Analysis Software Package Research Articles

Increasing Trend and Influencing Factors of Pre-term Labor in Iran from 2005 to 2019

Background: Each year, an estimated 15 million pre-term births occur worldwide, with the incidence of pre-term labor on the rise globally. Complications arising from pre-term labor are a leading cause of mortality among children under the age of 5. Despite this, there has been limited research on the trend of pre-term labor in Iran. Objectives: This study aimed to assess the trend of pre-term labor and identify influencing factors on pre-term labor in Arak city, Iran, from 2005 to 2019. Methods: We analyzed a total of 89 307 live birth cases in Arak city from 2005 to 2019. The trend of pre-term labor over this study period was evaluated using statistical analysis software packages, specifically SPSS version 25. Linear trend analyses, as well as univariate and multivariate logistic regression analyses, were performed for statistical analysis. Results: The mean percentage of pre-term labor incidence during the first, second, and third 5-year periods was 8.9%, 10.3%, and 12.1%, respectively. Multivariate logistic regression analysis showed an increasing trend in pre-term labor incidence, even after adjusting for confounding factors (P < 0.001). Conclusions: The observed increasing trend in pre-term labor incidence indicates the necessity for a comprehensive preventive strategy. This strategy should focus on identifying high-risk pregnancies and implementing effective interventions. The increasing incidence of pre-term labor in Arak city highlights the necessity for preventive measures to reduce the burden of this condition.

Evolution of digital transformation in SMEs management through a bibliometric analysis

This document performs a systematic review of the literature and bibliometrics on the orientation of digital transformation (DT) in the organizational and management processes of small and medium-sized enterprises (SMEs) in the 2015–2022 period. For this analysis, the bibliometrix and biblioshiny software packages have been used to perform the data extraction and quantitative analysis of the research articles, obtained from the Web of Science (WOS) and Scopus databases. 311 articles related to DT in SMEs were identified as the most representative publications of the subject to be analyzed. The results show that there is a clear orientation of DT to modify organizational processes in SMEs so that they are more agile and are thus able to respond to the sudden changes that originate in the markets. The elements that delimit DT in this study are the digital technologies to implement, the strategies to follow and the digital capabilities. Finally, the main limitations, problems and gaps in the research are presented.

Features of the local community involvement in the social tourism development (case study – Serik district, Antalya, Turkey)

Introduction of the research problem. Tourism activities have shown a shift from privileged individuals with high purchasing power to individuals with lower income levels due to increased leisure time. Along with a high economic potential, tourism has an important social significance; namely, it ensures the restoration of human life forces spent in the work process and contributes to the spiritual and intellectual development of the individual, thereby increasing the quality of labor resources. Orientation to the development of tourism in view of the principles of sustainable development, with an understanding of the need for the development of social tourism and promoting the improvement of the level and quality of life of the population, ensuring accessibility for all segments of the population does not lose its relevance and the need to implement science-based initiatives and measures that should be based on specific research results, primarily geographical. In order to understand the opportunities and obstacles to the development of social tourism, the following questions remain essential: What is the attitude of the local population to the intensive development of tourism in the region of residence? What is the involvement of the local population in tourism? What problems does the local population face when organizing leisure activities? What are the obstacles, challenges, and opportunities for the organization of social tourism? Given the limited geographical studies on social tourism, this study is seen as an original and distinctive contribution. The significance of this research lies in its potential to serve as an example for Turkey. The purpose of this research is to identify the participation of the local community living in urban and rural neighborhoods of Serik district, which constitutes one of the significant destination points in Antalya province, known as the tourism capital of Turkey, in tourism activities. Additionally, if there are any factors hindering their participation, the aim is to identify and highlight them. Results, scientific novelty, practical significance. Research method was employed, and a face-to-face survey was conducted using a random sampling method between December 2022 and April 2023, reaching a total of 466 participants. Out of these, 33 surveys were used for pilot testing, and due to incomplete data, 384 surveys were entered into the SPSS software package for analysis. According to the findings, it was observed that 44.8% of the local community residing in urban and rural areas of Serik district had not had the opportunity to go on vacation in 2022 or earlier. In this context, it is evident that the most significant factor influencing the participants' inability to go on vacation is financial insufficiency. Therefore, the necessity of public and civil institutions and organizations supporting the local population with various holiday programs arises.Therefore, it is deemed necessary to integrate social tourism activities to the maximum extent possible in the tourism planning for the local community.

