cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Harnessing nanomedicine to overcome the immunosuppressive tumor microenvironment
Creators: name: Wang, Andrew Z
name: Hyun, Hyesun
name: Li, Lian-tao
name: Sun, Bo
Publisher: name: Springer Nature
Year: 2020

description: Cancer immunotherapy has received extensive attention due to its ability to activate the innate or adaptive immune systems of patients to combat tumors. Despite a few clinical successes, further endeavors are still needed to tackle unresolved issues, including limited response rates, development of resistance, and immune-related toxicities. Accumulating evidence has pinpointed the tumor microenvironment (TME) as one of the major obstacles in cancer immunotherapy due to its detrimental impacts on tumor-infiltrating immune cells. Nanomedicine has been battling with the TME in the past several decades, and the experience obtained could be exploited to improve current paradigms of immunotherapy. Here, we discuss the metabolic features of the TME and its influence on different types of immune cells. The recent progress in nanoenabled cancer immunotherapy has been summarized with a highlight on the modulation of immune cells, tumor stroma, cytokines and enzymes to reverse the immunosuppressive TME.
Additional file 1 of Zinc supplementation and light intensity affect 2-acetyl-1-pyrroline (2AP) formation in fragrant rice
Creators: name: Shuochen, Jiang
name: Lihe, Zhang
name: Fenqin, Hu
name: Xiangru, Tang
name: Bin, Du
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Additional file 1: Supplementary Fig. 1. Maximum temperature, minimum temperature, mean temperature, daily rainfall and daily sunshine hours from April 1 to September 15 in the experiment conducted during 2019–2021.
Oxidizing Python: writing extensions in Rust
Creators: name: Luiz Carlos Irber Junior
Publisher: name: F1000 Research Limited
Year: 2018

description: Python has a mature ecosystem for extensions using C/C++, with Cython being part of the standard toolset for scientific programming. Even so, C/C++ still have many drawbacks, ranging from smaller annoyances (like library packaging, versioning and build systems) to serious one like buffer overflows and undefined behavior leading to security issues. Rust is a system programming language trying to avoid many of the C/C++ pitfalls, on top of providing a good development workflow and memory safety guarantees. This work presents a way to write extensions in Rust and use them in Python, using sourmash as an example.
sj-docx-1-fst-10.1177_10820132221147079 - Supplemental material for Development of novel heat-treated sausage with Pleurotus ostreatus: Low energy, enhanced bioactivity, reduced amount of meat and fat
Creators: name: Doğan, Cemhan
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 111199 Nutrition and Dietetics not elsewhere classified
subject: FOS: Health sciences

description: Supplemental material, sj-docx-1-fst-10.1177_10820132221147079 for Development of novel heat-treated sausage with Pleurotus ostreatus: Low energy, enhanced bioactivity, reduced amount of meat and fat by Cemhan Doğan in Food Science and Technology International
The ascent of water-rich magma and decompression heating: A thermodynamic analysis
Creators: name: Glazner, Allen F.
Publisher: name: Mineralogical Society of America
Year: 2019

description: The ascent of hydrous, silica-rich magmas from the lower crust drives volcanic eruptions, builds the upper crust, and concentrates metals such as Cu, Au, and Mo into ore deposits. Owing to the negative slope of the melting curve for granitic materials in the presence of water, it has long been assumed that water-saturated magmas move into the subsolidus field and freeze upon ascent; therefore, for magma to rise it must be water-undersaturated at a temperature well above the solidus. This assumption ignores the considerable energy released by crystallization. Here I show that if magma ascent is treated as an adiabatic, reversible process, then water-saturated magma can rise to the surface, following the solidus to shallow depth and higher temperature as it undergoes modest crystallization and vapor exsolution. Decompression heating is an alternative to magma recharge for explaining pre-eruptive reheating seen in many volcanic systems and accounts for paradoxical growth of quartz during a heating event. The viscosity increase that accompanies vapor exsolution as magma rises to shallow depth explains why silicic magmas tend to stop in the upper crust rather than erupting, producing the observed compositional dichotomy between plutonic and volcanic rocks.
BioXSD | BioJSON | BioYAML – towards unified formats for sequences, alignments, features, and annotations
Creators: name: Matúš Kalaš
name: Gundersen, Sveinung
name: Jonassen, Inge
name: BioXSD, The
Publisher: name: F1000 Research Limited
Year: 2018

description: Project website:  http://bioxsd.org
Source code:  https://github.com/bioxsd/bioxsd
Licence:  Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0). Additional Code of Conduct for development and derived work is stated in BioXSD-1.1.xsd.
Contact:  developers@bioxsd.org, @BioXSD

BioXSD has been developed as a tree-structured data model and exchange format for basic bioinformatics data, centered around bio-polymer sequence [1,2]. BioXSD allows integration of diverse features, information, measurements, and inferred values about a biological molecule or its part or context, annotated with provenance and reliability metadata, ontology concepts, scientific remarks, and conclusions.

BioJSON and BioYAML are alternatives to the XML serialization of BioXSD, following the same data model. As tree-structured data formats, BioXSD, BioJSON, and BioYAML are particularly suitable for programming in object-oriented languages, and for use with web applications and web APIs (Web services), while at the same time allowing a reasonable level of human readability. BioXSD|BioJSON|BioYAML are now further developed together with GTrack, GSuite, and BTrack (a family of universal tabular formats for features and metadata [2,3]),  under the umbrella of ELIXIR Norway, with an open group of international contributors. The BioXSD|GTrack family of generic, convenient, and interoperable data formats provides an added value for integrative bioinformatics and omics.

