Template Specificity Research Articles

B-108 Delta Check Performance Assessment by Using Real-WorldData at the Temple University Health System​

Abstract Background Delta check is a post-analytic tool focusing on pre-analytical, analytical and post-analytical errors. It can be sensitive in detecting isolated errors affecting a single patient, as opposed to moving patient averages, which is another QC tool for detecting errors that affect a cohort/population of patients. As a computer-based system on selected tests, delta checks are to detect excessive changes from prior value in the patient test result and to detect possible specimen errors such as misidentified or compromised samples before results are reported. It may also play a role in detecting examination(analytical) issues and clinically significant results. If delta checks exceed established limits, the result is flagged. There is a common agreement that measurands with low indices of individuality (<0.6) make good candidates for the identification of cases of sample misidentification than higher indices of individuality (>1.4). CLSI EP33 Use of Delta Checks in the Medical Laboratory guidelines recommends that laboratories assess the validity of current delta check parameters by reviewing retrospective data on flagged results to determine if errors are being identified efficiently. At Temple University Health System, delta check limits were established historically by using published data, however, its performance characteristics have not been verified previously. Verification of clinical performance of predefined delta check limits can be performed either through mathematical calculations or via clinical audits. Clinical audits are achieved by documenting the follow-up actions and outcomes of the samples flagged by a delta check rule(s). It has been suggested that this should be performed using a protocolized follow-up procedure to ensure uniformity in the investigation and management. Corey M. et al. shared an excel template, a mathematical model that can be adopted easily by replacing the example data with retrospectively extracted data and modifying the parameters to suit their laboratory’s requirements. Methods We collected up to 30,000 data points for each 12 measurand in the clinical chemistry lab retrospectively. By using the excel template, clinical sensitivity and clinical specificity has been calculated. Furthermore, we created ROC curves and evaluated them using the (YI) Youden Index and AUC (Area Under the Curve). Results In general, YI values were found to be very low, less than 0.6. Highest YI was used to establish new delta check limits for each analyte; only the current creatinine delta check limit was found as effective, and no change required. 11 out of 12 measurand were required a revision of delta check limits and were proposed to replace with lower delta checks. AUC values were found between 0.56-0.794. Na showed the highest AUC, which correlates its low individuality index (0.5) and its effects on effectiveness of the delta check system. Conclusions It is of vital importance to establish a solid follow-up evaluation for delta check alerts and distinguish between integrity issues and clinically significant changes. Conclusively, this endeavor can develop into extensive information for the application, evaluation, and follow-up of delta checks whilst improving diagnostic accuracy and quality assurance.

Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.

Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA)synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3' untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA-protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein-RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.

Appropriate Primer Selection Improves Molecular Bird Sexing Accuracy

Birds sexing utilize the Polymerase Chain Reaction (PCR) technique is increasingly being used by researchers and breeders. The PCR technique has high sensitivity, but its success is influenced by the specificity of the DNA template with the oligo primer used. This study aimed to evaluate 5 types of PCR primers P2/P8, 2550F/2718R, CHD1F/CHD1R, 1237L/1272H, and CHD1LF/CHD1LR to determine the sex of Phasianidae, Anatidae, Muscicapidae, and Psittacidae families. This research was conducted by tested primers mentioned above to amplify the target gene chromodomain helicase DNA binding 1 (CHD1) on DNA samples of each pair of males and females from four bird families, respectively. The results indicated that CHD1LF/CHD1LR PCR primer gave the best results and was recommended to determine the sex of four families tested. Some of other primers tested in this study failed to amplify targeted gene correctly, it is important to use appropriate primer to increase bird sexing accuracy.

The specificity of feature-based attentional guidance is equivalent under single- and dual-target search.

Individuals actively maintain attentional templates to prioritize target-matching inputs. While previous works have established that multiple templates can be held simultaneously, current understanding is limited with respect to the representational quality of such templates. We thus investigated: (a) whether the maintenance of two templates is limited to broad, coarse-grained representations, and if not, (b) whether there is nonetheless a decline in the achievable level of specificity when multiple attentional templates are held simultaneously. Using a spatial cueing procedure, we probed the breadth of attentional templates while participants maintained either one (Experiment 1) or two target colors (Experiment 2) under conditions of low- or high-similarity search and found specific template maintenance during high-similarity search for both single- and dual-target conditions. We then directly compared template specificity during single- and dual-target maintenance in Experiment 3, probing at the point of differentiation between target and nontarget feature values observed during single-target search. Here we found no difference in the selectivity of cue validity effects between single- and dual-target search, suggesting equivalent template specificity regardless of whether one or two features are relevant to search. Lastly, in Experiment 4, we established that such template specificity is dependent on access to visual working memory. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Diagnostic Performance of Response Assessment FDG-PET/CECT in HNSCC Treated With Definitive Radio(chemo)therapy Using NI-RADS.