A software package for efficient patient trajectory analysis applied to analyzing bladder cancer development.

We present the Patient Trajectory Analysis Library (PTRA), a software package for explorative analysis of patient development. PTRA provides the tools for extracting statistically relevant trajectories from the medical event histories of a patient population. These trajectories can additionally be clustered for visual inspection and identifying key events in patient progression. The algorithms of PTRA are based on a statistical method developed previously by Jensen et al, but we contribute several modifications and extensions to enable the implementation of a practical tool. This includes a new clustering strategy, filter mechanisms for controlling analysis to specific cohorts and for controlling trajectory output, a parallel implementation that executes on a single server rather than a high-performance computing (HPC) cluster, etc. PTRA is furthermore open source and the code is organized as a framework so researchers can reuse it to analyze new data sets. We illustrate our tool by discussing trajectories extracted from the TriNetX Dataworks database for analyzing bladder cancer development. We show this experiment uncovers medically sound trajectories for bladder cancer.

Effects of D-CAG chemotherapy regimen on cognitive function in patients with acute myeloid leukaemia: A resting-state functional magnetic resonance imaging study.

Post-chemotherapy cognitive impairment, also known as 'chemobrain', is a common neurotoxic complication induced by chemotherapy, which has been reported in many cancer survivors who have undergone chemotherapy. In this study, we aimed to explore the effects of D-neneneba dicitabine, C-nenenebb cytarabine, A-aclamycin, G-granulocyte colony-stimulating factor (D-CAG) chemotherapy on cognitive function in patients with acute myeloid leukaemia (AML) and its possible central mechanisms. Twenty patients with AML and 25 matched healthy controls (HC) were enrolled in this study. The cognitive function of patients before and after D-CAG chemotherapy was evaluated by the Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog). The resting-state functional magnetic resonance imaging data were collected from all patients before and after chemotherapy intervention, as well as HC. Then, resting-state functional magnetic resonance imaging data were preprocessed using DPABI software package and regional homogeneity (ReHo) values of brain regions were calculated. Finally, ReHo values between groups were compared by Resting-State fMRI Data Analysis software package with t-tests and Alphasim method was performed for multiple comparison correction. Moreover, associations between ReHo values of altered brain regions and the scores of FACT-Cog were analysed by Pearson correlation. The total FACT-Cog scores and four factor scores of AML patients increased significantly after treatment. ReHo values showed no significant changes in patients before treatment when compared with HC. Compared with HC, ReHo values of the right middle frontal gyrus, inferior frontal gyrus (opercular part), middle occipital gyrus, and left praecuneus decreased significantly, while ReHo values of the left inferior temporal gyrus, right middle temporal gyrus, and hippocampus increased significantly in patients after treatment. Compared with patients before treatment, ReHo values decreased significantly in the right middle frontal gyrus, inferior frontal gyrus (opercular part), and middle and inferior occipital gyri of patients after treatment. In addition, ReHo values of the right inferior frontal gyrus (opercular part) were negatively correlated with the total scores of FACT-Cog and factor scores of perceived cognitive impairment in patients after treatment. There were also negative correlations between ReHo values of the right middle frontal gyrus and perceived cognitive impairment scores. The present study confirmed that D-CAG chemotherapy might cause impaired subjective self-reported cognitive functioning in AML patients, which might be related to the decreased function of certain regions in the right prefrontal lobe. These findings provided further understanding of the mechanisms involved in post-chemotherapy cognitive impairment and would help develop new therapeutic strategies for 'chemobrain' in AML patients.