[1] Kalaš, M., Puntervoll, P., Joseph, A., Bartaševičiūtė (now Karosiene), E., Töpfer, A., Venkataraman, P., Pettifer, S., Bryne, J.C., Ison, J., Blanchet, C., Rapacki, K. and Jonassen, I. (2010). BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics, 26, i540-i546. DOI: 10.1093/bioinformatics/btq391 PMID: 20823319 Open Access

[2] Gundersen, S., Kalaš, M., Abul, O., Frigessi, A., Hovig, E. and Sandve, G.K. (2011). Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics, 212, 494. DOI: 10.1186/1471-2105-12-494 PMID: 22208806 Open Access

[3] Gundersen S., Kalaš M., Simovski B. et al. (2018). The GTrack ecosystem - expressive file formats for analysis of genomic track data [version 1; not peer reviewed]. F1000Research, 7(ELIXIR):270. Poster. DOI: 10.7490/f1000research.1115292.1 Open Access
sj-docx-1-aut-10.1177_13623613221144353 – Supplemental material for Health conditions and service use of autistic women and men: A retrospective population-based case–control study
Creators: name: Tint, Ami
name: Chung, Hannah
name: Lai, Meng-Chuan
name: Balogh, Robert
name: Lin, Elizabeth
name: Durbin, Anna
name: Lunsky, Yona
Publisher: name: SAGE Journals
Year: 2023
Subjects: Psychology not elsewhere classified
Psychiatry (incl. Psychotherapy)
Public Health and Health Services not elsewhere classified
Education
Special Education and Disability

description: Supplemental material, sj-docx-1-aut-10.1177_13623613221144353 for Health conditions and service use of autistic women and men: A retrospective population-based case–control study by Ami Tint, Hannah Chung, Meng-Chuan Lai, Robert Balogh, Elizabeth Lin, Anna Durbin and Yona Lunsky in Autism
title: Polycrystalline Lpcvd 3c-Sic Thin Films on Sio2 Using Alternating Supply Deposition
Creators: name: Moll, Philipp
name: Schwarz, Sabine
name: Pfusterschmied, Georg
name: Artner, Werner
name: Schmid, Ulrich
Publisher: name: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
Year: 2024
Subjects: 3C-SiC
alternating supply deposition
LPCVD, silicon carbide
SiO2

description: In this paper, we demonstrate the deposition of 3C-SiC thin films on SiO2 using the alternating supply deposition (ASD) technique in a low-pressure chemical vapor deposition (LPCVD) furnace. We provide data of the thin film properties showing strong dependencies on the process gas flow rates of silane, propane and hydrogen. For comparative reasons all gas flow compositions were performed on <100> silicon and SiO2. A decreased rate of growth per cycle of ∼37 % was discovered on SiO2. X-ray photoelectron spectroscopy (XPS) depth profiling revealed an oxygen content of 7.5 % ±2.5 % throughout the entire thin film when grown on SiO2. High resolution transmission electron microscopy (HRTEM) showed a 15 nm amorphous carbon layer at the 3C-SiC/Si interface. Conversely, on SiO2 a 10 nm graphite layer was determined as intermediate layer leading to prominent <111> 3C-SiC X-ray diffraction (XRD) peaks. Independent of the substrate type a similar microstructure is observed in cross-sectional analyses. Atomic force microscopy (AFM) surface roughness measurements showed for all SiO2 thin films lower values with a minimum of 4.9 nm (RMS), compared to 7 nm on Si. The electrical film resistivity was determined on SiO2 with CTLM analysis, depending on the process gas composition. The gained knowledge is beneficial for MEMS applications, where tailored 3C-SiC-on-SiO2 structures are desired.
Cheminformatics-driven discovery of polymeric micelle formulations for poorly soluble drugs
Creators: name: Andrade, Carolina H
name: Tropsha, Alexander
name: Kabanov, Alexander
name: Vinod, Natasha
name: Hwang, Duhyeong
name: Lim, Chaemin
name: Alves, Vinicius M
name: Sokolsky-Papkov, Marina
name: Muratov, Eugene
name: Varlamova, Ekaterina
Publisher: name: American Association for the Advancement of Science (AAAS)
Year: 2019

description: Many drug candidates fail therapeutic development because of poor aqueous solubility. We have conceived a computer-aided strategy to enable polymeric micelle-based delivery of poorly soluble drugs. We built models predicting both drug loading efficiency (LE) and loading capacity (LC) using novel descriptors of drug-polymer complexes. These models were employed for virtual screening of drug libraries, and eight drugs predicted to have either high LE and high LC or low LE and low LC were selected. Three putative positives, as well as three putative negative hits, were confirmed experimentally (implying 75% prediction accuracy). Fortuitously, simvastatin, a putative negative hit, was found to have the desired micelle solubility. Podophyllotoxin and simvastatin (LE of 95% and 87% and LC of 43% and 41%, respectively) were among the top five polymeric micelle-soluble compounds ever studied experimentally. The success of the strategy described herein suggests its broad utility for designing drug delivery systems.
sj-docx-1-hpq-10.1177_13591053221144442 – for Social support profiles correlate with depressive symptoms among Chinese parents during the COVID-19 pandemic: A latent profile analysis
Creators: name: Bai, Yashuang
name: Yang, Fan
name: Chen, Minglong
name: Zhang, Bo
name: Liu, Xiaohan
name: Huang, Ning
name: Riem, Madelon ME
name: Guo, Jing
Publisher: name: SAGE Journals
Year: 2023
Subjects: Psychology not elsewhere classified
Psychiatry (incl. Psychotherapy)
Public Health and Health Services not elsewhere classified