To assess the diagnostic performance of response assessment 18F-fluorodeoxyglucose positron emission tomography/contrast-enhanced computed tomography (FDG-PET/CECT) following definitive radio(chemo)therapy in head and neck squamous cell carcinoma (HNSCC) using Neck Imaging Reporting and Data System (NI-RADS). A retrospective analysis from a prospectively maintained dataset. Tertiary-care comprehensive cancer center in a low-middle-income country. Adults with newly diagnosed, biopsy-proven, nonmetastatic HNSCC treated with definitive radio(chemo)therapy were included. Posttreatment response assessment FDG-PET/CECT scans were retrospectively assigned NI-RADS categories (1-3) for the primary site, neck, and both sites combined. Locoregional recurrence occurring within 2-years was defined as the event of interest. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and overall accuracy were calculated. Locoregional control stratified by NI-RADS categories was computed with the Kaplan-Meier method and compared using the log-rank test. Posttreatment FDG-PET/CECT scans were available in 190 patients constituting the present study cohort. Sensitivity, specificity, PPV, NPV, and overall accuracy of the NI-RADS template for the primary site was 73.5%, 81.4%, 46.3%, 93.4%, and 80.0%, respectively. Similar metrics for the neck were 72.7%, 87.5%, 43.2%, 96.1%, and 85.8%, respectively. Combining primary site and neck, the corresponding metrics of diagnostic accuracy were 84.4%, 69.7%, 46.3%, 93.5%, and 73.2%, respectively. At a median follow-up of 40 months, Kaplan-Meier estimates of 2-year locoregional control were significantly higher for NI-RADS category 1 (94.2%) compared to NI-RADS category 2 (69.4%) and category 3 (20.4%), respectively (stratified log-rank p < .0001). FDG-PET/CECT using the NI-RADS template is associated with good diagnostic performance and prognostic utility in HNSCC treated with definitive radio(chemo)therapy.

ELGA Outpatient Clinic Report and ELGA Telehealth Note: Two HL7-CDA®-Based Modular Electronic Documents.

From 2022, the "Outpatient Clinic Report" and the "Telehealth Note" will complement the existing e-Reports in the Austrian Electronic Health Record system ELGA. The specification of two harmonized implementation guides with standardized structure for all types of outpatient clinics in hospitals on the one hand and for telemonitoring treatments on the other hand. With the participation of expert groups, the contents were harmonized, and a data model was created. Template specifications were modelled in ART-DECOR and approved in the course of an HL7 Austria ballot. Two sets of freely selectable building blocks and machine-readable content were created. The "Outpatient Clinic Report" and the "Telehealth Note" are currently being implemented. The use of these documents will be evaluated as well as if additional machine-readable content is needed.

Operational Rule Extraction and Construction Based on Task Scenario Analysis

Changes in the information age have induced the necessity for a more efficient and effective self-decision-making requirement. A method of extracting and constructing naval operations decision-making rules based on scenario analysis is proposed. The template specifications of Event Condition Action (ECA) rules are defined, and a consistency detection method of ECA rules based on SWRL is proposed. The logical relationships and state transitions of the naval operational process is analyzed in detail, and the association of objects, events, and behaviors is realized. Finally, the operation of the proposed methods is illustrated through an example process, showing the method can effectively solve the problems of self-decision-making rule extraction and construction among naval battlefield decision environment, and avoid relying on artificial intelligence, which may have brought some uncertain factors.

Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis.

Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10-20% of non-paired substitutions as well, underscoring the importance of the process.

How feature context alters attentional template switching.

