinking. However, golfers exhibit signs of loss aversion as the total payouts increase. Second, golfers are influenced by a reference bias, which we measure as the difference in their standing in a tournament compared to their world ranking at the time of the tournament. This bias is dynamic throughout the tournament, as risk taking rises as payouts become more imminent. Last, in Tiger Woods’s era of dominance (2004-2009 in our dataset), golfers took on more risk when Woods was in the field compared to events in which he was not. This finding suggests that the superstar forced his rivals to take on more risk than they would have liked, providing an explanation for the superstar effect found in Brown (2011).

Promise and Paradox

We used self-report surveys to gather information on a broad set of non-cognitive skills from 1,368 eighth graders. At the student level, scales measuring conscientiousness, self-control, grit, and growth mindset are positively correlated with attendance, behavior, and test-score gains between fourth grade and eighth grade. Conscientiousness, self-control, and grit are unrelated to test-score gains at the school level, however, and students attending over-subscribed charter schools score lower on these scales than do students attending district schools. Exploiting admissions lotteries, we find positive impacts of charter school attendance on achievement and attendance but negative impacts on these non-cognitive skills. We provide suggestive evidence that these paradoxical results are driven by reference bias or the tendency for survey responses to be influenced by social context.

Discouraged by Peer Excellence

People are exposed to exemplary peer performances often (and sometimes by design in interventions). In two studies, we showed that exposure to exemplary peer performances can undermine motivation and success by causing people to perceive that they cannot attain their peers’ high levels of performance. It also causes de-identification with the relevant domain. We examined such discouragement by peer excellence by exploiting the incidental exposure to peers’ abilities that occurs when students are asked to assess each other’s work. Study 1 was a natural experiment in a massive open online course that employed peer assessment (N = 5,740). Exposure to exemplary peer performances caused a large proportion of students to quit the course. Study 2 explored underlying psychological mechanisms in an online replication (N = 361). Discouragement by peer excellence has theoretical implications for work on social judgment, social comparison, and reference bias and has practical implications for interventions that induce social comparisons.

Meta-analysis of the accuracy of tools used for binary classification when the primary studies employ different references.

The quality of tools used in binary classification is evaluated by studies that assess the accuracy of the classification. The empirical evidence is summarized in 2 × 2 contingency tables. These provide the joint frequencies between the true status of a sample and the classification made by the test. The accuracy of the test is better estimated in a meta-analysis that synthesizes the results of a set of primary studies. The true status is determined by a reference that ideally is a gold standard, which means that it is error free. However, in psychology, it is rare that all the primary studies have employed the same reference, and often they have used an imperfect reference with suboptimal accuracy instead of an actual gold standard. An imperfect reference biases both the estimates of the accuracy of the test and the empirical prevalence of the target status in the primary studies. We discuss several strategies for meta-analysis when different references are employed. Special attention is paid to the simplest case, where the meta-analyst has 1 group of primary studies using a reference that can be considered a gold standard and a 2nd group of primary studies using an imperfect reference. A procedure is recommended in which the frequencies from the primary studies with the imperfect reference are corrected prior to the meta-analysis itself. Then, a hierarchical meta-analytic model is fitted. An example with actual data from SCOFF (Sick-Control-One-Fat-Food; Hill, Reid, Morgan, & Lacey, 2010; Morgan, Reid, & Lacey, 1999) a simple but efficient test for detecting eating disorders, is described.

M-free: Mask-independent scoring of the reference bias.

The M-free score is a heuristic to measure the reference bias in applications such as template matching and sub-tomogram averaging. In the original formulation the mask typically used in these applications had to be separated into a working and a testing area. Here we present a variant of the calculation of the M-free score, which under certain conditions does not require adapting the mask used during the processing. This is made possible by a modified algorithm that allows for arbitrary variances in the testing and in the working area. Consequently, the reference bias can be estimated with knowledge of only the starting reference, the final average and the mask used for processing. We show that the new formulation of the M-free score gives a reliable measure of the reference bias for any sub-tomogram average that has ancillary data, such as when the averaged structure contains density in the periphery, when a complex is attached to a membrane (membrane-associated complexes) or when one subunit is attached to others (e.g. in viruses). Further, we show that in contrast to correlation-based measurements, the M-free score is sensitive to wrong-alignments and contaminations present in the data set. The scope of this new calculation of the M-free score is to reduce the constraints of the previous approach and in certain cases to avoid an adaptation of the mask. The M-free score gives a separate reliability measure for sub-tomogram averaging and template matching.

