Copy Error Research Articles

Learning mimetic cuckoo call innovations from neighbors in a Chinese songbird

Some oscine passerines incorporate heterospecific sounds into their repertoires, including vocalizations of other bird species, sounds of other fauna, and even anthropogenic sounds, through vocal mimicry. However, few studies have investigated whether mimics learn heterospecific sounds from model species or from conspecific tutors. Here, we investigate mimicry acquisition using innovation in Cuculidae calls imitated by the Chinese blackbird (Turdus mandarinus). If the mimicry innovation arises and spreads among several neighbors and is not produced by model species, the mimicry must be acquired partially from conspecifics. We found that: (1) Cuculidae calls imitated by blackbirds were reasonably accurate, but with some differences between mimetic and real calls in acoustic structures. (2) We identified four unique mimetic units (mimicry innovation or copy errors), and these units only occurred at certain sites and were shared by several neighbors. In aggregate, frequency parameters (the first principal component) of unique mimetic units were higher than usual mimetic units (p < 0.001). Our findings provide further evidence that mimetic units can be partially learnt from conspecifics based on four cases of unique mimetic units. Our study and approach provide a reference and theoretical basis for the future understanding of social learning and development of vocal mimicry.

Phase I Pharmacokinetics Study of Oral Administration of Esperavir® (INN: Molnupiravir) (LLC "PROMOMED RUS", Russia)

Introduction. The pandemic of the new coronavirus infection COVID-19 (Coronavirus Disease 2019) was caused by a single-stranded RNA virus SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus 2). Molnupiravir is an antiviral drug with activity against RNA viruses including SARS-CoV-2. Molnupiravir exerts the antiviral effect by introducing copy errors during viral RNA replication – by that the replication of SARS-CoV-2 inhibits. For oral administration of molnupiravir the drug Esperavir® has been registered in Russia.Aim. The aim is pharmacokinetics study of Esperavir®, capsules 200 mg (the manufacturer is JSC "Biokhimic", LLC "PROMOMED RUS", Russia, as registration certificate holder) by a single dose (800 mg) and multiple doses oral administration (800 mg twice a day with a gap of 12 hours between doses) in healthy volunteers in a phase I pharmacokinetics study, comparison the obtained data of pharmacokinetic parameters with the literature data.Materials and methods. The clinical and analytical phases of the pharmacokinetic study as well as pharmacokinetic analyses have been performed as a part of a clinical trial of the drug Esperavir®, capsules 200 mg (the manufacturer is JSC "Biokhimic", LLC "PROMOMED RUS", Russia, as registration certificate holder). Chromatographic separation and detection by Nexera XR high-performance liquid chromatograph with triple quadrupole tandem mass spectrometry LCMS-8040 (Shimadzu Corporation, Japan). The pharmacokinetic parameters were calculated with the Boomer pharmacokinetic analysis add-in for Microsoft Excel (Department of Pharmacokinetics and Drug Metabolism, Allergan, Irvine, CA 92606, USA). Descriptive pharmacokinetic statistics were calculated with Microsoft Excel (Microsoft Corporation, USA).Results and discussion. Pharmacokinetic parameters for cohort 1 (800 mg single dose of Esperavir®) and for cohort 2 (800 mg of Esperavir® twice a day with a gap of 12 hours between doses) were calculated. Averaged pharmacokinetic profiles of mean NHC concentrations over time in linear and log-linear scales were plotted. The geometric mean of Cmax and T1/2, the median, minimum and maximum of Tmax showed the comparability of the obtained data after a single dose administration of 800 mg of Esperavir® and the available literature data.Conclusion. According to the concentrations from the analytical phase of the pharmacokinetic study the pharmacokinetic parameters were calculated, averaged pharmacokinetic profiles in linear and log-linear scales were plotted after a single dose and multiple doses of the drug Esperavir®, capsules (the manufacturer is JSC "Biokhimic", LLC "PROMOMED RUS", Russia, as registration certificate holder). The comparability of the obtained data and the available literature data was shown. The results justified the study of the subsequent phases of clinical trials of Esperavir®.