description: sj-docx-1-hpq-10.1177_13591053221144442 for Social support profiles correlate with depressive symptoms among Chinese parents during the COVID-19 pandemic: A latent profile analysis by Yashuang Bai, Fan Yang, Minglong Chen, Bo Zhang, Xiaohan Liu, Ning Huang, Madelon ME Riem and Jing Guo in Journal of Health Psychology
Additional file 1 of Dietary and lifestyle indices for hyperinsulinemia and colorectal cancer risk: a case-control study
Creators: name: Sicahni, Pegah Hadi
name: Makhtoomi, Maede
name: Leilami, Kimia
name: Shateri, Zainab
name: Mohammadi, Farzaneh
name: Nouri, Mehran
name: Omidbeigi, Niloofar
name: Mehrabani, Sanaz
name: Rashidkhani, Bahram
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Mental Health

description: Supplementary Material 1
Additional file 1 of Application of theoretical domains framework to explore the enablers and barriers to physical activity among university staff and students: a qualitative study
Creators: name: Ndupu, Lawrence Bismarck
name: Staples, Vicki
name: Lipka, Sigrid
name: Faghy, Mark
name: Bessadet, Nawel
name: Bussell, Chris
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1. Group interview guide. This table illustrates the lead researchers’ questions and potential prompts developed for physical activity using the theoretical domains framework (TDF).
sj-pdf-2-hpq-10.1177_13591053221144442 – for Social support profiles correlate with depressive symptoms among Chinese parents during the COVID-19 pandemic: A latent profile analysis
Creators: name: Bai, Yashuang
name: Yang, Fan
name: Chen, Minglong
name: Zhang, Bo
name: Liu, Xiaohan
name: Huang, Ning
name: Riem, Madelon ME
name: Guo, Jing
Publisher: name: SAGE Journals
Year: 2023
Subjects: Psychology not elsewhere classified
Psychiatry (incl. Psychotherapy)
Public Health and Health Services not elsewhere classified

description: sj-pdf-2-hpq-10.1177_13591053221144442 for Social support profiles correlate with depressive symptoms among Chinese parents during the COVID-19 pandemic: A latent profile analysis by Yashuang Bai, Fan Yang, Minglong Chen, Bo Zhang, Xiaohan Liu, Ning Huang, Madelon ME Riem and Jing Guo in Journal of Health Psychology
SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules
Creators: name: Rai, Ganesha
name: Yasgar, Adam
name: Korn, Daniel
name: Tropsha, Alexander
name: Zakharov, Alexey V.
name: Bowler, Kyle H.
name: Braga, Rodolpho C.
name: Capuzzi, Stephen J.
name: Muratov, Eugene N.
name: Simeonov, Anton
name: Alves, Vinicius M.
name: Hochuli, Joshua E.
Publisher: name: American Chemical Society (ACS)
Year: 2020

description: Small, colloidally aggregating molecules (SCAMs) are the most common source of false positives in high-throughput screening (HTS) campaigns. Although SCAMs can be experimentally detected and suppressed by the addition of detergent in the assay buffer, detergent sensitivity is not routinely monitored in HTS. Computational methods are thus needed to flag potential SCAMs during HTS triage. In this study, we have developed and rigorously validated quantitative structure-interference relationship (QSIR) models of detergent-sensitive aggregation in several HTS campaigns under various assay conditions and screening concentrations. In particular, we have modeled detergent-sensitive aggregation in an AmpC β-lactamase assay, the preferred HTS counter-screen for aggregation, as well as in another assay that measures cruzain inhibition. Our models increase the accuracy of aggregation prediction by ~53% in the β-lactamase assay and by ~46% in the cruzain assay compared to previously published methods. We also discuss the importance of both assay conditions and screening concentrations in the development of QSIR models for various interference mechanisms besides aggregation. The models developed in this study are publicly available for fast prediction within the SCAM detective web application (https://scamdetective.mml.unc.edu/).
sj-docx-1-ajr-10.1177_19458924221148566 - Supplemental material for Allegations of Failure to Obtain Informed Consent in Otolaryngology: Evidenced-Based Recommendations for Sinus Surgeons
Creators: name: Fritz, Christian G.
name: Romeo, Dominic J.
name: Lowery, Anne S.
name: Rajasekaran, Karthik
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 110315 Otorhinolaryngology
subject: FOS: Clinical medicine

description: Supplemental material, sj-docx-1-ajr-10.1177_19458924221148566 for Allegations of Failure to Obtain Informed Consent in Otolaryngology: Evidenced-Based Recommendations for Sinus Surgeons by Christian G. Fritz, Dominic J. Romeo and Anne S. Lowery, Karthik Rajasekaran in American Journal of Rhinology & Allergy
Emerging Nano-/Microapproaches for Cancer Immunotherapy
Creators: name: Mi, Yu
name: Wang, Andrew Z.
name: Vincent, Benjamin G.
name: Hagan, C. Tilden
Publisher: name: Wiley
Year: 2019

