In this study, we computationally analyzed published structures of Hepatitis B virus core protein (HBc) bound with different core protein assembly modulators (CAMs) that interfere with HBV assembly. We focused on comparing the difference in CAM binding between two mutations of HBc, one that forms flat sheets, and one that forms icosahedra similar to the wild type virus capsid. We did this by aligning all currently published HBc-CAM structures by their CAM binding pockets. This allowed us to both quantitatively and qualitatively compare the CAM binding pockets of these two different structure types. We find that there are critical differences in the angle of interaction, capsid orientation angle, CAM pocket shapes and sizes, and CAM interacting residues between icosahedral and sheet based HBc structures.
Title:
Assembly-active and -inactive forms of HBV capsid protein provide distinctly different binding sites for capsid assembly modulators
Polly, P. D. 2012. Phylogenetics for Mathematica. Version 2.1. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
Initial Jetstream Featured image. Based on CentOS 6 (6.7) Development. Patched up to date as of 3/29/16, turned off the following from default startup in GNOME: Bluetooth Power Manager Volume Control PulseAudio Package Manager
Date derived from a sample of OCLC records. Data was collected for research published by "Cataloging & Classification Quarterly." Full citation of the paper is: Park, Taemin Kim & Andrea M. Morrison (2017). The Nature and Characteristics of Bibliographic Relationships in RDA Cataloging Records in OCLC at the Beginning of RDA Implementation. Cataloging & Classification Quarterly, vol. 55, issue 6. http://www.tandfonline.com/doi/full/10.1080/01639374.2017.1319451. A post-print of the paper is available here: http://hdl.handle.net/2022/21657.
Zhang YL, Hu B, Teng Y, Tu K, Zhu C (2019) A library of BASIC scripts of reaction rates for geochemical modeling using PHREEQC. Computers & Geosciences
Title:
A library of BASIC scripts of rate equations for geochemical modeling using PHREEQC
List of base-pair substitutions in "The symmetrical pattern of base-pair substitutions rates across the chromosome in Escherichia coli has multiple causes"
Polly, P.D. and A. Goswami. 2010. Modularity for Mathematica, Version 1.0. Goswami, A. & Polly, P. D. 2010 Methods for studying morphological integration, modularity and covariance evolution. In Quantitative Methods in Paleobiology. Paleontological Society Short Course, October 30th, 2010, vol. The Paleontological Society Papers (ed. J. Alroy & G. Hunt), pp. 213-243. Chicago: The Paleontological Society.
Dataset for "Comparing Transaction Logs to ILL requests to Determine the Persistence of Library Patrons In Obtaining Materials" article.
Excel file contains all data in four worksheets
Zip file contains four csv files, one for each worksheet:
- Comparing Transaction Logs to ILL - 2016 ILL Raw Data.csv
- Comparing Transaction Logs to ILL - 2015 ILL Raw Data.csv
- Comparing Transaction Logs to ILL - 2016 Zero Search Raw Data.csv
- Comparing Transaction Logs to ILL - 2015 Zero Search Raw Data.csv
Polly, P. D. 2012. Geometric morphometrics for Mathematica. Version 9.0. Department of Geological Sciences, Indiana University: Bloomington, Indiana. http://mypage.iu.edu/~pdpolly/Software.html
Title:
Geometric Morphometrics for Mathematica (Ver. 9.0)
Data transcribed from authority records matching relevant search criteria submitted to OCLC. MARC records retrieved July 11, 2017 via OCLC Connexion Client. Data entry completed September, 12, 2017. Data entered in exact transcription, retaining any errors or typos found in the retrieved records.
There are two files: a README describing the main data file, and a main data file.
The main data file is plain ASCII, tab delimited, with header comments.
Title:
Data set for article "Links among inflammation, sexual activity and ovulation: Evolutionary trade-offs and clinical implications"
The purpose of this study was to examine how IMW affects the sensory and affective components of dyspnea, exercise performance, and NIRS-derived metaboreflex effects during a cycling time to exhaustion test. Additionally, to augment the ventilatory response for better elucidation of the cardiorespiratory effects of IMW, we added hypoxia as an intervention. Using both normoxic and hypoxic conditions, our hypotheses were: 1) both sensory and affective components of dyspnea would be attenuated following IMW in each condition, 2) the extent of skeletal muscle deoxygenation (i.e., a NIRS-derived surrogate for the metaboreflex) in the leg would be reduced after IMW in each condition, and 3) participants’ time to exhaustion would be prolonged following IMW in each condition.
The Concordant Crop Sequence Boundaries improves the stabilty and accuracy of the USDA Crop Sequence Boundaries by altering the agglomeration method to be based on the simiarilty of crop sequences rather than on the longest shared boundary.
This work aims to provide accurate temporal field boundaries for the Contiguous United States through time.
The stimuli consisted of 200 items, among which 100 critical items included 25 quadruples as in (1a-d), with 50 more English-like items in which the gender of the clitic or strong pronoun reflected the gender of the antecedent (1a, b), and 50 less English-like items in which the genitive pronoun agreed in gender with the head noun of the genitive structure rather than with the antecedent (1c, d). Of these second 50 items, 25 had a female antecedent in the matrix clause as in (1c), and 25 had a male antecedent as in (1d). Similarly, half of the more English-like items (1a, b) involved masculine pronouns le and lui ‘3p.sing.masc’ and half involved feminine pronouns la and elle ‘3p.sing.fem’. Crucially, antecedent-gender-specified pronouns la and elle and antecedent-gender-unspecified pronoun son all allow the retrieval of the matrix subject as the antecedent. The 100 distractor items involved complex interrogative structures and permutations like target items, counterbalanced so that no grouping stood out.