Research on the Influence of Traction Load on Transient Stability of Power Grid Based on Parameter Identification

The traction load of electrified railways is a special user of the power system, which will have a significant impact on and pose a challenge to the power system after grid connection. Considering the impact and fluctuation of traction load connected to the power grid, this paper proposed a method to study the influence of traction load on the transient stability of the power grid based on parameter identification. Firstly, according to the operation characteristics of traction load, a comprehensive traction load model based on the measurement-based method of induction motor parallel power function model is selected, and the objective function of parameter identification is determined. Then, the specific steps of using the improved gray wolf optimizer (IGWO) algorithm to achieve the parameter identification of the traction comprehensive load model are introduced, including chaotic map, nonlinear convergence factor, and individual position update. Next, with the IEEE39 bus system as the network background, the load parameters identified by the measured data of a line of the Beijing–Shanghai high-speed railway are imported into the Power System Analysis Software Package (PSASP) 7.0 for transient simulation to analyze the impact of traction load on the transient stability of the power grid. Finally, three typical load models are compared with the traction load model to draw relevant conclusions, and it is verified that the traction load characteristics are different from the general load model, which provides reference for the connection of electrified railway traction load to the power grid and the economic and technical construction of the power system.

Science Mapping of Meta-Analysis in Agricultural Science

As a powerful statistical method, meta-analysis has been applied increasingly in agricultural science with remarkable progress. However, meta-analysis research reports in the agricultural discipline still need to be systematically combed. Scientometrics is often used to quantitatively analyze research on certain themes. In this study, the literature from a 30-year period (1992–2021) was retrieved based on the Web of Science database, and a quantitative analysis was performed using the VOSviewer and CiteSpace visual analysis software packages. The objective of this study was to investigate the current application of meta-analysis in agricultural sciences, the latest research hotspots, and trends, and to identify influential authors, research institutions, countries, articles, and journal sources. Over the past 30 years, the volume of the meta-analysis literature in agriculture has increased rapidly. We identified the top three authors (Sauvant D, Kebreab E, and Huhtanen P), the top three contributing organizations (Chinese Academy of Sciences, National Institute for Agricultural Research, and Northwest A&F University), and top three productive countries (the USA, China, and France). Keyword cluster analysis shows that the meta-analysis research in agricultural sciences falls into four categories: climate change, crop yield, soil, and animal husbandry. Jeffrey (2011) is the most influential and cited research paper, with the highest utilization rate for the Journal of Dairy Science. This paper objectively evaluates the development of meta-analysis in the agricultural sciences using bibliometrics analysis, grasps the development frontier of agricultural research, and provides insights into the future of related research in the agricultural sciences.

An investigation on social impact performance assessment of the social enterprises: Identification of an ideal social entrepreneurship model

AbstractThis study examines the characteristics of ideal social entrepreneurship by assessing their social impact. The use of the contemporary design and triangulation approach allows for validating information gathered from different sources. Data were collected from in‐depth interviews, focus group interviews and documentary analysis, and MAXQDA (a qualitative analysis software package) was used for data management, coding and retrieval. The performance assessment logic model was used to assess the social performance of social enterprises. The findings show that selected social ventures have created a remarkable social value that explicitly resulted in economic empowerment, community improvement, career growth and political empowerment of its intended beneficiaries. We also found a significant variation in the linkage between social performance indicators, such as inputs, activities, outputs, outcomes and impact, across the five selected case studies.

An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator.

The adaptive immune system employs an array of receptors designed to respond with high specificity to pathogens or molecular aberrations faced by the host organism. Binding of these receptors to molecular fragments-collectively referred to as antigens-initiates immune responses. These antigenic targets are recognized in their native state on the surfaces of pathogens by antibodies, whereas T cell receptors (TCR) recognize processed antigens as short peptides, presented on major histocompatibility complex (MHC) molecules. Recent research has led to a wealth of immune repertoire data that are key to interrogating the nature of these molecular interactions. However, existing tools for the analysis of these large datasets typically focus on molecular sets of a single type, forcing researchers to separately analyze strongly coupled sequences of interacting molecules. Here, we introduce a software package for the integrated analysis of immune repertoire data, capable of identifying distinct biophysical differences in isolated TCR, MHC, peptide, antibody, and antigen sequence data. This integrated analytical approach allows for direct comparisons across immune repertoire subsets and provides a starting point for the identification of key interaction hotspots in complementary receptor-antigen pairs. The software (AIMS-Automated Immune Molecule Separator) is freely available as an open access package in GUI or command-line form.