Impact of panel size on minimum residual disease (MRD) assay performance.

e15022 Background: Sequencing circulating tumor DNA is a promising method for monitoring cancer treatment response and detecting recurrence, but sensitivity at the low tumor fractions typical of early-stage, post-treatment, and early recurrent tumors is limited by the small number of variants targeted in commercially available assays. Methods: We developed a tumor-informed minimum residual disease (MRD) assay using tumor-normal whole-genome sequencing (WGS) followed by interrogation of select somatic variants in cell-free DNA (cfDNA). We describe theoretical limits on panel designability as a function of tumor purity and sequencing depth using simulations and a discovery cohort of 31 patient samples. cfDNA assay performance was tested by creating serial dilutions of patient plasma before somatic enrichment and sequencing. Simulations and in-silico downsampling of target sites were used to test sensitivity as a function of panel size. A bioinformatics pipeline incorporating somatic calling, copy number inference, error assessment, and tumor-fraction estimation was developed to analyze results. Results: Across a range of tissues, tumor-normal WGS identified from hundreds to tens of thousands of somatic variants to inform an MRD capture panel. 97% of samples tested returned at least 300 high-confidence somatic variants, and targeted sequencing demonstrated over 95% positive predictive value in somatic variant calls. In cfDNA dilution experiments, we observed &gt; 99% sensitivity at a tumor fraction of 0.01%. Expanding the panel size from 16 to 300 target variants increased sensitivity at 0.005% tumor fraction from approximately 20% to &gt; 95%. Our tumor fraction model returned accurate quantification down to the parts per hundred thousand (0.001%) range, even when only a single tumor molecule could be observed at each target site. Conclusions: Increasing the number of targeted variants in an MRD assay increases sensitivity at low tumor fractions, and WGS-driven panel design ensures a sufficient number of interrogated variants while minimizing the failure rate due to panel designability. High sensitivity MRD has the potential to enable earlier recurrence detection while also giving researchers and clinicians new tools for monitoring patient treatment responses.

Cross-cultural forager myth transmission rules: Implications for the emergence of cumulative culture

For most of human evolution, accumulated cultural knowledge has been stored in memory and transmitted orally. This presents a daunting information management problem: how to store and transmit this knowledge in a portable format that resists corruption. One solution–widespread among foragers–is to encode knowledge in narrative. However, this strategy depends on accurate performance of the story. Significantly, some forager cultures have rules regulating myth performance, although the extent of this phenomenon is unknown. We hypothesize that these rules subserve high-fidelity transmission across generations. Accordingly, we predicted that, across forager cultures, myth-telling rules will mandate: (P1) transmission by the most proficient storytellers (P2) under low-distraction conditions with (P3) multiple individuals and (P4) multiple generations present, and the application of measures that (P5) prevent, identify, and/or correct errors, (P6) maintain audience attention, (P7) discourage rule violations and/or (P8) incentivize rule compliance. To test these predictions, we searched the forager ethnographic record for descriptions of myth performance, and coded them for prescriptions/proscriptions regarding narrator age, performance context, audience composition, narrative delivery, and audience comportment, as well as sanctions associated with rule transgression or compliance. Results indicate that rules regulating myth performance are widespread across forager cultures, and are characterized by features that reduce the likelihood of copy errors. These findings help elucidate the role that anthropogenic ratchets played in the emergence of cumulative culture.

Evidence for cumulative cultural evolution in bird song.

In studies of cumulative cultural evolution in non-human animals, the focus is most often on incremental changes that increase the efficacy of an existing form of socially learned behaviour, such as the refinement of migratory pathways. In this paper, we compare the songs of different species to describe patterns of evolution in the acoustic structure of bird songs, and explore the question of what building blocks might underlie cumulative cultural evolution of bird song using a comparative approach. We suggest that three steps occurred: first, imitation of independent sounds, or notes, via social learning; second, the formation of categories of note types; and third, assembling note types into sequences with defined structures. Simple sequences can then be repeated to form simple songs or concatenated with other sequences to form segmented songs, increasing complexity. Variant forms of both the notes and the sequencing rules may then arise due to copy errors and innovation. Some variants may become established in the population because of learning biases or selection, increasing signal efficiency, or because of cultural drift. Cumulative cultural evolution of bird songs thus arises from cognitive processes such as vocal imitation, categorization during memorization and learning biases applied to basic acoustic building blocks.This article is part of a discussion meeting issue ‘The emergence of collective knowledge and cumulative culture in animals, humans and machines’.

Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo

Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. The resulting data violates assumptions of variant callers developed for bulk sequencing. Thus, only dedicated models accounting for amplification bias and errors can provide accurate calls. We present ProSolo for calling single nucleotide variants from multiple displacement amplified (MDA) single cell DNA sequencing data. ProSolo probabilistically models a single cell jointly with a bulk sequencing sample and integrates all relevant MDA biases in a site-specific and scalable—because computationally efficient—manner. This achieves a higher accuracy in calling and genotyping single nucleotide variants in single cells in comparison to state-of-the-art tools and supports imputation of insufficiently covered genotypes, when downstream tools cannot handle missing data. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly. ProSolo is implemented in an extendable framework, with code and usage at: https://github.com/prosolo/prosolo

Geguritan Ni Sumala: Suatu Kajian Filologis

This research is entitled “Geguritan Ni Sumala: Philological Studies”. Assessment of Geguritan Ni Sumala uses philological theory. This study aims to obtain the text of Geguritan Ni Sumala which approaaches the original. The data supply phase uses the observation method and simak method helped by note taking technique. Next, in data analysis phase using comparative descriptive method, transliteration uses standard transliteration method, following by a comparation of three texts through text criticism, text edition using the legger method, the translation uses combination literal translation and idiomatic translation. In the stage of presenting the result of data analysis using formal and informal method by deductive-inductive tecnique also assisted by exposure, tables, and themes. The text edition is complemented by criticism apparatus which is presented separately and translation is also presented separately with the source text. The result of this study are, from the three of GNS manuscripts that have been compared through text criticism there are some copy/write errors from each text such as substitution, adition, omission, lakuna, interpolation, ditography, transposition, and corrupt. By correcting the copy error presented Geguritan Ni Sumala text which assumed to be correct based on the evidence three of contained manuscripts. Geguritan Ni Sumala uses Balinese Kawi language. Next in text edition for literacy guidelines used are Acri and Griffiths opinions (2014: 371-372) and combined with Damais opinions (1995: 125). aside from that, the spelling used in text edition are spelling guidelines for Balinese script pairs with Latin letters and Balinese letters also guidelines Pasang Aksara Bali. Indonesian translations are also included in the Geguritan Ni Sumala text.

A co-evolutionary model combined mixed-strategy and network adaptation by severing disassortative neighbors promotes cooperation in prisoner’s dilemma games

• The “assortative grouping” framework enhances cooperation in the dynamic network. • When a low network adaptation speed and a certain degree of strategy copy error are presumed, phenomenal network heterogeneity evolves. A co-evolutionary model of both network and mixed strategy is proposed in this study. The assigned strategy s i of agent i is defined by a real number ranging from 0 to 1, which probabilistically ordains a subsequent action of either cooperation or defection as the agent’s offer. We assume a network dynamic to support or hamper the enhancement of cooperation, where an agent severs a link with the neighbor who has the most disassortative strategy. This means that an agent tends to maintain interactions only with neighbors that resemble the agent. A series of numerical simulations reveal that our “assortative grouping” framework enhances cooperation. Interestingly, when a low network adaptation speed and a certain degree of strategy copy error are presumed, phenomenal network heterogeneity evolves, one that realizes more significant cooperation as compared to error-free cases.