In real-world tasks visual attention is rarely aimed at a single object. Humans rather "forage" the visual scene for information, dynamically switching attentional templates. Several visual search studies have found that observers often use suboptimal attentional control strategies, possibly to avoid effort. Here, we investigated with a foraging paradigm if observers' reluctance to switch between attentional templates increases with template specificity. To that end, we manipulated the feature context of displays in which participants "foraged" moving stimuli on a tablet-PC. Experiment 1 (N = 35) revealed a decline in switching tendency and foraging efficiency with increasing feature-space distance between target alternatives. Experiment 2 (N = 36) found even lower flexibility with distractor color close to target colors and strongest impairments with distractor color in between target colors. Our results demonstrate that visual information sampling is most flexible when broad (instead of very specific) templates and relational search strategies are possible (e.g., attending to "redder" objects), with implications for both attention research and applications, especially in visual-foraging-like tasks, such as baggage screening or medical image assessment. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Top-down and bottom-up guidance in normal aging during scene search.

Age-related differences in visual search have been extensively studied using simple item arrays, showing an attentional decline. Little is known about how aging affects attentional guidance during search in more complex scenes. To study this issue, we analyzed eye-movement behavior in realistic scene search. We examined age-related differences in top-down guidance, manipulating target template specificity (picture vs. word cue) and target-scene semantic consistency (consistent vs. inconsistent), and in bottom-up guidance, manipulating perceptual salience (high vs. low) of targets and distractors. Compared to young adults (YA), older adults (OA) were overall slower, from the first saccade in the scene. They showed a smaller benefit of a specific target template, suggesting that precision of visual information in working memory may decrease with age. The benefit of semantic consistency did not depend on age, suggesting a preserved ability in OA to use knowledge about object occurrence in scenes. OA showed greater bottom-up search facilitation due to target's high salience, which may depend on reduced selection of low-salience stimuli. Attentional capture by distractors was greater in OA than YA, with respect to engagement (probability of distractor fixation), but only following a picture cue, and disengagement (fixation duration on distractors) in all conditions. Overall, our study shows that age-related differences in visual selection of targets and distractors depend on specific task demands in terms of top-down and bottom-up guidance. It also indicates that scene search difficulties in OA can be limited by cognitive and perceptual forms of environmental support. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

When more is more: redundant modifiers can facilitate visual search

According to the Gricean Maxim of Quantity, speakers provide the amount of information listeners require to correctly interpret an utterance, and no more (Grice in Logic and conversation, 1975). However, speakers do tend to violate the Maxim of Quantity often, especially when the redundant information improves reference precision (Degen et al. in Psychol Rev 127(4):591–621, 2020). Redundant (non-contrastive) information may facilitate real-world search if it narrows the spatial scope under consideration, or improves target template specificity. The current study investigated whether non-contrastive modifiers that improve reference precision facilitate visual search in real-world scenes. In two visual search experiments, we compared search performance when perceptually relevant, but non-contrastive modifiers were included in the search instruction. Participants (NExp. 1 = 48, NExp. 2 = 48) searched for a unique target object following a search instruction that contained either no modifier, a location modifier (Experiment 1: on the top left, Experiment 2: on the shelf), or a color modifier (the black lamp). In Experiment 1 only, the target was located faster when the verbal instruction included either modifier, and there was an overall benefit of color modifiers in a combined analysis for scenes and conditions common to both experiments. The results suggest that violations of the Maxim of Quantity can facilitate search when the violations include task-relevant information that either augments the target template or constrains the search space, and when at least one modifier provides a highly reliable cue. Consistent with Degen et al. (2020), we conclude that listeners benefit from non-contrastive information that improves reference precision, and engage in rational reference comprehension.Significance statementThis study investigated whether providing more information than someone needs to find an object in a photograph helps them to find that object more easily, even though it means they need to interpret a more complicated sentence. Before searching a scene, participants were either given information about where the object would be located in the scene, what color the object was, or were only told what object to search for. The results showed that providing additional information helped participants locate an object in an image more easily only when at least one piece of information communicated what part of the scene the object was in, which suggests that more information can be beneficial as long as that information is specific and helps the recipient achieve a goal. We conclude that people will pay attention to redundant information when it supports their task. In practice, our results suggest that instructions in other contexts (e.g., real-world navigation, using a smartphone app, prescription instructions, etc.) can benefit from the inclusion of what appears to be redundant information.

