cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Entrepreneurship education 2-in-1: Helping young Bulgarians become more entrepreneurial in a 10-month parallel-group randomized trial
Creators: name: Vankov, Daniel
name: Vankov, Borislav
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Additional file 1. Appendix 1.
Relationships Between Soil Respiration and Crop Productivity in Different Crop Fields
Creators: name: Zhang, Miaomiao
name: Ding, Sicheng
name: Wang, Jin
name: Chen, Shutao
name: Hu, Zhenghua
Publisher: name: Taylor & Francis
Year: 2025
Subjects: 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: Plant Biology

description: Investigating the seasonal variations in soil respiration in different crop fields and their relationships with crop productivity is crucial to understanding the key biotic controls of soil respiration. A field experiment was performed during the 2020‒2021 winter wheat‒soybean, canola‒maize and broad bean‒sweet potato growing seasons. The seasonal variations in soil respiration, soil temperature and moisture were measured. The variables that were associated with crop productivity were also determined. The results showed that crop types significantly (p < .05) affected the mean seasonal soil respiration. Most variables that were associated with crop productivity exhibited obvious seasonal variation patterns. The soil temperature, moisture and crop productivity comprehensively influenced the soil respiration, and models based on these potential controlling factors explained 45.7%‒59.2% (R2 = 0.457‒0.592) of the variation in soil respiration in the different crop rotation fields. A model based on the mean seasonal soil temperature, moisture, leaf area index, and root carbon content explained 68.3% (R2 = 0.683) of the variation in the mean seasonal soil respiration across the different crop fields. We demonstrated the potential of effectively characterizing the variations in soil respiration in agroecosystems using temperature, moisture and crop productivity.
sj-docx-1-asn-10.1177_17590914211035036 - Supplemental material for Sevoflurane-Induced miR-211-5p Promotes Neuronal Apoptosis by Inhibiting Efemp2
Creators: name: Shen, Yousu
name: Zhou, Tao
name: Liu, Xiaobing
name: Liu, Yanlong
name: Li, Yaqi
name: Zeng, Dewu
name: Zhong, Wensheng
name: Zhang, Mingsheng
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: Medicine
subject: Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine

description: Supplemental material, sj-docx-1-asn-10.1177_17590914211035036 for Sevoflurane-Induced miR-211-5p Promotes Neuronal Apoptosis by Inhibiting Efemp2 by Yousu Shen, Tao Zhou, Xiaobing Liu, Yanlong Liu, Yaqi Li, Dewu Zeng, Wensheng Zhong and Mingsheng Zhang in ASN Neuro
Machine learning-based virtual screening and molecular modelling studies for identification of butyrylcholinesterase inhibitors as anti-Alzheimer’s agent
Creators: name: Ganeshpurkar, Ankit
name: Akotkar, Likhit
name: Kumar, Devendra
name: Kumar, Dileep
name: Ganeshpurkar, Aditya
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biochemistry
Medicine
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Butyrylcholinesterase (BChE) is a hydrolase involved in the metabolism and detoxification of specific esters in the blood. It is also implicated in the progression of Alzheimer’s disease, a type of dementia. As the disease progresses, the level of BChE tends to increase, opting for a major role as an acetylcholine-degrading enzyme and surpassing the role of acetylcholinesterase. Hence, the development of BChE inhibitors could be beneficial for the latter stages of the disease. In the present study, machine learning (ML) models were developed and employed to identify new BChE inhibitors. Further, the identified molecules were subjected to molecular property filters. The filtered ligands were studied through molecular modelling techniques, viz. molecular docking and molecular dynamics (MD). Support vector machine-based ML models resulted in the identification of 3291 compounds that would have predicted IC50 values less than 200 nM. The docking study showed that compounds ART13069594, ART17350769 and LEG19710163 have mean binding energies of −9.62, −9.26 and −8.93 kcal/mol, respectively. The MD study displayed that all the selected ligands showed stable complexes with BChE. The trajectories of all the ligands were stable similar to the standard BChE inhibitors.
Implementing anti-racist pedagogy in health professional education: a realist review
Creators: name: Diffey, Linda
name: Mignone, Javier
Publisher: name: F1000Research
Year: 2017

description: Background:  In response to the greater public awareness of anti-Indigenous racism within Canada’s health care system, the nation’s health education programs are under increasing pressure to incorporate anti-racist approaches in their training of health professionals.  But implementation of curricular content about racism has been slow to emerge in these programs and a focus on culture rather than racial oppression persists.  Few guidelines currently exist to assist in the application of anti-racist pedagogy in health education, and the published research in this area is relatively limited.