description: Cancer immunotherapy has achieved remarkable clinical efficacy through recent advances such as chimeric antigen receptor-T cell (CAR-T) therapy, immune checkpoint blockade (ICB) therapy, and neoantigen vaccines. However, application of immunotherapy in a clinical setting has been limited by low durable response rates and immune-related adverse events. The rapid development of nano-/microtechnologies in the past decade provides potential strategies to improve cancer immunotherapy. Advances of nano-/microparticles such as virus-like size, high surface to volume ratio, and modifiable surfaces for precise targeting of specific cell types can be exploited in the design of cancer vaccines and delivery of immunomodulators. Here, the emerging nano-/microapproaches in the field of cancer vaccines, immune checkpoint blockade, and adoptive or indirect immunotherapies are summarized. How nano-/microparticles improve the efficacy of these therapies, relevant immunological mechanisms, and how nano-/microparticle methods are able to accelerate the clinical translation of cancer immunotherapy are explored.
A Perspective and a New Integrated Computational Strategy for Skin Sensitization Assessment
Creators: name: Tropsha, Alexander
name: Capuzzi, Stephen J.
name: Andrade, Carolina Horta
name: Silva, Arthur C.
name: Muratov, Eugene N.
name: Hartung, Thomas
name: Braga, Rodolpho C.
name: Alves, Vinicius M.
name: Borba, Joyce V. B.
name: Luechtefeld, Thomas
Publisher: name: American Chemical Society (ACS)
Year: 2018

description: Traditionally, the skin sensitization potential of chemicals has been assessed using animal models. Due to growing ethical, political, and financial concerns, sustainable alternatives to animal testing need to be developed. As publicly available skin sensitization data continues to grow, computational approaches, such as alert-based systems, read-across, and QSAR models, are expected to reduce or replace animal testing for the prediction of human skin sensitization potential. Herein, we discuss current computational approaches to predicting skin sensitization and provide future perspectives of the field. As a proof-of-concept study, we have compiled the largest skin sensitization data set in the public domain and benchmarked several methods for building skin sensitization models. We propose a new comprehensive approach, which integrates multiple QSAR models developed with in vitro, in chemico, animal, and human data, and a Naive Bayes model for predicting human skin sensitization. Both the data sets and the KNIME implementation of the model allowing skin sensitization prediction for molecules of interest have been made freely available.
sj-docx-1-jia-10.1177_23259582221144448 - Supplemental material for “It’s Still in the Test Tube and Finding out How the Experiment Ends… ”. A Qualitative Study on Health and Aging in Older Gay Males Living with HIV in England
Creators: name: Licchelli, Stefano
name: King, Andrew
name: Smith, Kimberley J.
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: 111702 Aged Health Care
subject: 111799 Public Health and Health Services not elsewhere classified

description: Supplemental material, sj-docx-1-jia-10.1177_23259582221144448 for “It’s Still in the Test Tube and Finding out How the Experiment Ends… ”. A Qualitative Study on Health and Aging in Older Gay Males Living with HIV in England by Stefano Licchelli, Andrew King and Kimberley J. Smith in Journal of the International Association of Providers of AIDS Care (JIAPAC)
Supplemental Material, sj-docx-1-cpt-10.1177_10742484221146375 - Up-Titration of Sacubitril/Valsartan Among Patients With Heart Failure and Preserved Ejection Fraction
Creators: name: Matsumura, Koichiro
name: Ijichi, Takeshi
name: Morimoto, Junko
name: Takabayashi, Kensuke
name: Miho, Mitsunori
name: Ueno, Keisuke
name: Yagi, Eijiro
name: Takase, Toru
name: Ueno, Masafumi
name: Nakazawa, Gaku
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: Cardiology
subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: 110203 Respiratory Diseases
subject: 110323 Surgery

description: Supplemental Material, sj-docx-1-cpt-10.1177_10742484221146375 for Up-Titration of Sacubitril/Valsartan Among Patients With Heart Failure and Preserved Ejection Fraction by Koichiro Matsumura, Takeshi Ijichi, Junko Morimoto, Kensuke Takabayashi, Mitsunori Miho, Keisuke Ueno, Eijiro Yagi, Toru Takase, Masafumi Ueno and Gaku Nakazawa in Journal of Cardiovascular Pharmacology and Therapeutics
Additional file 2 of Dietary and lifestyle indices for hyperinsulinemia and colorectal cancer risk: a case-control study
Creators: name: Sicahni, Pegah Hadi
name: Makhtoomi, Maede
name: Leilami, Kimia
name: Shateri, Zainab
name: Mohammadi, Farzaneh
name: Nouri, Mehran
name: Omidbeigi, Niloofar
name: Mehrabani, Sanaz
name: Rashidkhani, Bahram
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Mental Health

description: Supplementary Material 2
sj-docx-2-cpc-10.1177_10556656221148902 - Supplemental material for Treatment of Asymmetric Crying Face by Fascia lata Grafting
Creators: name: Lei, Bowen
name: Huang, Qinghua
name: Li, Binghang
name: Ma, Hengyuan
name: Yang, Bin
Publisher: name: SAGE Journals
Year: 2023
Subjects: Surgery

description: Supplemental material, sj-docx-2-cpc-10.1177_10556656221148902 for Treatment of Asymmetric Crying Face by Fascia lata Grafting by Bowen Lei, MD, Qinghua Huang, MD, Binghang Li, MD, Hengyuan Ma, MD, and Bin Yang, MD, PHD in The Cleft Palate Craniofacial Journal
Identifying Security Critical Properties for the Dynamic Verification of a Processor
Creators: name: Griggs, Christopher
name: Chi, Andrew
name: Zhang, Rui
name: Sturton, Cynthia
name: Stanley, Natalie
Publisher: name: Association for Computing Machinery (ACM)
Year: 2017