A Newly Generated Seismic Ground Response Analysis Software Package -SeisGRASP- by International Institute of Earthquake Engineering and Seismology

A Newly Generated Seismic Ground Response Analysis Software Package -SeisGRASP- by International Institute of Earthquake Engineering and Seismology

Effect of Outdoor and Pasture Foraging Accessibility on Performance and Carcass Characteristics of Noiler Birds

This experiment was carried out to determine the effect of outdoor and pasture foraging accessibility on performance responses and carcass characteristics of Noiler birds. A total number of 320 Noiler birds were divided into 5 treatments and each treatment was replicated 4 times with 16 birds per replicate. At the end of the brooding phase (2 weeks), the birds were placed in a 2 x 2 factorial arrangement (outdoor durations and pasture accessibility were considered as factors) in a completely randomised design (CRD). T1 serves as control (indoor), T2 4 hours outdoor accessibility, 8 hours outdoor, 4 hours outdoor plus pasture foraging and 8 hours outdoor plus pasture foraging for T2, T3, T4 and T5 respectively. The data obtained in this study were subjected to Analysis of Variance (ANOVA) where means were separated using Duncan Multiple Range Test (DMRT) of the Statistical Analysis Software package (SAS). The birds in T2 had significantly (P<0.05) higher final weight; similarly, higher (P<0.05) weight gain were observed in birds reared in T2. The result revealed that there are no significant (P>0.05) differences in both carcass and visceral weight proportion across all the treatments. However, considerable numerical variations exist. Higher dress weight was observed in T3 (70.333%) followed by T5, T2, T4 and T1 with 67.853, 67.372, 63.901 and 59.888% respectively. The result however, suggests non-significant (P>0.05) differences in initial weight, feed conversion ratio, feed cost per kilogram diet. It is therefore concluded that outdoor and pasture foraging has a profound effect on the performance profile of Noiler birds. It is therefore recommended for enhanced body weight and weight gain birds should also be enriched with pasture foraging material and at least 4 hours outdoor accessibility.

PyApprox: A software package for sensitivity analysis, Bayesian inference, optimal experimental design, and multi-fidelity uncertainty quantification and surrogate modeling

PyApprox is a Python-based one-stop-shop for probabilistic analysis of numerical models such as those used in the earth, environmental and engineering sciences. Easy to use and extendable tools are provided for constructing surrogates, sensitivity analysis, Bayesian inference, experimental design, and forward uncertainty quantification. The algorithms implemented represent a wide range of methods for model analysis developed over the past two decades, including recent advances in multi-fidelity approaches that use multiple model discretizations and/or simplified physics to significantly reduce the computational cost of various types of analyses. An extensive set of Benchmarks from the literature is also provided to facilitate the easy comparison of new or existing algorithms for a wide range of model analyses. This paper introduces PyApprox and its various features, and presents results demonstrating the utility of PyApprox on a benchmark problem modeling the advection of a tracer in groundwater.

