Identical Templates Research Articles

Optimizing Resident Charge Capture with Disappearing Help Text in Note Templates.

To assist residents in selecting the correct Current Procedural Terminology (CPT) code for evaluation and management (E/M) services thru the addition of disappearing help text into a standardized note template. We created a disappearing text block that summarizes E/M requirements and embedded it into the note template used by residents at a pediatric urgent care clinic. An intervention cohort composed of post graduate year 1 (PGY 1) residents was instructed to use this note template, while senior residents (PGY 2-3) were instructed to use an identical template that lacked the help text. We evaluated the incidence of CPT change by the attending physician for each visit as a proxy for improvement in resident billing practices. Logistic regression with a primary outcome of whether the encounter CPT code was changed was completed. There were 2,869 encounters during the 255-day study period; the help text was used in 1,112 (38.8%) encounters. There was some crossover in note use; i.e., PGY 1s using the note without help text and PGY 2s using the note with help text. Nevertheless, all residents who used the help text had a lower unadjusted rate of CPT change (22.1% vs 30.6%, OR= 0.64, p < 0.0001). This pattern persisted when stratified by trainee level - PGY 1 (22.6% vs 45.3%, OR=0.35,p < 0.0001) and PGY 2-3 (12.2% vs 27.8%, p = 0.018). Adjusting for multiple factors, the use of help text was associated with a lower incidence of CPT change (odds ratio [OR] = 0.28, 95% confidence interval [CI]: 0.19-0.44). Residents' use of the disappearing help text was associated with a large decrease in CPT code adjustment by attending physicians, which demonstrates its promise for improved E/M coding and for other applications.

Complete synthesis of identity templates for quantum and reversible logic MCT circuits using SAT-solvers and proposal of suboptimality witness notion

Complete synthesis of identity templates for quantum and reversible logic MCT circuits using SAT-solvers and proposal of suboptimality witness notion

Projecting complex categories: biodynamic wine producers’ online identity

PurposeThis paper aims to investigate how producers of biodynamic and sustainable wine portray their brand identity online.Design/methodology/approachThe study uses an inductive approach to qualitative content analysis of wine producers’ websites. The authors use a theoretical starting point based on the categorizations literature related to institutional scripts and identity projection.FindingsProducers adopt identity templates similar to the provenance and glory templates established in extant research. They demonstrate templates of community, quality, spirituality and sustainability, but there is a break in the templates, and they adopt a pseudo-rationalist template, avoiding detailed descriptions of practices and underpinning philosophy, leaving any references to them opaque and ambiguous. This may be due to concerns over scientific skepticism or spiritual suspicion, or anticipation of a lack of consumer knowledge.Research limitations/implicationsThe geographical location of the sample poses limitations to the results of the study. However, the study provides an examination of the nuances of self-categorization as it relates to identity projection, prompting further investigation into its positive and negative potential.Practical implicationsResearch on the connection between quality perceptions and experience and credence attributes suggests producers should do more to emphasize the philosophy underpinning biodynamics.Originality/valueThe study contributes to research on marketing for inherently sustainable producers who may suffer potential negative reactions in general and biodynamic wine producers in particular. This study provides nuance to the understanding of negative reactions to novel and innovative wine production practices.

Validating Syntactic Correctness Using Unsupervised Clustering Algorithms

When developing a complex system in an open platform setting, users need to compose and maintain a systematic requirement specification. This paper proposes a solution to guarantee a syntactically accurate requirement specification that minimizes the ambiguity caused by ungrammatical sentences. Our system has a set of standard jargon and templates that are used as a guideline to write grammatically correct sentences. Given a database of standard technical Korean (STK) templates, the system that we have designed and implemented divides a new sentence into a specific cluster. If the system finds an identical template in a cluster, it confirms the new sentence as a sound one. Otherwise, the system uses unsupervised clustering algorithms to return the template that most closely resembles the syntax of the inputted sentence. We tested our proposed system in the field of open platform development for a railway train. In the experiment, our system learned to partition templates into clusters while reducing null attributes of an instance using the autoencoding procedure. Given a set of clusters, the system was able to successfully recommend templates that were syntactically similar to the structure of the inputted sentence. Since the degree of similarity for 500 instances was 97.00% on average, we conclude that our robust system can provide an appropriate template that users can use to modify their syntactically incorrect sentences.