Duo‐Trio Difference‐Preference Test with Two Replications: Use of Psychological Biases for Measuring Meaningful Preference

AbstractA new paradigm of the duo‐trio difference‐preference (DT‐Preference) test was developed as alternatives to the paired‐preference test with a no preference option, to correct the overestimation of preference responses. Triadic sample presentation in a preference test elicits odd sample bias, i.e., preferring the sample selected as the same as the reference. In the two replicated DT‐Preference test applied for fermented milk product testing using 208 consumers, this psychological bias in preference responses was apparent in the first test. This bias referred to as the tried first reference bias was eliminated by treating those responses that changed depending on which reference was presented as though no preference had been expressed, leading to more reliable sample preferences, meaningful to consumers. The perceptual discriminability in DT‐Preference tests was not decreased in comparison to the sole difference tests, while when the preferred sample was used as a reference, the discrimination increased.Practical ApplicationsConsumer acceptance mainly determines the sensory quality of products. Paired‐preference test with a no preference option is a broadly used sensory acceptance test method. Yet this preference test method suffers from preference bias caused by the order of sample presentation and/or hidden demand characteristic of the preference test. Such a psychological bias can generate preference responses toward either product presented in a pair for slight or no differences in sample preference, which is not meaningful for consumer behavior. The new paradigm of the duo‐trio difference‐preference test with a perceptual reference introduced in this article uses another type of psychological bias – odd sample bias – as a means to regulate such biased preferences expressed in a predictable manner. Using this approach, the validity and reliability of preference data analysis can be improved by finding more accurate response proportions of two‐way preference responses versus no preference responses.

Highly Reliable Reference Bitline Bias Designs for 64 Mb and 128 Mb Chain FeRAMs

This paper presents highly reliable reference bitline bias designs for 64 Mb and 128 Mb chain FeRAM™. The hysteresis shape deformation of ferroelectric capacitor due to temperature variation causes cell signal level shifts of both “1” and “0” data. The reference bitline bias of 64 Mb chip is designed to keep intermediate value of “1” and “0” data at any operating temperatures from ${-}40^{\circ}$ C to 85 $^{\circ}$ C by introducing a modified band-gap reference circuit with 3 bit temperature coefficient trimmers and 6 bit digital-to-analog converter (DAC) using laser fuses. The measured result shows the improvement of tail-to-tail cell signal windows by $\pm $ 22 mV. Moreover, a new reference bias circuit called the “elevator circuit” with 3 bit temperature coefficient trimmers using ferroelectric fuses installed in a 128 Mb chip compensates array operating voltage VAA fluctuation as well as temperature variation. The elevator circuit enables the temperature dependency control at low external VDD of 1.8 V. This improves cell signal window by $\pm $ 40 mV. The elevator circuit also varies reference bitline bias with array operating voltage VAA variation, resulting in improvement of cell signal windows by ${\pm}$ 44 mV in the range of 1.5 V $\pm$ 0.2 V VAA.

Approximate calculation of the potential profile in a graphene‐based device

The study of the transport and noise properties of graphene-based devices requires the computation of the potential profile as a function of the applied bias voltages. However, an exact solution for the potential profile involves a complete self-consistent treatment of the electrostatic and transport equations, which is computationally very expensive. Here, generalising the approach proposed by Das et al., the authors describe an approximate method that allows the evaluation of the potential profile by properly modifying, as a function of the bias voltages applied to the gates, the profile for a reference bias point, which is supposed to be known. The proposed approach is not very demanding from the computational point of view and can be useful for simulations aimed at the interpretation of experimental results or at device design.

Interacting hands: the role of attention for the joint Simon effect.