(1a) Quelle décision le concernant est-ce que Paul a dit t que Lydie avait rejetée t
which decision him regarding is-it that Paul has said that Lydie had rejected
sans hésitation ?
without hesitation
‘Which decision regarding him did Paul say that Lydie had rejected without hesitation?’
(1b) Quelle décision à propos de lui est-ce que Paul a dit t que Lydie avait rejetée t
which decision about him is-it that Paul has said that Lydie had rejected
sans hésitation ?
without hesitation
‘Which decision about him did Paul say that Lydie had rejected without hesitation?’
(1c) Quelle décision à son sujet est-ce que Paul a dit t que Lydie avait rejetée t
which decision about him/her is-it that Paul has said that Lydie had rejected
sans hésitation ?
without hesitation
‘Which decision regarding him did Paul say that Lydie had rejected without hesitation?
(1d) Quelle décision à son sujet est-ce que Lydie a dit t que Paul avait rejetée t
which decision about him is-it that Lydie has said that Paul had rejected
sans hésitation ?
without hesitation
‘Which decision about him did Lydie say that Paul had rejected without hesitation?’
E-Prime delivered the stimuli in a rapid serial visual presentation (RSVP) reading task. The stimuli appeared word by word at the center of the screen in 36-point Consolas font, using normal orthographic conventions. They appeared in four blocks presented in random order. Within each block, stimuli were also presented in random order. Participants sat in a chair facing a computer monitor at a distance of approximately four feet. A fixation cross at the center of the screen preceded each item, lasting 700ms. The task was found to be hard but manageable to advanced L2 speakers in stimuli preparation. Due to the time required for E-prime to load each word and for the monitor’s refresh rate, the total presentation time per word was 566ms (300ms presentation, 250ms interstimulus interval, and a 16ms refresh rate between words) accommodating L2 speakers without being unnaturally slow for L1 speakers.
Respondents were trained to read questions like the stimuli and then accept or reject follow-up comprehension statements, which were presented in their entirety for a maximum of 3500ms. These comprehension checks were of several types: Some examined the propensity for an anaphoric interpretation, while others queried other aspects of the sentences. Participants quickly responded to the statements by pressing the left arrow key for ‘Yes/True’ and the right arrow key for ‘No/False.’ There was a training session of six items, which could be repeated before moving on to the experiment. In the training, all items were followed by a comprehension statement; in the task, only two thirds were. However, L1 and L2 speakers alike interpreted the pronoun as referring to the gender-matched noun phrase 70% of the time in critical stimuli. Naturally, a set of questions like our stimuli seems plausible in only a limited set of situations. Thus, respondents were introduced to a context involving two characters who were devoted followers of a television series. One of the characters, however, had missed some episodes and asked the other character questions to catch up.
The data show performance on 19 tests of auditory abilities, with 340 subjects. The data include:
1. Percent correct for each of the 19 TBAC tests used in the 2007 study
2. Arcsine transformed values of the PC scores (names ending in “AS”)
3. Percentile values for the Arcsine-transformed scores (names ending in “ASp”)
4. Latent variable scores for four independent auditory factors, plus a general auditory ability factor, as described in KWG 2007.
Sex and race data are also included.
For a subset of subjects, SAT scores, GPA, and an IQ estimate (based on SAT scores) is also provided.
Kidd, G. R., Watson, C. S., & Gygi, B. (2007). Individual differences in auditory abilities. The Journal Of The Acoustical Society Of America, 122(1), 418-435.
Title:
Individual Differences in Auditory Abilities: The Expanded TBAC dataset
This dataset was generated as part of a multi‑year research effort examining differences in autism spectrum disorder (ASD) knowledge among caregivers and providers across disciplines and levels of experience . This dataset consists of de‑identified survey data from the Autism Knowledge Survey–Revised (AKS‑R) and is provided in SPSS (.sav) format with variable names, labels, and value labels embedded. The file includes item‑level responses, derived knowledge scores, and basic demographic variables related to participant role and experience. No direct or indirect personal identifiers are included.
The core data set are citations, typically in a basically Scopus dataset format, for 92 reports published between 1987 and 2025. Included are various views of the data set and tables summarizing some of the characteristics of the data set. Also included are a few sheets explaining calculations that do one of two things: convert Return On Investment (ROI) data from the form initially presented in a report to the units used in our analyses; or how Return on Investment figures were calculated from reports that included enough data to enable ROI calculation but within which an ROI figure was not calculated.
Snapp-Childs, W., Hancock, D., Smith, P., Towns, J., Stewart, C. (2025) "Overview of best practices for quantitative analysis of economic and academic benefits of research-enabling facilities." Indiana University. https://hdl.handle.net/2022/34680. https://hdl.handle.net/2022/34680
Title:
PRISMA Data and Analyses Regarding University-based Research-enabling Facilities and ROI
In addition to participant demographics, the number and type of herbs and spices used, supplements taken, specific diseases had, and number of prescription medications taken where analyzed in this dataset. Only this select information on the forms was loaded into the dataset. SPSS was used to run the dataset statistics.
The data was collected through an online Qualtrics survey. R and R Studio were used to subset the variables of interest that can be used in statistical analysis. No specific software or scripts, however, are required to access the final CSV file.
All data was processed in Microsoft Excel. An exception is the TIRF microscopy data, which led to Microsoft Excel for final computations and building the histogram. Across all data, measurements were taken from either the absorbance or the fluorescence of a fluorescent molecule (CAM-ALEXA488, 496/515 nm) and capsid protein (280 nm).