Development and Implementation of a Multisite Registry Using Structured Templates for Actionable Findings in the Kidney.

The aim of this study was to scale structured report templates categorizing actionable renal findings across health systems and create a centralized registry of patient and report data. In January 2017, three academic radiology departments agreed to prospectively include identical structured templates categorizing the malignant likelihood of renal findings in ≥90% of all adult ultrasound, MRI, and CT reports, a new approach for two sites. Between November 20, 2017, and September 30, 2019, deidentified HL7 report data were transmitted to a centralized ACR registry. An automated algorithm extracted categories. Radiologists were requested to addend reports with missing or incomplete templates after the first month. Separately, each site submitted patient sociodemographic and clinical data 12 months before and at least 3 months after enrollment. A total of 164,982 eligible radiology reports were transmitted to the registry; 4,159 (2.5%) were excluded because of missing categories or radiologist names. The final cohort included 160,823 examinations on 102,619 unique patients. Mean template use before and after addendum requests was 99.3% and 99.9% at SITE1, 86.5% and 94.6% at SITE2, and 91.4% and 96.0% at SITE3. Matching patient sociodemographic and clinical data were obtained on 96.9% of reports from SITE1, 94.2% from SITE2, and 96.0% from SITE3. Regulatory, cultural, and technology barriers to the creation of a multisite registry were identified. Barriers to the adoption of unified structured report templates for actionable kidney findings can be addressed. Deidentified report and patient data can be securely transmitted to an external registry. These data can facilitate the collection of diverse evidence-based population imaging outcomes.

Reproductive plasticity and oogenesis in the queen honey bee (Apis mellifera)

In the honey bee (Apis mellifera), queen and worker castes originate from identical genetic templates but develop into different phenotypes. Queens lay up to 2000 eggs daily whereas workers are sterile in the queen’s presence. Periodically queens stop laying: during swarming, when resources are scarce in winter, and when they are confined to a cage by beekeepers. We used confocal microscopy and gene expression assays to investigate the control of oogenesis in the ovaries of honey bee queens that were caged inside and outside the colony. We find evidence that queens use a different combination of ‘checkpoints’ to regulate oogenesis compared to honey bee workers and other insect species. However, both queen and worker castes likely use the same programmed cell death pathways to terminate oocyte development at their caste-specific checkpoints. Our results also suggest that a key factor driving the termination of oogenesis in queens is nutritional stress. Thus, queens may regulate oogenesis via the same regulatory pathways that were utilised by ancestral solitary species but likely have adjusted physiological checkpoints to suit their highly-derived life history.

The success of behavioral economics in improving patient retention within an intensive primary care practice

BackgroundA minority of the U.S. population comprises a majority of health care expenses. Health system interventions for high-cost populations aim to improve patient outcomes while reducing costly over-utilization. Missed and inconsistent appointments are associated with poor patient outcomes and increased health care utilization. PEAK Health— Mount Sinai’s intensive primary care clinic for high-cost patients— employed a novel behavioral economics-based intervention to reduce the rate of missed appointments at the practice. Behavioral economics has accomplished numerous successes across the health care field; the effect of a clinic-based behavioral economics intervention on reducing missed appointments has yet to be assessed.MethodsThis was a single-arm, pre-post trial conducted over 1 year involving all active patients at PEAK Health. The intervention consisted of: a) clinic signage, and b) appointment reminder cards containing behavioral economics messaging designed to increase the likelihood patients would complete their subsequent visit; appointment cards (t1) were transitioned to an identical EMR template (t2) at 6 months to boost provider utilization. The primary objective, the success of scheduled appointments, was assessed with visit adherence: the proportion of successful over all scheduled appointments, excluding those cancelled or rescheduled. The secondary objective, the consistency of appointments, was assessed with a 2-month visit constancy rate: the percentage of patients with at least one successful visit every 2 months for 1 year. Both metrics were assessed via a χ2 analysis and together define patient retention.ResultsThe visit adherence rate increased from 74.7% at baseline to 76.5% (p = .22) during t1 and 78.0% (p = .03) during t2. The 2-month visit constancy rate increased from 59.5% at baseline to 74.3% (p = .01) post-intervention.ConclusionsA low-resource, clinic-based behavioral economics intervention was capable of improving patient retention within a traditionally high-cost population. A renewed focus on patient retention— employing the metrics described here— could bolster chronic care efforts and significantly improve the outcomes of high-cost programs by reducing the deleterious effects of missed and inconsistent appointments.

Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae

Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.

Countering transphobic stigma: Identity work by self‐employed Keralan transpeople

AbstractTranspeople in India forge identities at the confluence of contradictory social forces. Interviews conducted in the state of Kerala suggest that the experience of transphobic stigma results in self‐employed transpeople being abjectified. Social abjectification, in turn, triggers their identity work within liminal social spaces located between the everyday lifeworld and postcolonial legal institutions. Through this work, the participants in this study navigated the contradictions between two identity‐constituting external structures: culture and law. Culture is a source of identity threat, but it also supplies a socially legitimated identity template—thehijra—used in the vital self‐formative work of mirroring and witnessing. Similarly, trans‐supportive social policies and laws provide institutional scaffolding for identities. Yet, despite the agential nature of the participants' identity work, the inherent limitations of the law and the vulnerability of embodiment render them susceptible to the ongoing threat posed by the transphobia emanating from ambient cultural norms.

Refinement of Protein Homology Model by Enhanced Directional Sampling Guided by Bioinformatics

An accurate protein structure is a prerequisite for computational drug discovery and mechanistic analysis of protein's interactions. Homology modelling is a widely used method to predict atomic-level structure of protein whose structure is experimentally undetermined. It predicts structure accurately even with moderate sequence identity (∼50 percent) template, however, its accuracy decreases when template has low sequence identity (<50 percent). We developed a homology model refinement method to obtain an accurate structure of those proteins for which high sequence identity template is not available but enough data on the history of protein's evolution is available.

Exploring Brain Dynamic Functional Connectivity Using Improved Principal Components Analysis Based on Template Matching.

Principle components analysis (PCA) can be used to detect repeating co-variant patterns of resting-state dynamic functional connectivity (DFC) of brain networks, accompanied with sliding-window technique. However, the robustness of PCA-based DFC-state extraction (DFC-PCA) is poorly studied. We investigated the reliability of PCA results and improved the robustness of DFC-PCA for a limited sample size. We first established how PCA-based DFC results varied with sample size and PC order in five rounds of bootstrapping with different sample sizes. The consistency across trials increased with increasing sample size and/or decreasing PC order. We then developed a framework based on PC matching and reordering to obtain a more reliable estimation of co-variant DFC patterns. With either the identical template generated by the surrogate dataset itself or with the external template obtained from existing results, the perceptual hash algorithm was used to reorder PCs according to their patterns. After order correction, reliable results were obtained by averaging across trials within each surrogate dataset. This newly developed framework allowed simultaneous measurement and improvement of DFC-PCA. This consistency could also be used as a criterion for PC selection and interpretation to support the reliability and validity of the conclusion.

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs.

As sequencing methodologies continue to advance, the availability of protein sequences far outpaces the ability of structure determination. Homology modeling is used to bridge this gap but relies on high-identity templates for accurate model building. G-protein coupled receptors (GPCRs) represent a significant target class for pharmaceutical therapies in which homology modeling could fill the knowledge gap for structure-based drug design. To date, only about 17% of druggable GPCRs have had their structures characterized at atomic resolution. However, modeling of the remaining 83% is hindered by the low sequence identity between receptors. Here we test key inputs in the model building process using GPCRs as a focus to improve the pipeline in two critical ways: Firstly, we use a blended sequence- and structure-based alignment that accounts for structure conservation in loop regions. Secondly, by merging multiple template structures into one comparative model, the best possible template for every region of a target can be used expanding the conformational space sampled in a meaningful way. This optimization allows for accurate modeling of receptors using templates as low as 20% sequence identity, which accounts for nearly the entire druggable space of GPCRs. A model database of all non-odorant GPCRs is made available at www.rosettagpcr.org. Additionally, all protocols are made available with insights into modifications that may improve accuracy at new targets.

Epigenetic regulator function through mouse gastrulation.

