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Programming languages in chemistry: a review of HTML5/JavaScript

Kevin J. Theisen

J Cheminform. 2019; 11: 11. Published online 2019 Feb 5. doi: 10.1186/s13321-019-0331-1

PMCID:: PMC6689888

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Detecting non-natural language artifacts for de-noising bug reports

Thomas Hirsch, Birgit Hofer

Autom Softw Eng. 2022; 29(2): 52. Published online 2022 Aug 24. doi: 10.1007/s10515-022-00350-0

PMCID:: PMC9439617

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Neurobiological Causal Models of Language Processing

Hartmut Fitz, Peter Hagoort, Karl Magnus Petersson

Neurobiol Lang (Camb) 2024; 5(1): 225–247. Published online 2024 Apr 1. doi: 10.1162/nol_a_00133

PMCID:: PMC11025648

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Parametric CAD modeling for open source scientific hardware: Comparing OpenSCAD and FreeCAD Python scripts

Felipe Machado, Norberto Malpica, Susana Borromeo

PLoS One. 2019; 14(12): e0225795. Published online 2019 Dec 5. doi: 10.1371/journal.pone.0225795

PMCID:: PMC6894851

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A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

Stefan Badelt, Casey Grun, Karthik V. Sarma, Brian Wolfe, Seung Woo Shin, Erik Winfree

J R Soc Interface. 2020 Jun; 17(167): 20190866. Published online 2020 Jun 3. doi: 10.1098/rsif.2019.0866

PMCID:: PMC7328391

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chem^f: A purely functional chemistry toolkit

Stefan Höck, Rainer Riedl

J Cheminform. 2012; 4: 38. Published online 2012 Dec 20. doi: 10.1186/1758-2946-4-38

PMCID:: PMC3660204

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A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank

Andrey Smelter, Morgan Astra, Hunter N. B. Moseley

BMC Bioinformatics. 2017; 18: 175. Published online 2017 Mar 17. doi: 10.1186/s12859-017-1580-5

PMCID:: PMC5356280

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Artificial intelligence driven design of catalysts and materials for ring opening polymerization using a domain-specific language

Nathaniel H. Park, Matteo Manica, Jannis Born, James L. Hedrick, Tim Erdmann, Dmitry Yu. Zubarev, Nil Adell-Mill, Pedro L. Arrechea

Nat Commun. 2023; 14: 3686. Published online 2023 Jun 21. doi: 10.1038/s41467-023-39396-3

Correction in:: Nat Commun. 2023; 14: 4469.

PMCID:: PMC10284867

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Bellman’s GAP—a language and compiler for dynamic programming in sequence analysis

Georg Sauthoff, Mathias Möhl, Stefan Janssen, Robert Giegerich

Bioinformatics. 2013 Mar 1; 29(5): 551–560. Published online 2013 Jan 25. doi: 10.1093/bioinformatics/btt022

PMCID:: PMC3582264

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owlcpp: a C++ library for working with OWL ontologies

Mikhail K. Levin, Lindsay G. Cowell

J Biomed Semantics. 2015; 6: 35. Published online 2015 Sep 16. doi: 10.1186/s13326-015-0035-z

PMCID:: PMC4574266

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StreamQRE: Modular Specification and Efficient Evaluation of Quantitative Queries over Streaming Data

Konstantinos Mamouras, Mukund Raghothaman, Rajeev Alur, Zachary G. Ives, Sanjeev Khanna

Proc ACM SIGPLAN Conf Program Lang Des Implement. Author manuscript; available in PMC 2018 Jun 1.

Published in final edited form as: Proc ACM SIGPLAN Conf Program Lang Des Implement. 2017 Jun; 52(6): 693–708. doi: 10.1145/3140587.3062369

PMCID:: PMC5687100

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A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository

Andrey Smelter, Hunter N. B. Moseley

Metabolomics. 2018; 14(5): 64. Published online 2018 Apr 20. doi: 10.1007/s11306-018-1356-6

PMCID:: PMC5910482

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Linguistic aspects of stuttering: research updates on the language-fluency interface

Shelley B. Brundage, Nan Bernstein Ratner

Top Lang Disord. Author manuscript; available in PMC 2023 Jan 1.