Methods:  The purpose of this systematic review was to explore the peer-reviewed literature to identify the factors and processes that influence the implementation of anti-racist teaching in a health context.  A critical realism framework was used to help understand the complex relationship among context, human actors, and processes involved in this pedagogical approach.

Results:  Of the 4042 papers identified, 287 were selected for full-text retrieval and 31 met the inclusion criteria for this review.  Factors that either facilitate or limit the implementation of anti-racist pedagogy in health education programs were identified, including instructor training and mentorship, institutional commitment, and the socio-political climate of the community.  Specific teaching processes that assisted or impeded learning were also identified.

Discussion:  Employing an anti-racist approach to health education challenges the status quo and is often met with resistance from students, faculty and administrators, a reaction which tends to reflect the racial tensions and worldview of the larger social context outside the classroom.  Despite these challenges, this review identified a number of factors and strategies that may be used by health educators to overcome the barriers.

Conclusions:  Recommendations from this review highlight the need for faculty support and mentorship, community engagement, and institutional-level commitment to ensure the successful implementation of anti-racist pedagogy in health education.

What this project adds:  The findings from this project will contribute to the ongoing efforts to develop Canadian medical education curricula that seek to address the systemic racism that results in the health inequities experienced by Indigenous peoples.
Additional file 1 of Beyond gait speed: exploring the added value of Inertial Measurement Unit-based measurements of gait in the estimation of the walking ability in daily life
Creators: name: Felius, R. A. W.
name: Wouda, N. C.
name: Geerars, M.
name: Bruijn, S. M.
name: van Dieën, J. H.
name: Punt, M.
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Supplementary Material 1.
sj-pdf-1-han-10.1177_15589447211049517 – Supplemental material for Trends in the Management of Pediatric Trigger Thumb in the United States
Creators: name: Park, Keon Min
name: Immerman, Igor
name: Rahgozar, Paymon
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: Medicine
subject: 110314 Orthopaedics
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine
subject: FOS: Health sciences

description: Supplemental material, sj-pdf-1-han-10.1177_15589447211049517 for Trends in the Management of Pediatric Trigger Thumb in the United States by Keon Min Park, Igor Immerman and Paymon Rahgozar in HAND
Synthesis, spectroscopic analysis, and computational-based investigations on ‘azo-coumarin-Co(II)-galangin’ hybrids exhibit multipotential activities
Creators: name: Swain, Shasank Sekhar
name: Sahoo, Alaka
name: Singh, Satya Ranjan
name: Sahoo, Jyotirmaya
name: Paidesetty, Sudhir Kumar
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: The present study synthesized a series of cobalt (II) metal ion frame hybrid candidates (6a–6f) bearing phyto-flavonol galangin with substituted aryl diazenyl coumarins, and further structural confirmation was validated by various spectral techniques, including NMR, ATR-FTIR, UV-vis, HPLC, XRD, etc. Therapeutic potency was investigated via PASS (prediction of activity spectra for substances), molecular docking, molecular dynamics simulation, prediction of toxicity, pharmacokinetics, and drug-likeness scores, along with the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), with their energy gaps (ΔEH–L) to locate the most potential therapeutic candidates. The PASS prediction (Pa > Pi score) showed that proposed metal complexes have kinase inhibitors, antioxidative, and antischistosomal activities with potential molecular docking scores (> −7 kcal/mol) against selected targeted enzymes. Further, the MD-simulation (RMSD, RMSF, Rg, and H-bonds) of the most potential docking complex, ‘HER2-6d’, showed a minimum deviation similar to the standard drug (lapatinib) at 100 ns, indicating that 6d could be a potential noncovalent anticancer inhibitor. In addition, metal complexes possess a non-toxic and ideal drug-ability profiles, and positive electron space in an excited state increases the binding affinity towards target enzymes. Among all six ligands, 6c and 6d were the two most multipotent therapeutic agents from the above analyses. In summary, this could be a feasible approach towards the utilization of phytochemicals in mainstream therapeutic applications, where bioinformatics tools help to select a lead drug candidate at an early stage and guide for higher experimental success by proceeding with potential candidates.
Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches
Creators: name: Gupta, Swati
name: Pal, Debnath
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inverted nucleotide repeat detection for identification of RNA hairpin, while the latter a pair-potential function – the hairpin energy score evaluation being identical for both. We find INTERPIN more sensitive than WebGeSTer with about 6% and 51% additional predictions for ITTs in chromosomal and plasmid operons, respectively. INTERPIN hairpins are relatively shorter in length with ungapped stem, and even located in AT-rich segments, compared to GC-rich longer hairpins with a gapped stem in WebGeSTer. The GC%, length, and energy score from INTERPIN transcription units (TUs) are best inter-correlated while the lowest energy single hairpins from WebGeSTer, considered suitable for ITT, being the worst. Around 72% TUs from the two databases overlap, and ∼60% of all alternate ITT sites downstream of TUs overlap, of which 65% are cluster hairpins. This helps highlight hairpin features that can be used to identify termination sites in bacteria across different prediction methods. Overall, the pair-potential-function-based hairpins screened appear to be more consistent with the kinetic and thermodynamics processes of ITT known to date.
Additional file 1 of Real-time earthquake magnitude estimation via a deep learning network based on waveform and text mixed modal
Creators: name: Hou, Baorui
name: Zhou, Yueyong
name: Li, Shanyou
name: Wei, Yongxiang
name: Song, Jindong
Publisher: name: figshare
Year: 2024
Subjects: subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mental Health