description: We present a methodology for identifying security critical properties for use in the dynamic verification of a processor. Such verification has been shown to be an effective way to prevent exploits of vulnerabilities in the processor, given a meaningful set of security properties. We use known processor errata to establish an initial set of security-critical invariants of the processor. We then use machine learning to infer an additional set of invariants that are not tied to any particular, known vulnerability, yet are critical to security. We build a tool chain implementing the approach and evaluate it for the open-source OR1200 RISC processor. We find that our tool can identify 19 (86.4%) of the 22 manually crafted security-critical properties from prior work and generates 3 new security properties not covered in prior work.
sj-docx-1-hss-10.1177_15563316221145156 – Supplemental material for Lumbar Lordosis Distribution in Asymptomatic Adult Volunteers: A Systematic Review
Creators: name: Ge, Tenghui
name: Xie, Linzhen
name: Li, Jianing
name: Ao, Jintao
name: Wu, Jingye
name: Sun, Yuqing
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 110323 Surgery
subject: FOS: Clinical medicine

description: Supplemental material, sj-docx-1-hss-10.1177_15563316221145156 for Lumbar Lordosis Distribution in Asymptomatic Adult Volunteers: A Systematic Review by Tenghui Ge, Linzhen Xie, Jianing Li, Jintao Ao, Jingye Wu and Yuqing Sun in HSS Journal®: The Musculoskeletal Journal of Hospital for Special Surgery
Additional file 2 of Application of theoretical domains framework to explore the enablers and barriers to physical activity among university staff and students: a qualitative study
Creators: name: Ndupu, Lawrence Bismarck
name: Staples, Vicki
name: Lipka, Sigrid
name: Faghy, Mark
name: Bessadet, Nawel
name: Bussell, Chris
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 2. This table provides all the enablers and barriers to physical activity among university staff and students, with description of the TDF domains, sub-themes, and sample quotes from the participants.
Assessing Clinical Relevance of Uremic Toxins
Creators: name: Hostetter, Thomas H
name: Flythe, Jennifer E
Publisher: name: Wolters Kluwer
Year: 2019

description: Standard hemodialysis works. Indeed, this procedure maintains life in hundreds of thousands of people with little or no kidney function. Moreover, severe symptoms of uremia—coma, seizures, acidosis, hyperkalemia, and pulmonary edema—are readily reversed by dialysis. However, it is also now conspicuous that life on maintenance hemodialysis is short, with about 20%of the ESKDpopulation in the United States dying each year, yielding a 3–5years survival rate of only 50%. Although mortality is appallingly high, patient symptom burden is great, and for many patients, these symptoms are more daunting than the dismal mortality prospects. Quality of life has remained consistently poor for patients on hemodialysis. A recent survey reported that the physical symptoms of insomnia, fatigue, andcramping, andmoodsymptoms of anxiety, depression, and frustration were paramount concerns among patients
Additional file 3 of Dietary and lifestyle indices for hyperinsulinemia and colorectal cancer risk: a case-control study
Creators: name: Sicahni, Pegah Hadi
name: Makhtoomi, Maede
name: Leilami, Kimia
name: Shateri, Zainab
name: Mohammadi, Farzaneh
name: Nouri, Mehran
name: Omidbeigi, Niloofar
name: Mehrabani, Sanaz
name: Rashidkhani, Bahram
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Mental Health

description: Supplementary Material 3
Additional file 1 of The angiotensin II receptors type 1 and 2 modulate astrocytes and their crosstalk with microglia and neurons in an in vitro model of ischemic stroke
Creators: name: Olschewski, Daniel Navin
name: Nazarzadeh, Nilufar
name: Lange, Felix
name: Koenig, Anna Maria
name: Kulka, Christina
name: Abraham, Jella-Andrea
name: Blaschke, Stefan Johannes
name: Merkel, Rudolf
name: Hoffmann, Bernd
name: Fink, Gereon Rudolf
name: Schroeter, Michael
name: Rueger, Maria Adele
name: Vay, Sabine Ulrike
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Mental Health

description: Additional file 1: Figure S1.
sj-docx-5-hss-10.1177_15563316221145156 – Supplemental material for Lumbar Lordosis Distribution in Asymptomatic Adult Volunteers: A Systematic Review
Creators: name: Ge, Tenghui
name: Xie, Linzhen
name: Li, Jianing
name: Ao, Jintao
name: Wu, Jingye
name: Sun, Yuqing
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 110323 Surgery
subject: FOS: Clinical medicine

description: Supplemental material, sj-docx-5-hss-10.1177_15563316221145156 for Lumbar Lordosis Distribution in Asymptomatic Adult Volunteers: A Systematic Review by Tenghui Ge, Linzhen Xie, Jianing Li, Jintao Ao, Jingye Wu and Yuqing Sun in HSS Journal®: The Musculoskeletal Journal of Hospital for Special Surgery
CWLProv – Interoperable retrospective provenance capture and its challenges
Creators: name: Khan, Farah Zaib
name: Soiland-Reyes, Stian
name: Sinnott, Richard O.
name: Lonie, Andrew
name: Crusoe, Michael R.
Publisher: name: F1000 Research Limited
Year: 2018

description: Source Code snapshot: https://github.com/common-workflow-language/cwltool/tree/921fc1d387930a0a5fede332c43f039697f6a4de	License: https://www.apache.org/licenses/LICENSE-2.0	Research Object: https://doi.org/10.5281/zenodo.1215611Abstract (accepted for poster and talk at BOSC2018)

The automation of data analysis in the form of scientific workflows is a widely adopted practice in many fields of research nowadays. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still a number of challenges associated with the effective sharing, publication, understandability and reproducibility of such workflows due to the incomplete capture of provenance and the dependence on the particular technical (software) platforms.