Published in final edited form as: Top Lang Disord. 2022 Jan-Mar; 42(1): 5–23. doi: 10.1097/TLD.0000000000000269

PMCID:: PMC8936424

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AUX: A scripting language for auditory signal processing and software packages for psychoacoustic experiments and education

Bomjun J. Kwon

Behav Res Methods. 2012; 44(2): 361–373. Published online 2011 Nov 20. doi: 10.3758/s13428-011-0161-1

PMCID:: PMC3356523

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Clinical bracket failure rates between different bonding techniques: a systematic review and meta-analysis

Csaba Dudás, László Márk Czumbel, Szabolcs Kiss, Noémi Gede, Péter Hegyi, Krisztina Mártha, Gábor Varga

Eur J Orthod. 2023 Apr; 45(2): 175–185. Published online 2022 Oct 12. doi: 10.1093/ejo/cjac050

PMCID:: PMC10065138

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Identifying Developmental Language Disorder in Vietnamese Children

Giang T. Pham, Sonja Pruitt-Lord, Catherine E. Snow, Yen Hoang Thi Nguyen, Ben Phạm, Thuy Bich Thi Dao, Ngoc Bich Thi Tran, Linh Thuy Pham, Hien Thu Hoang, Quynh Diem Dam

J Speech Lang Hear Res. 2019 May; 62(5): 1452–1467. Published online 2019 Apr 17. doi: 10.1044/2019_JSLHR-L-18-0305

PMCID:: PMC6808316

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An integrated platform for intuitive mathematical programming modeling using LaTeX

Charalampos P. Triantafyllidis, Lazaros G. Papageorgiou

PeerJ Comput Sci. 2018; 4: e161. Published online 2018 Sep 10. doi: 10.7717/peerj-cs.161

PMCID:: PMC7924498

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Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber, Vincent J. Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S. Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D. Hansen, Rafael A. Irizarry, Michael Lawrence, Michael I. Love, James MacDonald, Valerie Obenchain, Andrzej K. Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K. Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan

Nat Methods. Author manuscript; available in PMC 2015 Jul 21.

Published in final edited form as: Nat Methods. 2015 Feb; 12(2): 115–121. doi: 10.1038/nmeth.3252

PMCID:: PMC4509590

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Biotite: new tools for a versatile Python bioinformatics library

Patrick Kunzmann, Tom David Müller, Maximilian Greil, Jan Hendrik Krumbach, Jacob Marcel Anter, Daniel Bauer, Faisal Islam, Kay Hamacher

BMC Bioinformatics. 2023; 24: 236. Published online 2023 Jun 5. doi: 10.1186/s12859-023-05345-6

PMCID:: PMC10243083

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Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface

Konrad Hinsen

PeerJ Comput Sci. 2018; 4: e158. Published online 2018 Jul 23. doi: 10.7717/peerj-cs.158

PMCID:: PMC7924627

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Fig. 4

Lateralization indexes (LIs), significant group lateralizations, and between-group comparisons using combined tasks analysis (CTA), within single (right panel) and extended (left panel) ROIs. The box plots depict group lateralization for each ROI, with positive and negative LIs reflecting left and right, respectively, and with significant left or right lateralizations (p<0.05) outlined by bold lines. The p-values of between-group comparisons are indicated, with significant between-group differences outlined by a square bracket with a star.
^ap-value from two-sided two sample t-test.
IFG=inferior frontal gyrus; STG=superior temporal gyrus; SMG=supramarginal gyrus.
“Temporo-parietal language ROI”=STG and SMG; “Frontal language ROI”=IFG (opercularis and triangularis) and insula; “Language ROI”=“frontal language” and “temporo-parietal language” ROIs; “Non-language ROI”=whole brain (i.e. all AAL ROIs) except “language ROI”.

Abnormal functional lateralization and activity of language brain areas in typical specific language impairment (developmental dysphasia)

Brain. ;134(Pt 10):3044-3058.
Fig. 3

Laterality indexes (LIs), significant group lateralizations, and between-group comparisons within the ROIs for each single language task. The box plots depict group lateralization for each ROI, with positive and negative LIs reflecting left and right, respectively, and with significant left or right lateralizations (p<0.05) outlined by bold lines. The p-values of between-group comparisons are indicated, with significant between-group differences outlined by a square bracket with a star.
^ap-value of group factor from analysis of covariance with factors age and group.
Oper=opercularis; Tri=triangularis; Sup=superior.

Abnormal functional lateralization and activity of language brain areas in typical specific language impairment (developmental dysphasia)

Brain. ;134(Pt 10):3044-3058.
Fig. 2

Multigroup SEM of the mediated contribution of language on vaccination across T1 and T2 Note. Coefficients are non-standardized. Total effects are in parentheses. Coefficients with brackets indicate significant differences between groups, such that T1 coefficients are displayed outside the bracket and T2 coefficients are inside the brackets. ***p < .001.

The relation between conspiracism, government trust, and COVID-19 vaccination intentions: The key role of motivation

Soc Sci Med. 2022 May;301:114926-114926.
Figure 1:Whole-cohort testing characteristics.

Asterisk on x-axis label indicates significant group difference below testing norms (p<0.05); starred bracket indicates significant discrepancy in performance between domains (p<0.05). T-scores are normed against typical validation groups with mean scores of 50 and a standard deviation of 10.

Preschool language outcomes following perinatal hypoxic-ischemic encephalopathy in the age of therapeutic hypothermia

Dev Neurosci. :1-11.