description: Additional file 1: Figure S1. Earthquake map and data distribution of the subset-region. The subfigure a indicates the distribution of the seismometers and earthquake epicenters. Different colors indicate the earthquake depth range and different shapes indicate different geographical regions. Subfigure b indicates the distribution between depths and magnitudes. Subfigure c indicates the distribution between the depths and epicenter distances. The subfigures d to e indicate the frequency distribution of depths and epicenter distances. The different colors indicate different geographical regions.
Discovery of small molecule entry inhibitors targeting the linoleic acid binding pocket of SARS-CoV-2 spike protein
Creators: name: Prasad, Roshny
name: Kadam, Anil
name: Padippurackal, Vinitha Vinod
name: Balasubramanian, Aparna Pulikuttymadom
name: Chandrakumaran, Naveen Kumar
name: Rangari, Kartik Suresh
name: Khangar, Pawan Dnyaneshwar
name: Ajith, Harikrishnan
name: Natarajan, Kathiresan
name: Chandramohanadas, Rajesh
name: Nelson-Sathi, Shijulal
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Virology

description: Spike glycoprotein has a significant role in the entry of SARS-CoV-2 to host cells, which makes it a potential drug target. Continued accumulation of non-synonymous mutations in the receptor binding domain of spike protein poses great challenges in identifying antiviral drugs targeting this protein. This study aims to identify potential entry inhibitors of SARS-CoV-2 using virtual screening and molecular dynamics (MD) simulations from three distinct chemical libraries including Pandemic Response Box, Drugbank and DrugCentral, comprising 6971 small molecules. The molecules were screened against a binding pocket identified in the receptor-binding domain (RBD) region of the spike protein which is known as the linoleic acid binding pocket, a highly conserved motif among several SARS-CoV-2 variants. Through virtual screening and binding free energy calculations, we identified four top-scoring compounds, MMV1579787 ([2-Oxo-2-[2-(3-phenoxyphenyl)ethylamino]ethyl]phosphonic acid), Tretinoin, MMV1633963 ((2E,4E)-5-[3-(3,5-dichlorophenoxy)phenyl]penta-2,4-dienoic acid) and Polydatin, which were previously reported to have antibacterial, antifungal or antiviral properties. These molecules showed stable binding on MD simulations over 100 ns and maintained stable interactions with TYR365, PHE338, PHE342, PHE377, TYR369, PHE374 and LEU368 of the spike protein RBD that are found to be conserved among SARS-CoV-2 variants. Our findings were further validated with free energy landscape, principal component analysis and dynamic cross-correlation analysis. Our in silico analysis of binding mode and MD simulation analyses suggest that the identified compounds may impede viral entrance by interacting with the linoleic acid binding site of the spike protein of SARS-CoV-2 regardless of its variants, and they thus demand for further in vitro and in vivo research.
“They share more than we think they are sharing”: a mixed-methods evaluation of post-natal clubs in South Africa
Creators: name: Duvivier, Hélène
name: Nelson, Aurelie
name: Cassidy, Tali
name: Duran, Laura Trivino
name: Shroufi, Amir
name: Hoxha, Ana
name: Buchanan, Kate
name: Uenishi, Rinako
name: Mpumi Mantangana
name: Mdani, Leticia
name: Venables, Emilie
name: Shariefa Abrahams
name: Azevedo, Virginia De
name: Igumbor, Jude
name: Hofmeyr, Clare
name: Zodwa Mbakaza
name: Sibanda, Beryl
name: Nopinky Matinise
name: Nikiwe Mkhosana
name: Isaakidis, Petros
name: Pieters, Pauline
name: Cotton, Mark
name: Maritz, Jean
name: Decroo, Tom
Publisher: name: F1000 Research Limited
Year: 2018