We present CWLProv, an approach for retrospective provenance-capture utilizing open source community-driven standards involving application and customization of workflow-centric Research Objects (ROs). The ROs are produced as an output of a workflow enactment defined in the Common Workflow Language (CWL) using reference implementation cwltool.

The approach aggregates and annotates all the resources involved in the scientific investigation including inputs, outputs, workflow specification, command line tool specifications and input parameter settings. The resources are linked within the RO to enable re-enactment of an analysis without depending on external resources. The workflow provenance profile is represented in W3C standardized PROV-N and PROV-JSON format and captures retrospective provenance of the workflow enactment.

The workflow-centric RO produced as an output of a CWL workflow enactment is expected to be interoperable, reusable, shareable and portable across different platforms. Our work describes the need and motivation for CWLProv and the lessons learned in applying it for ROs using CWL in the bioinformatics domain. The complete capture of provenance along with the aggregated resources used in a workflow enactment will mitigate the workflow decay and allow applications of provenance to make experiments transparent, reproducible and authentic.

We believe that underlying principles of the standards utilized to implement CWLProv will result in a semantically rich executable workflow objects such that any platform supporting CWL and CWLProv will be able to reproduce them. We ultimately aim to achieve a solution that is compliant with all four dimensions of FAIR principles. Currently CWLProv is implemented using the reference implementation, cwltool. This study can further be extended to support Provenance Capture on other platforms supporting CWL to demonstrate interoperability of analysis methods.
Association of Continuation of Loop Diuretics at Hemodialysis Initiation with Clinical Outcomes
Creators: name: Flythe, Jennifer
name: Walker, Adam G
name: Colson, Carey
name: Sibbel, Scott
name: Brunelli, Steven M
name: Tentori, Francesca
Publisher: name: Wolters Kluwer
Year: 2018

description: BACKGROUND AND OBJECTIVES: Loop diuretics are commonly used to manage nondialysis-dependent CKD. Despite benefits of augmented urine output, loop diuretics are often discontinued after dialysis initiation. Here, we assessed the association of the early decision to continue loop diuretics at hemodialysis start with clinical outcomes during the first year of dialysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We considered all patients on in-center hemodialysis at a large dialysis organization (2006-2013) with Medicare Part A and D benefits who had an active supply of a loop diuretic at dialysis initiation (n=11,297). Active therapy was determined on the basis of whether loop diuretic prescription was refilled after dialysis initiation and within 30 days of exhaustion of prior supply. Patients were followed under an intention-to-treat paradigm for up to 12 months for rates of death, hospitalization, and intradialytic hypotension and mean monthly values of interdialytic weight gain, serum potassium, predialysis systolic BP, and ultrafiltration rates. RESULTS: We identified 5219 patients who refilled a loop diuretic and 6078 eligible controls who did not. After adjustments for patient mix and clinical differences, continuation of loop diuretics was associated with lower hospitalization (adjusted incidence rate ratio, 0.93; 95% confidence interval, 0.89 to 0.98) and intradialytic hypotension (adjusted incidence rate ratio, 0.95; 95% confidence interval, 0.92 to 0.99) rates, no difference in death rate (adjusted hazard ratio, 0.92; 95% confidence interval, 0.84 to 1.01), and lower interdialytic weight gain (P=0.03). CONCLUSIONS: Continuation of loop diuretics after hemodialysis initiation was associated with lower rates of hospitalization and intradialytic hypotension as well as lower interdialytic weight gain, but there was no difference in mortality over the first year of dialysis.
Dynamics of HBsAg clearance in a UK cohort of chronic HBV infection
Creators: name: Downs, Louise
name: Meha Patel
name: Ansari, Azim
name: McNaughton, Anna
name: Smith, David
name: Andersson, Monique
name: Barnes, Eleanor
name: Jeffery, Katie
name: Matthews, Philippa C
Publisher: name: F1000 Research Limited
Year: 2018

description: This poster describes the dynamics of HBsAg (hepatitis B surface antigen) clearance in a cohort of adults with chronic HBV (hepatitis B virus) infection. There is increasing interest in using HBsAg as a biomarker, with potential clinical use in predicting prognosis and stratifying treatment. Identification of the individuals who clear infection may allow us to develop better insights into the immune mechanisms of control and clearance.
Consistency and overfitting of multi-omics methods on experimental data
Creators: name: Lin, Dan-Yu
name: McCabe, Sean D
name: Love, Michael I
Publisher: name: Oxford University Press (OUP)
Year: 2019

description: Knowledge on the relationship between different biological modalities (RNA, chromatin, etc.) can help further our understanding of the processes through which biological components interact. The ready availability of multi-omics datasets has led to the development of numerous methods for identifying sources of common variation across biological modalities. However, evaluation of the performance of these methods, in terms of consistency, has been difficult because most methods are unsupervised. We present a comparison of sparse multiple canonical correlation analysis (Sparse mCCA), angle-based joint and individual variation explained (AJIVE) and multi-omics factor analysis (MOFA) using a cross-validation approach to assess overfitting and consistency. Both large and small-sample datasets were used to evaluate performance, and a permuted null dataset was used to identify overfitting through the application of our framework and approach. In the large-sample setting, we found that all methods demonstrated consistency and lack of overfitting; however, in the small-sample size setting, AJIVE provided the most stable results. We provide an R package so that our framework and approach can be applied to evaluate other methods and datasets.
Supplemental Material - Aide and Client Safety “Should Go Hand-In-Hand”: Qualitative Findings From Home Care Aides, Clients, and Agency Leaders
Creators: name: Brouillette, Natalie M.
name: Markkanen, Pia K.
name: Quinn, Margaret M.
name: Galligan, Catherine J.
name: Sama, Susan R.
name: Lindberg, John E.
name: Karlsson, Nicole D.
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 110308 Geriatrics and Gerontology
subject: 111799 Public Health and Health Services not elsewhere classified
subject: FOS: Health sciences