Summary paragraph:During ontogeny, proliferating cells become restricted in their fate through the combined action of cell-type specific transcription factors and ubiquitous epigenetic machinery, which recognize universally available histone residues or nucleotides but are nonetheless deployed in a highly context-dependent manner1,2. The molecular functions of these regulators are generally well understood, but assigning direct developmental roles is hampered by complex mutant phenotypes that often emerge following gastrulation3,4. Recently, single-cell RNA sequencing (scRNA-seq) and analytical approaches have explored this highly conserved process across numerous model organisms5–8, including mouse9–18. To elaborate on these strategies, we investigated a panel of ten essential regulators using a combined zygotic perturbation, scRNA-seq platform where many mutant embryos can be assayed simultaneously to recover robust transcriptional and morphological information. Deeper analysis of central Polycomb Repressive Complex (PRC) 1 and 2 members indicate substantial cooperativity, but distinguishes a PRC2-dominant role in restricting the germline that emerges from gross molecular changes within the initial conceptus. We believe our experimental framework will eventually allow for a fully quantitative view of how cellular diversity emerges using an identical genetic template and from a single totipotent cell.

One Thing Leads to Another: Anticipating Visual Object Identity Based on Associative-Memory Templates.

Probabilistic associations between stimuli afford memory templates that guide perception through proactive anticipatory mechanisms. A great deal of work has examined the behavioral consequences and human electrophysiological substrates of anticipation following probabilistic memory cues that carry spatial or temporal information to guide perception. However, less is understood about the electrophysiological substrates linked to anticipating the sensory content of events based on recurring associations between successive events. Here, we demonstrate behavioral and electrophysiological signatures of using associative-memory templates to guide perception, while equating spatial and temporal anticipation (experiments 1 and 2), as well as target probability and response demands (experiment 2). By recording the electroencephalogram in the two experiments (N = 55; 24 females), we show that two markers in human electrophysiology implicated in spatial and temporal anticipation also contribute to the anticipation of perceptual identity, as follows: attenuation of alpha-band oscillations and the contingent negative variation (CNV). Together, our results show that memory-guided identity templates proactively impact perception and are associated with anticipatory states of attenuated alpha oscillations and the CNV. Furthermore, by isolating object-identity anticipation from spatial and temporal anticipation, our results suggest a role for alpha attenuation and the CNV in specific visual content anticipation beyond general changes in neural excitability or readiness.SIGNIFICANCE STATEMENT Probabilistic associations between stimuli afford memory templates that guide perception through proactive anticipatory mechanisms. The current work isolates the behavioral benefits and electrophysiological signatures of memory-guided identity-based anticipation, while equating anticipation of space, time, motor responses, and task relevance. Our results show that anticipation of the specific identity of a forthcoming percept impacts performance and is associated with states of attenuated alpha oscillations and the contingent negative variation, extending previous work implicating these neural substrates in spatial and temporal preparatory attention. Together, this work bridges fields of attention, memory, and perception, providing new insights into the neural mechanisms that support complex attentional templates.

From diary narrative to the referential Self: how questionnaires and quizzes reshaped online self-writing

This article discusses the evolution of self-inscription from the soul-searching autobiographical narratives characteristic of personal diaries to the highly referential and indirect language articulated in today’s social media. To trace the origins of this shift, this study considers blogs of the first decade of the 21st century where traditional diary narrative started to transform into a new type of ego-text. It suggests that the spread of online quizzes and questionnaires in the beginning of the 21st century played an important role in the creation of the referential Self characteristic of today’s online rhetoric. Entering the realm of traditional ego-text, these prestructured tools replaced evident self-narration with a disguised indirect version, providing ready-made identity templates and establishing clear rules of information circulation.

No Acoustic Correlates of Grammatical Class: A Critical Re-Examination of Sereno and Jongman (1995)

The present article describes an extended replication of a reading study by Sereno and Jongman (1995) that reported acoustic differences between noun and verb pronunciations of English disyllabic, non-stress-shifting homophone pairs, for example, answer (v) versus answer (n). The original findings point to a gradual influence of the typical stress patterns of both grammatical categories, with noun readings exhibiting a tendency toward trochaic and verb readings toward iambic pronunciation. However, the effects found by Sereno and Jongman (1995) did not consistently reach statistical significance and were based on a very small sample size. Employing a considerably larger group of speakers, the current replication fails to find the reported effects of the grammatical category. The null result obtained can be accounted for within speech production models that assume identical metrical templates for the homophone pairs tested and no direct influence of the grammatical category on the phonetics of stress assignment.