Memory for distractors during hybrid search: The effect of target template specificity

Memory for distractors during hybrid search: The effect of target template specificity

PERCEPTUAL GUIDANCE IMPROVES VISUAL SEARCH IN AGING AND IN ALZHEIMER’S DISEASE: EVIDENCE FROM EYE-MOVEMENT BEHAVIOR WITHIN REAL-WORLD SCENES

Elderly people and, especially, patients with Alzheimer's disease (AD) show impaired performance in visual search. This seems to arise from inefficient strategies, with an increased number of eye fixations and longer fixation durations. As many activities of daily living require efficient search of objects within complex environments, visual search deficits of AD patients may have a key role in reducing their functional autonomy. However, while previous studies have examined patients’ search in simple object arrays, little is know about their search behaviour in real-world scenes. Using an EyeLink 1000, we recorded eye movements of 12 mild AD patients, 24 healthy age-matched individuals (“elderly controls”) and 32 young individuals (“young controls”) during search within real-world scenes. We examined whether any group difference in eye guidance during search depends on target template specificity (name vs. precise picture), target visual salience (low vs. high) and reliability of scene semantics (consistent vs. inconsistent targets). We analysed data using linear mixed effect models, considering search initiation (first search saccade), scene scanning (until first target fixations) and target verification (dwell time on target). Aging (elderly vs. young controls) and AD (patients vs. elderly controls) led to less effective behaviour in all search phases, with fewer first saccades directed toward the target, longer scanning time and longer verification time. While these patterns were not affected by scene semantic guidance, a greater amount of target perceptual guidance was especially beneficial for the elderly controls and, even more, for the AD patients. In particular, higher target salience reduced performance gaps between elderly and young controls during scene scanning and target verification, and – when combined with a pictorial template – between patients and elderly controls during scene scanning. Eye-movement analysis enables to examine the time course of fine impairments during real-world scene search. Enhancing target visual salience and providing a priori knowledge of the perceptual appearance of the specific target objects seem promising ways of improving visual search behaviour in healthy elderly individuals and in AD patients. This understanding may contribute to the development of more appropriate information systems and living places, promoting individual's everyday functional autonomy.

For Want of a Template

For Want of a Template

Hepatitis E virus RNA-dependent RNA polymerase: RNA template specificities, recruitment and synthesis.

Hepatitis E virus (HEV) is a positive-sense RNA virus and member of the genus Orthohepevirus in the family Hepeviridae. Although HEV RNA-dependent RNA polymerase (HEV-RdRp) plays an important role in the HEV life cycle, its template specificities are not completely understood. We expressed HEV-RdRp protein with His-tag in a bacterial system and analysed template specificities using different putative cis-regulatory elements in the HEV genome. The enzyme showed highest affinity for the 3' non-coding region (NCR), then for the 5'NCR and least for the putative subgenomic promoter (SgP). The enzyme could co-bind to 3'NCR and putative SgP templates together, as evident from the supershift in binding assay, indicating presence of different binding sites for these elements. Proteomic analysis revealed that the RNA elements share two common peptides for binding, while a third peptide, which is highly conserved across different HEV genotypes, is specific for 3'NCR. We propose that, during the early phases of replication, as negative sense antigenome copies accumulate at the replication site, they probably initiate promoter swapping from 3'NCR to SgP, to favour synthesis of subgenomic RNA and to prevent synthesis of genomic RNA. The conserved site for 3'NCR binding could be potential antiviral target and needs further evaluation.

PRACTICAL APPLICATION OF BRTL APPROACH FOR FINANCIAL REPORTING DOMAIN

Business rules are evidently important for organisations as they describe how they are doing business. Business rules templates are often proposed as a means of the specification of business rules. Business rules templates language (BRTL) is a language developed for the specification of business rules templates. This paper documents the findings of an experiment aimed at determining the extent to which business rules specified using BRTL can be used within the model driven development of the financial reporting systems. The results of the experiment are compared with the data available from the four historical projects of the same domain.

Serum cholesterol selectively regulates glucocorticoid sensitivity through activation of JNK.