Identidad y delimitación textual del poema 29 de Ausiàs March

La poesía 29 de Ausiàs March Si com lo taur se’n va fuyt pel desert, formada por una única estrofa, es una de las más populares y difundidas de su Cancionero. Se conserva en la mayor parte de los testimonios manuscritos e impresos. Sin embargo, posiblemente debido a un error de copia, la poesía 29 se difundió junto con la 30, Vengut és temps que será conegut, como si de una sola composición se tratase. Este posible error coincide en una serie de testimonios. La hipótesis de una filiación entre los diferentes manuscritos y el tratamiento de la poesía en los impresos puede contribuir a conocer mejor la tradición textual. La redacción conjunta de las dos poesías se debe a un problema de transmisión pues por su temática no son textos relacionables. En este trabajo observaremos el comportamiento de los dos textos y las posibles razones de su localización conjunta, así como también la decisión de editarlas por separado. The poem 29 by Ausiàs March, Si com lo taur se’n va fuyt pel desert, consisting of a single stanza, is one of the most popular and widespread of this author. It is preserved in most of the handwritten and printed testimonies. However, possibly due to a copy error, the poem 29 was spread together with the poem 30, Vengut és temps que será conegut, like a single composition. This possible error coincides in a series of testimonies. Perhaps, the relation between certain manuscripts and the presence of the poetry in the printed books can contribute to a better understanding of the textual tradition. The joint writing of the two poems is due to a problem of transmission because they are not relatable texts in terms of subject matter. In this work we will observe the behavior of the two texts and the possible reasons for their joint location, as well as the decision to edit them separately.

Reconciling and Reassessing the Accumulated Copying Error Model's Population‐Level Predictions for Continuous Cultural Traits

ABSTRACTThe accumulated copying error (ACE) model exploits the fact that limits to human visual perception introduce proportional copying errors during cultural transmission of a continuous trait, such as the length of a tool. Archaeologists have used ACE to infer the mechanisms of cultural transmission employed in the past. But ACE's predictions apply only under “idealized” conditions in which the population contains infinitely many vertical transmission chains and the continuous trait can take any positive value. Here, I relax each assumption to show: (1) the mean and variance of a vertically transmitted continuous trait are functions of population size and number of transmission events, and (2) functional constraints weaken the cumulative effects of proportional copying error. Incorporating the effects of population size and functional constraints in future work will reduce Type I errors (falsely rejecting a true null) when inferring the cultural transmission mechanisms responsible for population‐level variation in continuous traits. [cultural evolution, cultural transmission, finite population size, functional constraints, Paleolithic, simulation, social learning]

A-198 Major Errors on BVRT Determine Specific Cognitive Deficit in a Veteran Sample

Abstract Objective The goal of the study is to examine the underlying conceptual factors that account for major performance errors of the Benton Visual Retention Test (BVRT) using indices of the Weschler Adult Intelligence Scale, 3rd Edition (WAIS-III) as gold-standard comparison variables. Method One hundred thirty participants with mixed cognitive and psychiatric diagnoses who were referred to the neuropsychological assessment clinic at the VA Palo Alto Health Care System and completed the BVRT and WAIS-III measures were included in the analysis of the data. Factor Analysis of BVRT major memory and copy errors (rotations, distortions, and perseverations) and WAIS-III indices were conducted using SPSS 25. Results BVRT major memory and copy errors factored onto WAIS-III index variables using Principal Components Analysis with Equamax rotation yielded a four-factor model explaining 79% of total variance. Major errors on the immediate recall trial of the BVRT were found to be specifically and inversely related to performance on the WAIS-III Perceptual Organization and Processing Speed Indices. Major errors on the copy trial of the BVRT showed an inverse relationship with performance on the WAIS-III Verbal Comprehension and Working Memory Indices. Conclusions BVRT recall errors are related to failures in visual perceptual processing. Conversely, copy errors on the BVRT are potentially attributable to deficits in auditory-verbal-attentional information processing. The results of the study provide evidence for the BVRT as a viable measurement tool to determine domain-specific cognitive impairment when considering error types on recall and copy trials.