ANALYSIS AND DESIGN OF BUILDING (B+G+10) WITH FLAT SLABS IN ZONE ‘II’ USING ETABS AND SAFE SOFTWARE

Structural Engineering is a Branch of civil engineering which deals in the determination of behaviour of structures in order to predict the responses of real structures like bridges, Buildings, etc. under the improvement of expected loading and external environment during the service life of the structure. Structural Engineers these days are up against the challenging task of striving for the most efficient and most economical design with accuracy in solution while guaranteeing the final design of a building is serviceable for its design lifetime. In reality it’s very difficult to predict with certainty how much damage a building will experience for a given level of ground motion, because there are number of factors that affect the behaviour of the structural systems. The objective is to emphasize on structural behaviour of a commercial building (basement + ground+10 stories) installed with flat slabs for Bangalore (Zone 2) pertaining to medium soil. The building model is designed and analysed using ETABS (Extended Three dimensional analysis of Building System) and SAFE. ETABS is the ultimate integrated software package for the structural analysis and design of buildings. SAFE is the ultimate tool for designing concrete floor and foundation systems. The lateral loads induced from wind and earthquakes in the design and analysis of building is considered. The dead loads are calculated as per IS 875(part 1)-1987, live load is taken as per IS 875(part 2)-1987, earthquake load has been taken as per IS 1893-2002(part 1) and wind load has been taken from IS 875 (part 3)1987. The manual calculations for the design of structural members were compared with the software results which were found to be satisfactory. All the design and detailing procedures for structural members were carried out as per the guidelines of Bureau of Indian Standard code books.

Running Critical Power: A Comparison Of Different Theoretical Models.

This study aimed (i) to compare the critical power (CP) and work capacity over CP (W´) values reported by the different CP models available in current analysis software packages (Golden Cheetah and Stryd platform), (ii) to locate the CP values in the power-duration curve (PDC), and (iii) to determine the influence of the CP model used on the W´ balance. Fifteen trained athletes performed four time trials (i. e., 3, 5, 10, 20 minutes) to define their PDC through different CP models: work-time (CPwork), power-1/time (CP1/time), Morton hyperbolic (CPhyp), Stryd platform (CPstryd), and Bioenergetic Golden Cheetah (CPCheetah). Three additional time trials were performed: two to locate the CP values in the PDC (30 and 60 minutes), and one to test the validity of the W' balance model (4 minutes). Significant differences (p<0.001) were reported between models for the estimated parameters (CP, W´). CPcheetah was associated with the power output developed between 10 to 20 minutes, CP1/time, CPstryd CPwork and CPhyp. The W´ reported by the three-parameter CP models overestimated the actual 4 minutes time to exhaustion, with CPwork (0.48 [- 0.19 to 1.16] minutes); and CP1/time (0.40 [- 0.13 to 0.94] minutes) being the only valid models (p≥0.240).

Long-term results of profundoplasty in patients with atherosclerotic lesions of the arteries of the lower extremities depending on the state of the distal bed

Objective. To evaluate the effectiveness of profundoplasty in patients with atherosclerotic lesions of the arteries of the lower extremities, depending on the state of the distal bed.Materials and methods. A retrospective analysis of 50 medical records and a survey of patients were carried out. The patients were divided into two groups: the first group (n=32) — patients with a satisfactory distal bed (without occlusion of the popliteal artery (PCA) and the presence of at least one tibial artery), the second group (n=18) — patients with occlusion of the PCA and / or tibial arteries. The results of the study were processed using applied statistics methods using MS Excel and the software package for statistical analysis “Statistica v. 8.0”. Differences were considered statistically significant at p &lt; 0.05.Results. The vast majority of patients who underwent profundoplasty were patients with critical lower extremities’ ischemia (F = 0.026; p&lt;0.05). Among patients with occlusion of the popliteal segment, the lower limb was saved during the first year in 44 % of cases. Among patients with a satisfactory distal bed during the year, the limb was saved in 84 % of cases.Conclusion. The state of the distal bed has a significant impact on the result of profundoplasty in the late postoperative period (p=0.008). Patients with peripheral arterial disease in the postoperative period have low compliance with ongoing conservative therapy and modification of risk factors (p&gt;0.05).