Recent research in monkeys and humans has shown that the presence of the hands near an object enhances spatial processing for objects presented near the hand. This study aimed to test the effect of hand position on the joint Simon effect. In Experiment 1, two human co-actors shared a Simon task while placing their response hands either near the objects appearing on the monitor or away from the monitor. Experiment 2 varied each co-actor’s hand position independently. Experiment 3 tested whether enhanced spatial processing for objects presented near the hand is obtained when replacing one of the two co-actors by a non-human event-producing rubber hand. Experiment 1 provided evidence for a Simon effect. Hand position significantly modulated the size of the Simon effect in the joint Simon task showing an increased Simon effect when the hands of both actors were located near the objects on the monitor, than when they were located away from the monitor. Experiment 2 replicated this finding showing an increased Simon effect when the actor’s hand was located near the objects on the monitor, but only when the co-actor also produced action events in spatial reference. A similar hand position effect was observed in Experiment 3 when a non-human rubber hand replaced the human co-actor. These findings suggest that external action events that are produced in spatial reference bias the distribution of attention to the area near the hand. This strengthens the weight of the spatial response codes (referential coding) and hence increases the joint Simon effect.

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses: Criticality (keff) Predictions

One of the most significant remaining challenges associated with expanded implementation of burnup credit in the United States is the validation of depletion and criticality calculations used in the safety evaluation—in particular, the availability and use of applicable measured data to support validation, especially for fission products (FPs). Applicants and regulatory reviewers have been constrained by both a scarcity of data and a lack of clear technical basis or approach for use of the data. This paper describes a validation approach for commercial spent nuclear fuel (SNF) criticality safety (keff) evaluations based on best-available data and methods and applies the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The criticality validation approach utilizes not only available laboratory critical experiment (LCE) data from the International Handbook of Evaluated Criticality Safety Benchmark Experiments and the French Haut Taux de Combustion program to support validation of the principal actinides but also calculated sensitivities, nuclear data uncertainties, and limited available FP LCE data to predict and verify individual biases for relevant minor actinides and FPs. The results demonstrate that (a) sufficient critical experiment data exist to adequately validate keff calculations via conventional validation approaches for the primary actinides, (b) sensitivity-based critical experiment selection is more appropriate for generating accurate application model bias and uncertainty, and (c) calculated sensitivities and nuclear data uncertainties can be used for generating conservative estimates of bias for minor actinides and FPs. Results based on the SCALE 6.1 and the ENDF/B-VII.0 cross-section libraries indicate that a conservative estimate of the bias for the minor actinides and FPs is 1.5% of their worth within the application model. This paper provides a detailed description of the approach and its technical bases, describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models, and provides reference bias results based on the prerelease SCALE 6.1 code package and ENDF/B-VII nuclear cross-section data.

Validation of MIPAS IMK/IAA V5R_O3_224 ozone profiles

Abstract. We present the results of an extensive validation program of the most recent version of ozone vertical profiles retrieved with the IMK/IAA (Institute for Meteorology and Climate Research/Instituto de Astrofísica de Andalucía) MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) research level 2 processor from version 5 spectral level 1 data. The time period covered corresponds to the reduced spectral resolution period of the MIPAS instrument, i.e., January 2005–April 2012. The comparison with satellite instruments includes all post-2005 satellite limb and occultation sensors that have measured the vertical profiles of tropospheric and stratospheric ozone: ACE-FTS, GOMOS, HALOE, HIRDLS, MLS, OSIRIS, POAM, SAGE II, SCIAMACHY, SMILES, and SMR. In addition, balloon-borne MkIV solar occultation measurements and ground-based Umkehr measurements have been included, as well as two nadir sensors: IASI and SBUV. For each reference data set, bias determination and precision assessment are performed. Better agreement with reference instruments than for the previous data version, V5R_O3_220 (Laeng et al., 2014), is found: the known high bias around the ozone vmr (volume mixing ratio) peak is significantly reduced and the vertical resolution at 35 km has been improved. The agreement with limb and solar occultation reference instruments that have a known small bias vs. ozonesondes is within 7% in the lower and middle stratosphere and 5% in the upper troposphere. Around the ozone vmr peak, the agreement with most of the satellite reference instruments is within 5%; this bias is as low as 3% for ACE-FTS, MLS, OSIRIS, POAM and SBUV.