description: Post-natal mother-to-child transmission of HIV in South Africa is high; 4.3% at 18 months, and uptake of infant HIV testing is poor. Data from the infant diagnosis cascade in Khayelitsha between Nov 2014 and Jul 2016 (781 tested at birth) has shown poor retention in care, with only 25% of infants being tested at 18 months, and 38% after contact tracing. To address these problems, since July 2016, we have established an integrated PMTCT model of care. Post-natal clubs (PNCs) provide maternal and child healthcare together with HIV services to HIV-positive mothers and their infants. PNCs enroll groups of two to ten mother-infant pairs each and meet 1-3 monthly until 18 months.
Pregnancy and Ebola: survival outcomes for pregnant women admitted to MSF Ebola treatment centres in the West Africa outbreak
Creators: name: Caluwaerts, Séverine
name: Herp, Michel Van
name: Cuesta, Julita Gil
name: Crestani, Rosa
name: Ronsse, Axelle
name: Lagrou, Daphne
name: Weber, Patricia
name: Jean-François  Saint-Sauveur
name: Black, Benjamin
name: Caleo, Grazia
name: Guild, Carissa
name: Furaha Walumpumpu
name: Iza Ciglenecki
name: Squire, James
name: Mosoka Fallah
name: Sow, Mamadou
name: Antierens, Annick
Publisher: name: F1000 Research Limited
Year: 2018

description: Data on pregnancy and Ebola virus disease (EVD) are scarce but suggest high maternal (90%) and neonatal (100%) mortality. During the 2014-2016 West Africa EVD outbreak, MSF managed nine Ebola treatment centres (ETCs) in Guinea, Sierra Leone, and Liberia. We compared survival outcomes for EVD-confirmed pregnant women with those of EVD-confirmed clinically and self-reported non-pregnant women of reproductive age (WRA) attending ETCs.
Additional file 1 of Sex differences in foraging ecology of a zooplanktivorous little auk Alle alle during the pre-laying period: insights from remote sensing and animal-tracking
Creators: name: Jakubas, Dariusz
name: Wojczulanis-Jakubas, Katarzyna
name: Iliszko, Lech Marek
Publisher: name: figshare
Year: 2024
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Supplementary Material 1.
Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics
Creators: name: Rubavathy, S. M. Esther
name: Rajapandian, V.
name: Prakash, M.
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic. However, most HDAC inhibitors lack subclass or isoform selectivity, which can be dangerous. Featuring both enhanced selectivity and toxicity profiles, slow-binding HDAC inhibitors offer promising treatment options for a variety of disorders. Diseases like cardiac, neurodegenerative disorders and diabetes are mainly associated with the HDAC1, HDAC2 and HDAC3 enzymes. The AI-based virtual screening tool PyRMD is implemented to identify the potential inhibitors from ∼2 million compounds. Based on the IC50 values, the top 10 compounds were selected for molecular docking. From the docking and ADMET study, the top-ranked three compounds were selected for molecular dynamics (MD) simulations. Further, to get more insights into the binding/unbinding mechanism of the ligand, we have employed the steered molecular dynamics (SMD) simulations. This study assists in developing Amber force field parameters for the HDAC1, HDAC2 and HDAC3 proteins and sheds light on the discovery of a potent drug. Our study suggests that hydroxamic acid derivative (i.e. referred to as Comp-1, CHEMBL600072) is the potential inhibitor for the series of HDAC-related diseases.
Choice and equal access in early childhood education and care: The case of Germany
Creators: name: Hogrebe, Nina
Publisher: name: Universität Münster / Institut für Musikwissenschaft und Musikpädagogik
Year: 2017
Subjects: 300 Sozialwissenschaften, Soziologie, Anthropologie
360 Soziale Probleme, Sozialdienste

description: Der Beitrag trägt zu den Diskussionen bei, wie unterschiedlich ausgestaltete Systeme frühkindlicher Bildung, Betreuung und Erziehung (FBBE) mit elterlicher Wahlfreiheit, Qualität und Gleichheit in Verbindung stehen. Basierend auf einer kurzen Skizzierung von generellen Ausgestaltungsoptionen von FBBE in Europa und ihrer Umsetzung in Deutschland wird dargelegt, dass die genrelle Gesetzgebung auf nationaler Ebene hierzulande sowohl elterliche Wahlfreiheit als auch gleichen Zugang zu qualitativ hochwertigen Angeboten für alle Kinder zu gewährleisten scheint. Allerdings verdeckt die ausschließliche Betrachtung auf Landesebene Segregationsprozesse auf lokaler Ebene, die zu Ungleichheiten führen. Der Beitag illustriert trägerspezifische Segregationsmuster auf kommunaler Ebene auf der Basis von Daten der Schuleingangsuntersuchung einer mittelgroßen Stadt in Nordrhein-Westfalen.
Enhancing multi‐site autism research through the development of a collaborative data platform
Creators: name: Anderson, Jeffrey T
name: Roth, Jeffrey D
name: Rosenau, Kashia A
name: Dwyer, Patrick
name: Kuo, Alice A
name: Martinez‐Agosto, Julian A
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 520105
subject: Psychological methodology, design and analysis
classificationCode: 5203
subject: Clinical and health psychology
classificationCode: 3209
subject: Neurosciences
subject: FOS: Clinical medicine
classificationCode: 52
subject: Psychology
subject: FOS: Psychology
classificationCode: 5201
subject: Applied and developmental psychology