A-196 BVRT Copy and Memory Trial Omission Errors Are Associated With Working Memory and Auditory Comprehension Deficits

Abstract Objective The goal of this study is to examine the cognitive factors that account for omission errors on the Benton Visual Retention Test (BVRT) copy and memory trials using factorial indices based on raw subtest scores of the Wechsler Adult Intelligence Scale-III (WAIS-III) and the Multilingual Aphasia Examination (MAE). Method Participants were referred for assessment at the VA Palo Alto Health Care System. One hundred and forty-three participants were sampled. BVRT omission error scores for the copy and memory trials were factor analyzed with age, education level, WAIS-III Digit Span Forward (DSpF), and Letter-Number Sequencing (LNS). These variables were refactored with the spoken language components of the MAE (naming, repetition, verbal fluency, and auditory comprehension). Results BVRT copy and memory omission scores were factorially grouped with age and inversely correlated with LNS. A second factor was composed of positive loadings on DSpF, LNS, and education. The BVRT Copy-and-Memory-Omissions-Age-LNS component was inversely and specifically related to the MAE measure of auditory comprehension. The Digit Span Forward-LNS-Education variable loaded strongly on the MAE Repetition component and secondarily on the MAE Verbal Fluency and Naming components. Conclusions BVRT copy and memory trial omission errors are strongly and specifically related to failure of auditory comprehension. Errors of this type are not related to the other three components of spoken language.

Population Size Limits the Coefficient of Variation in Continuous Traits Affected by Proportional Copying Error (and Why This Matters for Studying Cultural Transmission)

The accumulated copying error model (ACE) combines findings on the proportional nature of human visual perception error with cultural transmission theory. Previous studies have employed ACE to provide population-level expectations of the coefficient of variation (CV) of a continuous trait, such as the thickness of ceramic vessels. To date, empirical departures from expected CV values have been interpreted as evidence of biased cultural transmission or functional constraints without consideration for how population size might affect population-level cultural variation in the presence of proportional perception error. Here, I employ agent-based simulation experiments to investigate the ways in which population size affects the CV of a continuous cultural trait under different cultural transmission mechanisms. Results show that the CV of a continuous cultural trait is a function of its cultural equivalent N and effective population size (Ne) as well as the relative strength of cultural selection. The results also demonstrate that different combinations of N and cultural transmission yield identical CV values. The study highlights a new set of difficulties with inferring individual-level process—the mechanism(s) by which cultural information is transmitted among individuals—from population-level pattern—the CV of a continuous cultural trait. In light of these results, I identify and discuss one avenue through which we might improve our ability to infer past cultural transmission from archeological data.

Assembly of heteropolymers via a network of reaction coordinates.

In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a sequence of discrete chemical reactions between intermediate metastable states. In this paper, we use ideas from reaction rate theory and describe nonequilibrium assembly of a heteropolymer via a continuous reaction coordinate. Our approach allows for estimating the copy error and incorporation speed from the Gibbs free energy landscape of the process. We apply our theory to several examples from a simple reaction characterized by a free energy barrier to more complex cases incorporating error correction mechanisms, such as kinetic proofreading.

A-43 Factorial Relationships Among Copy and Memory Trials of the Benton Visual Retention Test

Abstract Objective We investigated the factorial relationships among categorical error groups on the Benton Visual Retention Test (BVRT) copy and memory trials. Methods A sample of 523 ambulatory American Veteran patients who presented for clinical evaluation with a wide variety of mixed neuropsychiatric diagnoses and general medical diagnoses were studied. There were no demographic or diagnostic exclusion criteria. Results Frequency summary scores for the six types of BVRT errors (omission, misplacement, size, distortion, perseveration, and rotation errors) were factored jointly by means of principal component analysis. Omission, misplacement, and size errors grouped factorially across copy and memory domains by error type. Results showed the factorial relationships are primarily defined by the type of error. Omission, size, and misplacement errors were grouped together regardless of whether they occurred on copy or memory trials. Rotation, distortion, and perseveration errors were factorially grouped on both the copy and memory trials, but the groupings of these similar error groups formed independent factors for the copy and memory trials. The copy error factor explained the most variance and the memory error factor o explained the least variance. Conclusions Omission, size, and misplacement errors on the BVRT copy and memory trials appear to be due to similar encoding process errors. Distortion, rotation, and perseveration errors on the BVRT copy and memory trials are related to each other within each trial type but different cognitive processes account for errors of this kind on the copy and memory trials.