Quantitative lead determination in coating paint on children׳s outwear by LA-ICP-MS: A practical calibration strategy for solid samples

Lead is a hazardous compound that affects the central nervous system in people, particularly children, and may cause some reversible and irreversible diseases. Legal regulations try to prevent the exposure from products especially produced for children such as coating paints, jewelry, toys, bed linen, textile, etc. The aim of this study was to determine the lead levels of coating paints on children׳s outwear selling in district bazaar by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and to specify the percent of non-complying samples. Here we described the solid matrix calibration method and confirmed the results with the microwave-assisted acid digestion method. Both comparative methods were validated by analysis of the certified reference materials (NIST SRM-612 glass matrix, NIST SRM-2582 powdered paint and ERM-EC681k) and bias% for accuracy and RSD% for precision were calculated lower than 6.8% and 7.3%, respectively. The recovery ranges of laser ablation and microwave-assisted acid digestion method for Pb were found to be between 88.2–98.1% and 95.3–101.3%, respectively. The limits of detection values were determined as 0.162mgkg−1 for direct sampling in the ablation chamber and 0.002ngmL−1 for aqueous solutions. Correlation result of 16 samples (r=0.99) examined in both methods was satisfactory. In coating paint samples, 14.65% of 198 (n=29) did not comply with the 90mgkg−1 lead limit according to regulation. Validated quantitative laser ablation method may be preferred to quickly and reliably determine the Pb levels in other solid samples as well as coating paints.

A 12 bit 200 MS/s Zero-Crossing-Based Pipelined ADC With Early Sub-ADC Decision and Output Residue Background Calibration

A 12 bit 200 MS/s analog-to-digital converter (ADC) applies techniques of zero-crossing-based circuits as a replacement for high-gain high-speed op-amps. High accuracy in the residue amplifier is achieved by using a coarse phase in ZCBC followed by a level-shifting capacitor for fine phase. Sub-ADC flash comparators are strobed immediately after the coarse phase to achieve a high sampling rate. The systematic offset voltage between the coarse and fine phase manifests itself as systematic offset in the sub-ADC comparators. This offset is caused by the coarse phase undershoot and the fine phase overshoot. In this work, the offset is cancelled with background calibration by residue range correction circuits in the following stage's sub-ADC. In addition, the sub-ADC's random comparator offset is calibrated with a discrete-time charge-pump based background calibration technique. The reference buffer, bias circuitry, and digital error correction circuits are all integrated on a single chip. The ADC occupies an area of 0.282 mm $^{2}$ in 55 nm CMOS technology and dissipates 30.7 mW. It achieves 64.6 dB SNDR and 82.9 dBc SFDR at 200 MS/s for a FOM of 111 fJ/conversion-step. The SNDR degrades gracefully above the designed sampling frequency to 62.9 dB at 250 MS/s, and remains above 50 dB at 300 MS/s.

M-free: scoring the reference bias in sub-tomogram averaging and template matching.

Cryo-electron tomography provides a snapshot of the cellular proteome. With template matching, the spatial positions of various macromolecular complexes within their native cellular context can be detected. However, the growing awareness of the reference bias introduced by the cross-correlation based approaches, and more importantly the lack of a reliable confidence measurement in the selection of these macromolecular complexes, has restricted the use of these applications. Here we propose a heuristic, in which the reference bias is measured in real space in an analogous way to the R-free value in X-ray crystallography. We measure the reference bias within the mask used to outline the area of the template, and do not modify the template itself. The heuristic works by splitting the mask into a working and a testing area in a volume ratio of 9:1. While the working area is used during the calculation of the cross-correlation function, the information from both areas is explored to calculate the M-free score. We show using artificial data, that the M-free score gives a reliable measure for the reference bias. The heuristic can be applied in template matching and in sub-tomogram averaging. We further test the applicability of the heuristic in tomograms of purified macromolecules, and tomograms of whole Mycoplasma cells.