description: Data repositories, particularly those storing data on vulnerable populations, increasingly need to carefully consider not only what data is being collected, but how it will be used. As such, the Autism Intervention Research Network on Physical Health (AIR-P) has created the Infrastructure for Collaborative Research (ICR) to establish standards on data collection practices in Autism repositories. The ICR will strive to encourage inter-site collaboration, amplify autistic voices, and widen accessibility to data. The ICR is staged as a three-tiered framework consisting of (1) a request for proposals system, (2) a REDCap-based data repository, and (3) public data dashboards to display aggregate de-identified data. Coupled with a review process including autistic and non-autistic researchers, this framework aims to propel the implementation of equitable autism research, enhance standardization within and between studies, and boost transparency and dissemination of findings. In addition, the inclusion of a contact registry that study participants can opt into creates the base for a robust participant pool. As such, researchers can leverage the platform to identify, reach, and distribute electronic materials to a greater proportion of potential participants who likely fall within their eligibility criteria. By incorporating practices that promote effective communication between researchers and participants, the ICR can facilitate research that is both considerate of and a benefit to autistic people.
sj-pdf-1-wso-10.1177_17474930211053140 - Supplemental material for Are low doses of non-vitamin K antagonists effective in Chinese patients with atrial fibrillation? A report from the Optimal Thromboprophylaxis in Elderly Chinese Patients with Atrial Fibrillation (ChiOTEAF) registry
Creators: name: Kotalczyk, Agnieszka
name: Guo, Yutao
name: Wang, Yutang
name: Lip, Gregory YH
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: Cardiology
subject: Medicine
subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine

description: Supplemental material, sj-pdf-1-wso-10.1177_17474930211053140 for Are low doses of non-vitamin K antagonists effective in Chinese patients with atrial fibrillation? A report from the Optimal Thromboprophylaxis in Elderly Chinese Patients with Atrial Fibrillation (ChiOTEAF) registry by Agnieszka Kotalczyk, Yutao Guo, Yutang Wang, Gregory YH Lip and on behalf of the ChiOTEAF Registry Investigators in International Journal of Stroke
Additional file 2 of Effects of tissue type and season on the detection of regulated sugarcane viruses by high throughput sequencing
Creators: name: Bolus, Stephen
name: Wathen-Dunn, Kate
name: Grinstead, Samuel C.
name: Hu, Xiaojun
name: Malapi, Martha
name: Mollov, Dimitre
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Table S1. Accession numbers from the National Center for Biotechnology Information (NCBI) used for read mapping in reads per kilobase per million reads (RPKM) measurements and depth of sequencing analysis.
Multistate B- to A- transition in protein-DNA Binding – How well is it described by current AMBER force fields?
Creators: name: Jurečka, Petr
name: Zgarbová, Marie
name: Černý, Filip
name: Salomon, Jan
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Cancer

description: When DNA interacts with a protein, its structure often undergoes a significant conformational adaptation, usually involving a transition from B-DNA towards the A-DNA form. This is not a two-state, but rather a multistate transition. The A- and B- forms differ mainly in sugar pucker (north/south) and glycosidic torsion χ (anti/high-anti). The combination of A-like pucker and B-like χ (and vice versa) represents the nature of the intermediate states between the pure A- and B- forms. Here we study how the A/B equilibrium and the A/B intermediate states at protein-DNA interfaces are modeled by current AMBER force fields. Eight diverse protein-DNA complexes and their naked (unbound) DNAs were simulated with OL15 and bsc1 force fields and an experimental combination OL15χOL3. We found that while the geometries of the A-like intermediate states agree well with the native X-ray geometries, their populations (stabilities) are significantly underestimated. Different force fields predict different propensities for A-like states growing in the order OL15 < bsc1 < OL15χOL3, yet all underestimate A-like form populations. Interestingly, the force fields seem to predict the correct sequence-dependent A-form propensity, as they predict larger populations of the A-like form in unbound DNA in those steps that acquire A-like conformations in protein-DNA complexes. The instability of A-like geometries in current force fields significantly alters the geometry of simulated protein-DNA complexes and destabilizes the binding motif, suggesting that refinement is required to improve description of protein-DNA interactions in AMBER force fields.
Additional file 1 of Community coalition efforts to prevent childhood obesity: two-year results of the Shape Up Under 5 study
Creators: name: Economos, Christina D.
name: Calancie, Larissa
name: Korn, Ariella R.
name: Allender, Steven
name: Appel, Julia M.
name: Bakun, Peter
name: Hennessy, Erin
name: Hovmand, Peter S.
name: Kasman, Matt
name: Nichols, Melanie
name: Pachucki, Mark C.
name: Swinburn, Boyd A.
name: Tovar, Alison
name: Hammond, Ross A.
Publisher: name: figshare
Year: 2024
Subjects: subject: Sociology
subject: FOS: Sociology