Neural Network Architecture and Transient Evoked Otoacoustic Emission (TEOAE) Biometrics for Identification and Verification

This study presents a deep neural network architecture that achieves state of the art multi-session verification and identification performance for Transient Evoked Otoacoustic Emission (TEOAE) biometric system. TEOAE is a 20ms long response generated by the ear that is naturally strong against falsification, and replay attacks. It can be measured using a device with a speaker and multiple microphones. Previous TEAOE authentication methods focused on single-session or mixed-session performance. Our method focuses on multi-session authentication performance. We train a neural network model that generates a TEOAE embedding that is separable in Euclidean space by using the triplet loss function. These embeddings are used to create identity templates which are used to authenticate the user. We achieved identification accuracy of 99.3 ± 1.04%, and achieved an EER(Equal Error Rate) of 0.187 ± 0.146% for verification scenarios. Our method has achieved 7.56% performance increase for identification scenarios and 13.3% performance increase for verification scenarios over previous methods when averaged across all tests.

Optimised insert design for improved single-molecule imaging and quantification through CRISPR-Cas9 mediated knock-in

The use of CRISPR-Cas9 genome editing to introduce endogenously expressed tags has the potential to address a number of the classical limitations of single molecule localisation microscopy. In this work we present the first systematic comparison of inserts introduced through CRISPR-knock in, with the aim of optimising this approach for single molecule imaging. We show that more highly monomeric and codon optimised variants of mEos result in improved expression at the TubA1B locus, despite the use of identical guides, homology templates, and selection strategies. We apply this approach to target the G protein-coupled receptor (GPCR) CXCR4 and show a further insert dependent effect on expression and protein function. Finally, we show that compared to over-expressed CXCR4, endogenously labelled samples allow for accurate single molecule quantification on ligand treatment. This suggests that despite the complications evident in CRISPR mediated labelling, the development of CRISPR-PALM has substantial quantitative benefits.

Multiplex Detection of Nucleic Acids Using Recombinase Polymerase Amplification and a Molecular Colorimetric 7-Segment Display.

Nucleic acid analysis has become highly relevant for point-of-care (POC) diagnostics since the advent of isothermal amplification methods that do not require thermal cycling. In particular, recombinase polymerase amplification (RPA) combined with lateral flow detection offers a rapid and simple solution for field-amenable low-resource nucleic acid testing. Expanding POC nucleic acid tests for the detection of multiple analytes is vital to improve diagnostic efficiency because increased multiplexing capacity enables higher information density combined with reduced assay time and costs. Here, we investigate expanding RPA POC detection by identifying a generic multiplex RPA format that can be combined with a generic multiplex lateral flow device (LFD) to enable binary and molecular encoding for the compaction of diagnostic data. This new technology relies on the incorporation of molecular labels to differentiate nucleic acid species spatially on a lateral flow membrane. In particular, we identified additional five molecular labels that can be incorporated during the RPA reaction for subsequent coupling with LFD detection. Combined with two previously demonstrated successful labels, we demonstrate potential to enable hepta-plex detection of RPA reactions coupled to multiplex LFD detection. When this hepta-plex detection is combined with binary and molecular encoding, an intuitive 7-segment output display can be produced. We note that in all experiments, we used an identical DNA template, except for the 5′ label on the forward primer, to eliminate any effects of nucleic acid sequence amplification bias. Our proof-of-concept technology demonstration is highly relevant for developing information-compact POC diagnostics where space and time are premium commodities.

An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein-monosaccharide complexes.

Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conformational diversity. In the present work we have analyzed conventional and solvent-site biased autodock4 performance concerning receptor conformational diversity as derived from different crystal structures (apo and holo), Molecular Dynamics snapshots and Homology-based models, for 14 different lectin-monosaccharide complexes. Our results show that both conventional and biased docking yield accurate lectin-monosaccharide complexes, starting from either apo or homology-based structures, even when only moderate (45%) sequence identity templates are available. An essential element for success is a proper combination of a middle-sized (10-100 structures) conformational ensemble, derived either from Molecular dynamics or multiple homology model building. Consistent with our previous works, results show that solvent-site biased methods improve overall performance, but that results are still highly system dependent. Finally, our results also show that docking can select the correct receptor structure within the ensemble, underscoring the relevance of joint evaluation of both ligand pose and receptor conformation.