Noteworthy Disparities With Four CAQDAS Tools: Explorations in Organising Live Twitter Data

Qualitative data analysis software (QDAS) packages that support live data extraction are a relatively recent innovation. Little has been written concerning the research implications of differences in such QDAS packages’ functionalities, and how such disparities might contribute to contrasting analytical opportunities. Consequently, early-stage researchers may experience difficulties in choosing an apt QDAS for Twitter analysis. In response to both methodological gaps, this paper presents a software comparison across the four QDAS tools that support live Twitter data imports, namely, ATLAS.ti™, NVivo™, MAXQDA™ and QDA Miner™. The authors’ QDAS features checklist for these tools spotlights many differences in their functionalities. These disparities were tested through data imports and thematic coding that was derived from the same queries and codebook. The authors’ resultant QDAS experiences were compared during the first activity of a broad qualitative analysis process, ‘organising data’. Notwithstanding large difference in QDAS pricing, it was surprising how much the tools varied for aspects of qualitative research organisation. Notably, the quantum of data extracted for the same query differed, largely due to contrasts in the types and amount of data that the four QDAS could extract. Variations in how each supported visual organisation also shaped researchers’ opportunities for becoming familiar with Twitter users and their tweet content. Such disparities suggest that choosing a suitable QDAS for organising live Twitter data must dovetail with a researcher’s focus: ATLAS.ti accommodates scholars focused on wrangling unstructured data for personal meaning-making, while MAXQDA suits the mixed-methods researcher. QDA Miner’s easy-to-learn user interface suits a highly efficient implementation of methods, whilst NVivo supports relatively rapid analysis of tweet content. Such findings may help guide Twitter social science researchers and others in QDAS tool selection. Future research can explore disparities in other qualitative research phases, or contrast data extraction routes for a variety of microblogging services.

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.

On an Equation in the Ricci Solitons Theory with a Semisymmetric Connection

The study of Ricci solitons and invariant Ricci solitons with connections of various types has garnered much attention from many mathematicians. Metric connections with vector torsion, or semisymmetric connections, were first studied by E. Cartan on (pseudo) Riemannian manifolds. Later, K. Yano and I. Agricola studied tensor fields and geodesic lines of such connections, while P.N. Klepikov, E.D. Rodionov, and O.P. Khromova considered the Einstein equation of semisymmetric connections on three-dimensional locally homogeneous (pseudo) Riemannian manifolds.&#x0D; In the previous paper, the authors studied invariant Ricci solitons with a semisymmetric connection. They are an important subclass of the class of homogeneous Ricci solitons. We obtained the classification of invariant Ricci solitons on three-dimensional Lie groups with a left-invariant Riemannian metric and a semisymmetric connection different from the Levi-Civita connection. Also, the existence of invariant Ricci solitons with a non-conformal Killing vector field was proved for the such case. Moreover, a part of the proofs was obtained using the analytical calculation software packages.&#x0D; In this paper, we investigate invariant Ricci solitons on three-dimensional nonunimodular Lie groups with a left-invariant Riemannian metric and a semisymmet-ric connection. Analytical proofs of all theorems completing the classification of such solitons are presented.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1'-β-d-2'-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find G-Z pairs have stability comparable to that of A-T pairs and should therefore be included as base pairs in structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing it with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases in which Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.

RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein-RNA Cross-Linking/Mass Spectrometry Data.

Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein-protein XL-MS data, supporting stable isotope-labeled cross-linking reagents. Resultant paired peaks in mass spectra aid sensitivity and specificity of data analysis. The recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach extends the XL-MS concept to protein-RNA interactions, also employing isotope-labeled cross-link (XL) species to facilitate data analysis. Data from CLIR-MS experiments are broadly compatible with core xQuest functionality, but the required analysis approach for this novel data type presents several technical challenges not optimally served by the original xQuest package. Here we introduce RNxQuest, a Python package extension for xQuest, which automates the analysis approach required for CLIR-MS data, providing bespoke, state-of-the-art processing and visualization functionality for this novel data type. Using functions included with RNxQuest, we evaluate three false discovery rate control approaches for CLIR-MS data. We demonstrate the versatility of the RNxQuest-enabled data analysis pipeline by also reanalyzing published protein-RNA XL-MS data sets that lack isotope-labeled RNA. This study demonstrates that RNxQuest provides a sensitive and specific data analysis pipeline for detection of isotope-labeled XLs in protein-RNA XL-MS experiments.