description: Additional file 1: Supplemental Table 1. Knowledge scores among Shape Up Under 5 neighborhood networks at each data collection point over the two-year pilot study. Mean (SD) knowledge and engagement scores range from 0 (low) to 1 (high). Neighborhood networks sizes (n) increase cumulatively over time. Supplemental Table 2. Engagement scores among Shape Up Under 5 neighborhood networks at each data collection point over the two-year pilot study. Mean (SD) knowledge and engagement scores range from 0 (low) to 1 (high). Neighborhood networks sizes (n) increase cumulatively over time.
Supplemental Material, sj-pdf-1-vet-10.1177_03009858211025794 - Experimental porcine astrovirus type 3-associated polioencephalomyelitis in swine
Creators: name: Ferreyra, Franco Matias
name: Arruda, Paulo E. H.
name: Bradner, Laura K.
name: Harmon, Karen M.
name: Zhang, Min
name: Giménez-Lirola, Luis
name: Arruda, Bailey L.
Publisher: name: SAGE Journals
Year: 2021
Subjects: Pharmacology and Pharmaceutical Sciences not elsewhere classified
Veterinary Medicine

description: Supplemental Material, sj-pdf-1-vet-10.1177_03009858211025794 for Experimental porcine astrovirus type 3-associated polioencephalomyelitis in swine by Franco Matias Ferreyra, Paulo E. H. Arruda, Laura K. Bradner, Karen M. Harmon, Min Zhang, Luis Giménez-Lirola and Bailey L. Arruda in Veterinary Pathology
Tepotinib and tivantinib as potential inhibitors for the serine/threonine kinase of the mpox virus: insights from structural bioinformatics analysis
Creators: name: Abduljalil, Jameel M.
name: Elfiky, Abdo A.
name: AlKhazindar, Maha M.
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The serine/threonine kinase (STK) plays a central role as the primary kinase in poxviruses, directing phosphoryl transfer reactions. Such reactions are pivotal for the activation of certain proteins during viral replication, assembly, and maturation. Therefore, targeting this key protein is anticipated to impede virus replication. In this work, a structural bioinformatics approach was employed to evaluate the potential of drug-like kinase inhibitors in binding to the ATP-binding pocket on the STK of the Mpox virus. Virtual screening of known kinase inhibitors revealed that the top 10 inhibitors exhibited binding affinities ranging from −8.59 to −12.05 kcal/mol. The rescoring of compounds using the deep-learning default model in GNINA was performed to predict accurate binding poses. Subsequently, the top three inhibitors underwent unbiased molecular dynamics (MD) simulations for 100 ns. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and Principal Component Analysis (PCA) suggested tepotinib as a competitive inhibitor for Mpox virus STK as evidenced by its binding free energy and the induction of similar conformational behavior of the enzyme. Nevertheless, it is sensible to experimentally test all top 10 compounds, as scoring functions and energy calculations may not consistently align with experimental findings. These insights are poised to provide an attempt to identify an effective inhibitor for the Mpox virus.
Additional file 1 of A robust deep learning workflow to predict CD8 + T-cell epitopes
Creators: name: Lee, Chloe H.
name: Huh, Jaesung
name: Buckley, Paul R.
name: Jang, Myeongjun
name: Pinho, Mariana Pereira
name: Fernandes, Ricardo A.
name: Antanaviciute, Agne
name: Simmons, Alison
name: Koohy, Hashem
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Fig. S1. Screnshot of TRAP web application. Fig. S2. Cross-species variation and HLA-bias. Fig. S3. Effect of anchor and contact positions on peptide immunogenicity. Fig. S4. Intra vs. Inter-HLA variability. Fig. S5. Pathogenic and self-antigen datasets. Fig. S6. Sequence patterns discriminating epitopes versus non-epitopes. Fig. S7. Out-of-distribution detection. Fig. S8. Benchmark TRAP performance.
An integrated network pharmacology approach to discover therapeutic mechanisms of Commiphora wightii for the treatment of Bell’s palsy
Creators: name: Tabassum, Ayesha
name: Nadeem, Habibullah
name: Azeem, Farrukh
name: Siddique, Muhammad Hussnain
name: Zubair, Muhammad
name: Kanwal, Aqsa
name: Rasul, Ijaz
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biochemistry
Cell Biology
Molecular Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer
Mental Health