description: Supplemental Material for Aide and Client Safety “Should Go Hand-In-Hand”: Qualitative Findings From Home Care Aides, Clients, and Agency Leaders by Natalie M. Brouillette, Pia K. Markkanen, Margaret M. Quinn, Catherine J. Galligan, Susan R. Sama, John E. Lindberg, and Nicole D. Karlsson in Journal of Applied Gerontology
Additional file 1 of Tensor decomposition for painting analysis. Part 1: pigment characterization
Creators: name: Ciortan, Irina M.
name: Poulsson, Tina G.
name: George, Sony
name: Hardeberg, Jon Y.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1: The supplementary file attached to this paper includes a code snippet for a better understanding of the implementation details, as well as plots with all the measured and modelled spectra of the samples in the central and left lantern.
Sickle cell trait is not associated with an increased risk of heart failure or abnormalities of cardiac structure and function
Creators: name: Carty, Cara L.
name: Egede, Leonard D.
name: Adams, Robert J.
name: Derebail, Vimal K.
name: Roetker, Nicholas S.
name: Gee, Beatrice E.
name: Hughes, Austin L.
name: Manson, JoAnn E.
name: Shah, Amil M.
name: Naik, Rakhi P.
name: Konety, Suma H.
name: Correa, Adolfo
name: Reiner, Alexander P.
name: Choudhary, Gaurav
name: Allison, Matthew
name: Solomon, Scott D.
name: Key, Nigel S.
name: Longstreth, W.T.
name: Wilson, James G.
name: Kshirsagar, Abhijit V.
name: Burke, Gregory L.
name: Hyacinth, Hyacinth I.
name: Seals, Samantha R.
name: Folsom, Aaron R.
name: Bello, Natalie A.
Publisher: name: American Society of Hematology
Year: 2016

description: Sickle cell trait (SCT), defined as heterozygosity for the sickle cell b-globin gene mutation (HbAS), is present in ~8% to 12% of African Americans. Despite a lack of longitudinal studies of individuals with SCT, it is generally thought that these heterozygous carriers exhibit a normal lifespan. On the other hand, SCT has been associated with an increased rate of venous thromboembolism, ischemic stroke, and renal dysfunction. It has also been associated with exertional sudden death, but a very recent study has challenged this finding when reporting a strong association with rhabdomyolysis. Several studies of patients with sickle cell disease (SCD) have shown an association with abnormalities of cardiac structure and function. In particular, an elevated tricuspid regurgitant velocity (TRV) is associated with early mortality in SCD, whereas another study reported a significant association between SCD and myocardial ischemia. The association of SCT with cardiac dysfunction and incident heart failure (HF) has not been comprehensively studied. We examined the association of SCT with (1) risk of HF and (2) abnormalities of cardiac structure and function.
sj-pdf-1-eso-10.1177_23969873221148267 – Supplemental material for Age of onset of cerebral venous thrombosis: the BEAST study
Creators: name: Ranjan, Redoy
name: Ken-Dror, Gie
name: Martinelli, Ida
name: Grandone, Elvira
name: Hiltunen, Sini
name: Lindgren, Erik
name: Margaglione, Maurizio
name: Le Cam Duchez, Veronique
name: Bagan Triquenot, Aude
name: Zedde, Marialuisa
name: Mancuso, Michelangelo
name: Ruigrok, Ynte M
name: Worrall, Brad
name: Majersik, Jennifer J
name: Putaala, Jukka
name: Haapaniemi, Elena
name: Zuurbier, Susanna M
name: Brouwer, Matthijs C
name: Passamonti, Serena M
name: Abbattista, Maria
name: Bucciarelli, Paolo
name: Lemmens, Robin
name: Pappalardo, Emanuela
name: Costa, Paolo
name: Colombi, Marina
name: Aguiar de Sousa, Diana
name: Rodrigues, Sofia
name: Canhao, Patrícia
name: Tkach, Aleksander
name: Santacroce, Rosa
name: Favuzzi, Giovanni
name: Arauz, Antonio
name: Colaizzo, Donatella
name: Spengos, Kostas
name: Hodge, Amanda
name: Ditta, Reina
name: Han, Thang S
name: Pezzini, Alessandro
name: Coutinho, Jonathan M
name: Thijs, Vincent
name: Jood, Katarina
name: Tatlisumak, Turgut
name: Ferro, José M
name: Sharma, Pankaj
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: Cardiology
subject: Medicine
subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine

description: Supplemental material, sj-pdf-1-eso-10.1177_23969873221148267 for Age of onset of cerebral venous thrombosis: the BEAST study by Redoy Ranjan, Gie Ken-Dror, Ida Martinelli, Elvira Grandone, Sini Hiltunen, Erik Lindgren, Maurizio Margaglione, Veronique Le Cam Duchez, Aude Bagan Triquenot, Marialuisa Zedde, Michelangelo Mancuso, Ynte M Ruigrok, Brad Worrall, Jennifer J Majersik, Jukka Putaala, Elena Haapaniemi, Susanna M Zuurbier, Matthijs C Brouwer, Serena M Passamonti, Maria Abbattista, Paolo Bucciarelli, Robin Lemmens, Emanuela Pappalardo, Paolo Costa, Marina Colombi, Diana Aguiar de Sousa, Sofia Rodrigues, Patrícia Canhao, Aleksander Tkach, Rosa Santacroce, Giovanni Favuzzi, Antonio Arauz, Donatella Colaizzo, Kostas Spengos, Amanda Hodge, Reina Ditta, Thang S Han, Alessandro Pezzini, Jonathan M Coutinho, Vincent Thijs, Katarina Jood, Turgut Tatlisumak, José M Ferro and Pankaj Sharma in European Stroke Journal
STopTox: An in Silico Alternative to Animal Testing for Acute Systemic and Topical Toxicity
Creators: name: Borba, Joyce V.B.
name: Overdahl, Erik
name: Muratov, Eugene N.
name: Alves, Vinicius M.
name: Overdahl, Kirsten
name: Allen, David
name: Korn, Daniel R.
name: Andrade, Carolina Horta
name: Strickland, Judy
name: Hall, Steven U.S.
name: Tropsha, Alexander
name: Braga, Rodolpho C.
name: Silva, Arthur C.
name: Kleinstreuer, Nicole
Publisher: name: Environmental Health Perspectives
Year: 2022

description: BACKGROUND: Modern chemical toxicology is facing a growing need to Reduce, Refine, and Replace animal tests (Russell 1959) for hazard identification. The most common type of animal assays for acute toxicity assessment of chemicals used as pesticides, pharmaceuticals, or in cosmetic products is known as a "6-pack" battery of tests, including three topical (skin sensitization, skin irritation and corrosion, and eye irritation and corrosion) and three systemic (acute oral toxicity, acute inhalation toxicity, and acute dermal toxicity) end points. METHODS: We compiled, curated, and integrated, to the best of our knowledge, the largest publicly available data sets and developed an ensemble of quantitative structure-activity relationship (QSAR) models for all six end points. All models were validated according to the Organisation for Economic Co-operation and Development (OECD) QSAR principles, using data on compounds not included in the training sets. RESULTS: In addition to high internal accuracy assessed by cross-validation, all models demonstrated an external correct classification rate ranging from 70% to 77%. We established a publicly accessible Systemic and Topical chemical Toxicity (STopTox) web portal (https://stoptox.mml.unc.edu/) integrating all developed models for 6-pack assays. CONCLUSIONS: We developed STopTox, a comprehensive collection of computational models that can be used as an alternative to in vivo 6-pack tests for predicting the toxicity hazard of small organic molecules. Models were established following the best practices for the development and validation of QSAR models. Scientists and regulators can use the STopTox portal to identify putative toxicants or nontoxicants in chemical libraries of interest. https://doi.org/10.1289/EHP9341.
Phantom PAINS: Problems with the Utility of Alerts for Pan€‘Assay INterference CompoundS
Creators: name: Capuzzi, Stephen J.
name: Muratov, Eugene N.
name: Tropsha, Alexander
Publisher: name: American Chemical Society (ACS)
Year: 2017

description: The use of substructural alerts to identify Pan-Assay INterference compoundS (PAINS) has become a common component of the triage process in biological screening campaigns. These alerts, however, were originally derived from a proprietary library tested in just six assays measuring protein-protein interaction (PPI) inhibition using the AlphaScreen detection technology only; moreover, 68% (328 out of the 480 alerts) were derived from four or fewer compounds. In an effort to assess the reliability of these alerts as indicators of pan-assay interference, we performed a large-scale analysis of the impact of PAINS alerts on compound promiscuity in bioassays using publicly available data in PubChem. We found that the majority (97%) of all compounds containing PAINS alerts were actually infrequent hitters in AlphaScreen assays measuring PPI inhibition. We also found that the presence of PAINS alerts, contrary to expectations, did not reflect any heightened assay activity trends across all assays in PubChem including AlphaScreen, luciferase, beta-lactamase, or fluorescence-based assays. In addition, 109 PAINS alerts were present in 3570 extensively assayed, but consistently inactive compounds called Dark Chemical Matter. Finally, we observed that 87 small molecule FDA-approved drugs contained PAINS alerts and profiled their bioassay activity. Based on this detailed analysis of PAINS alerts in nonproprietary compound libraries, we caution against the blind use of PAINS filters to detect and triage compounds with possible PAINS liabilities and recommend that such conclusions should be drawn only by conducting orthogonal experiments.
Supplemental Material - The Relationship Between Uterine Activity, Oxytocin Dosing, Labor Progress, and Mode of Birth in Nulliparas with Obesity: Minimal Usefulness of Montevideo Unit Measurement
Creators: name: Kissler, Katherine J.
name: Hernandez, Teri L.
name: Carlson, Nicole
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: 111099 Nursing not elsewhere classified
subject: FOS: Health sciences

description: Supplemental Material for The Relationship Between Uterine Activity, Oxytocin Dosing, Labor Progress, and Mode of Birth in Nulliparas with Obesity: Minimal Usefulness of Montevideo Unit Measurement by Katherine J. Kissler, Teri L. Hernandez, and Nicole Carlson in Biological Research For Nursing