THE HARDER THE TASK, THE HIGHER THE SCORE: FINDINGS OF A DIFFICULTY BIAS

Studies have found that going first or last in a sequential order contest leads to a biased outcome, commonly called order bias (or primacy and recency). Studies have also found that judges have a tendency to reward contestants they recognize with additional points, called reference bias. Controlling for known biases, we test for a new type of bias we refer to as “difficulty bias,” which reveals that athletes attempting more difficult routines receive higher execution scores, even when difficulty and execution are judged separately. Despite some identification challenges, we add to the literature by finding strong evidence of a difficulty bias in gymnastics. We also provide generalizations beyond athletics. (JEL L10, L83, D81, J70, Z1)

Evaluating seasonal loading models and their impact on global and regional reference frame alignment

Seasonal variations are observed in GPS time series, but are not included in the International Terrestrial Reference Frame (ITRF) models. Unmodeled seasonal variations at sites used for reference frame alignment are aliased into the reference frame parameters and bias all coordinates in the transformed solution. We augment ITRF2008 with seasonal loading models based either on Gravity Recovery and Climate Experiment (GRACE) measurements or a suite of models for atmospheric pressure, continental hydrology, and nontidal ocean loading. We model the seasonal components using either annual and semiannual terms or a nonparametric approach. When we include a seasonal variation model, the weighted root-mean-square misfit after seven-parameter transformation decreases for 70–90% of the daily GPS solutions depending on the network and seasonal model used, relative to a baseline case using ITRF2008. When seasonal variations are included in the reference frame solution, the observed seasonal variations are more consistent with the GRACE-based model at 80–85% of the GPS sites that were not used in the frame alignment. The suite of forward models performs nearly as well as the GRACE-based model for North America, but substantially worse for other parts of the world. We interpret these findings to mean that the use of ITRF2008 without seasonal terms causes the amplitude of seasonal variations in the coordinate time series to be damped down relative to the true loading deformation and that the observed GPS time series are more consistent with a TRF model that includes seasonal variations. At present, a seasonal model derived from GRACE captures seasonal variations more faithfully than one based on hydrologic models.

Determination of Boron in Silicon Carbide by ICP-OES and ICP-MS after Sample Preparation using Pyrohydrolysis

Pyrohydrolysis was used for sample preparation of silicon carbide (SiC) and subsequent determination of B using inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS). Important parameters for pyrohydrolysis method as temperature, air and water flow rates, reaction time and use of V2O5 were evaluated. In addition, a study of W spectral interference on B emission lines was evaluated for ICP-OES determination. Accuracy was evaluated using certified reference material (CRM BAM S003) and bias value lower than 1% between the certified and determined value was achieved. Limit of detection (LOD) of 0.010 μg g−1 was obtained using pyrohydrolysis and ICP-MS. Pyrohydrolysis is a very simple sample preparation method that allowed the use of deionized water as absorbing solution for B determination in SiC.

Finding trimeric HIV-1 envelope glycoproteins in random noise

In two recent papers, Mao et al. (1, 2) present the trimeric structure of the HIV-1 gp160 trimer at 11- and 6-A resolutions, respectively. The authors repeatedly emphasize their “reference-free,” “gold standard” methodology, but in neither of their papers do they state how the particles were selected from the electron micrographs. They do state (figure S3 in ref. 1): “Each row shows a sequence of average images from the same projection class, progressing from the initial average to the converged average,” and “refinements started without an external or prior reference images and did not assume any symmetry.” These projection classes thus must have existed prior to the refinements, as the result of an explicit search for specific molecular views, namely projection images generated from an earlier 3D structure. Because the reference bias is introduced at this earlier stage, it becomes irrelevant that the projection classes can be averaged without using further references or symmetry assumptions. In contrast to local-variance particle detection (3), correlation function picking looks for specific views in specific orientations and may introduce reference bias (4), as do all forms of reference-based alignment (4, 5). My best guess is that an earlier structure (EMDataBank EMD-5019) was used to pick particles in ref. 1.