description: Bell’s palsy (BP) can result in facial paralysis. Inflammation or injury to the cranial nerves that regulate the facial muscles is primarily responsible for that disease. Commiphora wightii remains recognized as a cure for a few human ailments. This study focused on therapeutic phenomena of C. wightii for the treatment of Bell’s palsy, utilizing the network drug discovery and molecular docking techniques. Active biological constituents of C. wightii were retrieved from literature and independent databases. Potential therapeutic targets (431) of 13 bioactive phytochemicals were fetched via SwissTargetPrediction tool. Putative intersecting targets (855) of Bell’s palsy were computed through the DisGeNET and GeneCards datasets. Subsequently, by the analysis of potential shared targets (87) of C. wightii and Bell’s palsy, a Venn diagram was drawn. DAVID database was used to evaluate gene functional annotations and enriched pathways that are involved in Bell’s palsy. STRING database was used for generating the protein–protein relationship complex. Visual presentations of the interactions of potential targets to active chemical constituents were done by the Cytoscape. Whereas, the conformational research sorted out 10 key targets through the protein–protein interactions network. Moreover, the capacity of therapeutic ingredients to interact with a target inhibiting Bell’s palsy was confirmed by molecular docking, which might ratify the findings of network pharmacology. In the molecular complex of AKT1–cholesterol, a 100-ns simulation unveiled a graceful stability, with a minimal 0.167 Å ligand shift and resilient hydrogen bonds (ASN54 and SER205). The final 20 ns showcased a P1 motif pirouette, gracefully forming aromatic bonds with H165 and W186, underscoring the complex’s dynamic finesse. This study evaluated compound–target interactions and their impact on disease-related genes. It revealed that five genes (AKT1, TNF, MAPK3, EGFR and SRC) of C. wightii might be useful therapeutic targets for the treatment of Bell’s palsy, as well as helping in lowering down the blood pressure. Communicated by Ramaswamy H. Sarma
sj-pdf-1-jad-10.1177_10870547211045743 – Supplemental material for Networks of ADHD and SCT Symptoms in Emerging Adulthood
Creators: name: Lee, Christine A.
name: Goh, Patrick K.
name: Shelton, Christopher R.
name: Hartung, Cynthia M.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: Education
subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology

description: Supplemental material, sj-pdf-1-jad-10.1177_10870547211045743 for Networks of ADHD and SCT Symptoms in Emerging Adulthood by Christine A. Lee, Patrick K. Goh, Christopher R. Shelton and Cynthia M. Hartung in Journal of Attention Disorders
title:  Ecce bombyx. Fonti, drappi e pitture nella Roma altomedievale
Creators: name: Bordi, Giulia
Publisher: name: Roma Tre University
publisherIdentifier: https://ror.org/05vf0dg29
publisherIdentifierScheme: ROR
Year: 2025

description: Per riflettere sui limiti delle fonti e sul loro uso è stato scelto come campo di indagine quello della produzione e circolazione tessile nella Roma altomedievale. Poche sono le notizie, scarsi gli indicatori archeologici diretti e indiretti emersi dagli scavi e davvero esiguo è il numero di tessuti giunti sino a noi, tutti conservati in frammenti spesso di dimensioni davvero ridotte. Tuttavia, attraverso lo studio integrato di fonti documentarie, come il Liber Pontificalis e gli inventari di beni ecclesiastici su papiro, dei rari reperti archeologici, dei pochi tessuti giunti a noi e delle pitture che imitano tessuti serici o di lino conservate nelle chiese dell’Urbe, iniziano a aprirsi nuove prospettive di ricerca sulla manifattura tessile romana e sui canali di importazione di seta e lino.