Glucocorticoids (Gc) are potent anti-inflammatory agents with wide clinical application. We have previously shown that increased serum concentration significantly attenuates regulation of a simple Gc-responsive reporter. We now find that glucocorticoid receptor (GR) regulation of some endogenous transactivated but not transrepressed genes is impaired, suggesting template specificity. Serum did not directly affect GR expression, activity or trafficking, implicating GR crosstalk with other signalling pathways. Indeed, a JNK inhibitor completely abolished the serum effect. We identified the Gc modulating serum component as cholesterol. Cholesterol loading mimicked the serum effect, which was readily reversed by JNK inhibition. Chelation of serum cholesterol with methyl-β-cyclodextrin or inhibition of cellular cholesterol synthesis with simvastatin potentiated the Gc response. To explore the effect in vivo we used ApoE −/− mice, a model of hypercholesterolaemia. Consistent with our in vitro studies, we find no impact of elevated cholesterol on the expression of GR, or on the hypothalamic–pituitary–adrenal axis, measured by dexamethasone suppression test. Instead we find selective Gc resistance on some hepatic target genes in ApoE −/− mice. Therefore, we have discovered an unexpected role for cholesterol as a selective modulator of Gc action in vivo. Taken together these findings reveal a new environmental constraint on Gc action with relevance to both inflammation and cancer.

How context information and target information guide the eyes from the first epoch of search in real-world scenes

This study investigated how the visual system utilizes context and task information during the different phases of a visual search task. The specificity of the target template (the picture or the name of the target) and the plausibility of target position in real-world scenes were manipulated orthogonally. Our findings showed that both target template information and guidance of spatial context are utilized to guide eye movements from the beginning of scene inspection. In both search initiation and subsequent scene scanning, the availability of a specific visual template was particularly useful when the spatial context of the scene was misleading and the availability of a reliable scene context facilitated search mainly when the template was abstract. Target verification was affected principally by the level of detail of target template, and was quicker in the case of a picture cue. The results indicate that the visual system can utilize target template guidance and context guidance flexibly from the beginning of scene inspection, depending upon the amount and the quality of the available information supplied by either of these high-level sources. This allows for optimization of oculomotor behavior throughout the different phases of search within a real-world scene.

The PriA Replication Restart Protein Blocks Replicase Access Prior to Helicase Assembly and Directs Template Specificity through Its ATPase Activity

The PriA protein serves as an initiator for the restart of DNA replication on stalled replication forks and as a checkpoint protein that prevents the replicase from advancing in a strand displacement reaction on forks that do not contain a functional replicative helicase. We have developed a primosomal protein-dependent fluorescence resonance energy transfer (FRET) assay using a minimal fork substrate composed of synthetic oligonucleotides. We demonstrate that a self-loading reaction, which proceeds at high helicase concentrations, occurs by threading of a preassembled helicase over free 5'-ends, an event that can be blocked by attaching a steric block to the 5'-end or coating DNA with single-stranded DNA binding protein. The specificity of PriA for replication forks is regulated by its intrinsic ATPase. ATPase-defective PriA K230R shows a strong preference for substrates that contain no gap between the leading strand and the duplex portion of the fork, as demonstrated previously. Wild-type PriA prefers substrates with larger gaps, showing maximal activity on substrates on which PriA K230R is inactive. We demonstrate that PriA blocks replicase function on forks by blocking its binding.

Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase

Viroids are a unique class of noncoding RNAs: composed of only a circular, single-stranded molecule of 246-401 nt, they manage to replicate, move, circumvent host defenses, and frequently induce disease in higher plants. Viroids replicate through an RNA-to-RNA rolling-circle mechanism consisting of transcription of oligomeric viroid RNA intermediates, cleavage to unit-length strands, and circularization. Though the host RNA polymerase II (redirected to accept RNA templates) mediates RNA synthesis and a type-III RNase presumably cleavage of Potato spindle tuber viroid (PSTVd) and closely related members of the family Pospiviroidae, the host enzyme catalyzing the final circularization step, has remained elusive. In this study we propose that PSTVd subverts host DNA ligase 1, converting it to an RNA ligase, for the final step. To support this hypothesis, we show that the tomato (Solanum lycopersicum L.) DNA ligase 1 specifically and efficiently catalyzes circularization of the genuine PSTVd monomeric linear replication intermediate opened at position G95-G96 and containing 5'-phosphomonoester and 3'-hydroxyl terminal groups. Moreover, we also show a decreased PSTVd accumulation and a reduced ratio of monomeric circular to total monomeric PSTVd forms in Nicotiana benthamiana Domin plants in which the endogenous DNA ligase 1 was silenced. Thus, in a remarkable example of parasitic strategy, viroids reprogram for their replication the template and substrate specificity of a DNA-dependent RNA polymerase and a DNA ligase to act as RNA-dependent RNA polymerase and RNA ligase, respectively.