“Gott, nimm dich ferner unser an”

Bach’s motet Singet dem Herrn , presumed by the author to have been composed between late May 1726 and June 1727, has until now been misunderstood. Taking into account Kuhnau’s copy errors, an analysis of Bach’s advice to repeat the second movement leads to the conclusion that his intention-alternating choruses that sing the repeat with the same text- had a self-referencial purpose in that all members of both choirs would then sing the aria “Gott, nimm dich ferner unser an.” Based on an array of evidence, the author asserts that this motet is actually funeral music for the St. Thomas Boy’s Choir themselves, on the occasion of the death of the first young singer Bach accepted into the ensemble.

Breaking the speed-power-accuracy trade-off in current mirror with non-linear CCII feedback

Design of analog integrated circuit is a matter of trade-offs. Elementary blocks as simple as current mirrors must balance power, speed and accuracy as soon as they have to face dynamic inputs. In this paper, we propose a new structure of high-performance current mirror that overcomes the classical speed-power-accuracy limits. The structure combines a precise cascode current mirror with a custom low-power current conveyor used as a current mode non-linear feedback circuit. It is particularly suitable for fast multipolar current sources with high driving capabilities and small step response time over a large current dynamic. Design method and practical implementation are discussed in details. The circuit realized in AMS CMOS 0.18 μm technology at 1.8 V supply exhibits a large output current dynamic ranging from 160 μA to 2 m A, an average relative current copy error of 0.3% for worst-cases, a maximal settling time of 730 ns for full range step and a maximum quiescent power consumption of 142 μW.

Checksum-Filtered List Decoding Applied to H.264 and H.265 Video Error Correction

The latest video coding standards, H.264 and H.265, are highly vulnerable in error-prone networks. Reconstructed packets may exhibit significant degradation in terms of peak signal-to-noise ratio and visual quality. This paper presents a novel list-decoding approach exploiting the receiver side user datagram protocol (UDP) checksum. The proposed method identifies the possible locations of errors by analyzing the pattern of the calculated UDP checksum. This permits considerably reducing the number of candidate bitstreams in comparison to conventional list decoding approaches. When a packet composed of $N$ bits contains a single-bit error, instead of considering $N$ candidate bitstreams, as is the case in conventional list decoding approaches, the proposed approach considers $N/32$ candidate bitstreams, leading to a reduction of 97% of the number of candidates. For a two-bit error, the reduction increases to 99.6%. The method’s performance is evaluated using H.264 and H.265 test model software. Our simulation results reveal that, on average, the error was corrected perfectly 80%–90% of the time (the original bitstream was recovered). In addition, the proposed approach provides, on average, a 2.79-dB gain over frame copy (FC) error concealment using the joint model and a 3.57-dB gain over our implementation of FC error concealment in the High Efficiency Video Coding test model.

Various error settings bring different noise-driven effects on network reciprocity in spatial prisoner's dilemma

In view of stochastic resonance effect, this paper reports what type of additional noise can draw more enhanced network reciprocity in spatial prisoner's dilemma (SPD) games presuming different underlying networks as well as strategy updating rules. Relying on a series of simulations comprehensively designed, we explored various noise models namely action error, copy error, observation error, by either placing random agents or biased agents and variant settings of those. We found that the influence by adding noise significantly differs depending on the type of noise as well as the combination of what underlying network and update rule are presumed. Action error when added to SPD games presuming deterministic updating rule shows relatively large enhancement for cooperation.

Author Correction: Disruption of the beclin 1-BCL2 autophagy regulatory complex promotes longevity in mice.

In this Letter, the graphs in Fig. 2a and c were inadvertently the same owing to a copy and paste error from the original graphs in Prism. The Source Data files containing the raw data were correct. Fig. 2c has been corrected online.