To reflect on the limitations of sources and their use, the chosen field of investigation is the production and circulation of textiles in early medieval Rome. There is little information, few direct and indirect archaeological indicators from excavations, and a very limited number of textiles have survived to this day, all preserved in fragments, often in very small sizes. However, through the integrated study of documentary sources, such as the Liber Pontificalis and inventories of ecclesiastical assets on papyrus, the rare archaeological finds, the few textiles that have come down to us, and the paintings that imitate silk or linen fabrics preserved in the churches of Rome, new research perspectives are beginning to open on Roman textile manufacturing and on the channels for importing silk and linen.
description: EvoMedio. Rivista interdisciplinare di Studi Medievali – I/2024
sj-docx-1-hhc-10.1177_10848223211056928 – Supplemental material for A Systematic Review of the Needs of Dementia Caregivers Across Care Settings
Creators: name: Mueller, Anne
name: Thao, Lesley
name: Condon, Olivia
name: Liebzeit, Daniel
name: Fields, Beth
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: 111099 Nursing not elsewhere classified
subject: 111702 Aged Health Care
subject: 111799 Public Health and Health Services not elsewhere classified

description: Supplemental material, sj-docx-1-hhc-10.1177_10848223211056928 for A Systematic Review of the Needs of Dementia Caregivers Across Care Settings by Anne Mueller, Lesley Thao, Olivia Condon, Daniel Liebzeit and Beth Fields in Home Health Care Management & Practice
sj-pdf-6-tct-10.1177_15330338211052150 - Supplemental material for LncRNA OIP5-AS1 Promotes the Autophagy-Related Imatinib Resistance in Chronic Myeloid Leukemia Cells by Regulating miR-30e-5p/ATG12 Axis
Creators: name: Dai, Hongdan
name: Wang, Jianming
name: Huang, Zhenglan
name: Zhang, Hui
name: Wang, Xin
name: Li, Qian
name: Feng, Wenli
Publisher: name: SAGE Journals
Year: 2021
Subjects: Oncology and Carcinogenesis not elsewhere classified
Radiology and Organ Imaging
Biochemistry

description: Supplemental material, sj-pdf-6-tct-10.1177_15330338211052150 for LncRNA OIP5-AS1 Promotes the Autophagy-Related Imatinib Resistance in Chronic Myeloid Leukemia Cells by Regulating miR-30e-5p/ATG12 Axis by Hongdan Dai, Jianming Wang, Zhenglan Huang, Hui Zhang, Xin Wang, Qian Li and Wenli Feng in Technology in Cancer Research & Treatment
sj-docx-1-cre-10.1177_02692155211044137 - Supplemental material for Effectiveness of early versus delayed rehabilitation following total shoulder replacement: A systematic review
Creators: name: Moffatt, Maria
name: Whelan, Gareth
name: Gill, Peter
name: Mazuquin, Bruno
name: Edwards, Peter
name: Peach, Chris
name: Davies, Ronnie
name: Morgan, Marie
name: Littlewood, Chris
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: 110314 Orthopaedics
subject: 110604 Sports Medicine
subject: FOS: Health sciences

description: Supplemental material, sj-docx-1-cre-10.1177_02692155211044137 for Effectiveness of early versus delayed rehabilitation following total shoulder replacement: A systematic review by Maria Moffatt, Gareth Whelan, Peter Gill, Bruno Mazuquin, Peter Edwards, Chris Peach, Ronnie Davies, Marie Morgan and Chris Littlewood in Clinical Rehabilitation
sj-docx-2-cre-10.1177_02692155211044137 - Supplemental material for Effectiveness of early versus delayed rehabilitation following total shoulder replacement: A systematic review
Creators: name: Moffatt, Maria
name: Whelan, Gareth
name: Gill, Peter
name: Mazuquin, Bruno
name: Edwards, Peter
name: Peach, Chris
name: Davies, Ronnie
name: Morgan, Marie
name: Littlewood, Chris
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: 110314 Orthopaedics
subject: 110604 Sports Medicine
subject: FOS: Health sciences

description: Supplemental material, sj-docx-2-cre-10.1177_02692155211044137 for Effectiveness of early versus delayed rehabilitation following total shoulder replacement: A systematic review by Maria Moffatt, Gareth Whelan, Peter Gill, Bruno Mazuquin, Peter Edwards, Chris Peach, Ronnie Davies, Marie Morgan and Chris Littlewood in Clinical Rehabilitation
АССОЦИАЦИИ ПОЛИМОРФИЗМОВ В ГЕНЕ КОАКТИВАТОРА-1 АЛЬФА-РЕЦЕПТОРА ГАММА-РЕЦЕПТОРА, АКТИВИРУЕМОГО ПРОЛИФЕРАТОРАМИ ПЕРОКСИСОМ, С ПОСЛЕДУЮЩЕЙ ИШЕМИЧЕСКОЙ БОЛЕЗНЬЮ СЕРДЦА
Creators: name: Назарова, Нигина
name: Жаббаров, Озимбой
Publisher: name: Zenodo
Year: 2024

description: Мы стремились исследовать влияние трех различных однонуклеотидных полиморфизмов (SNP) в гене PPARGC1A на риск последующей ИБС в популяции с установленной ИБС.
sj-docx-1-jdr-10.1177_00220345211040459 – Supplemental material for Toward Clinically Applicable 3-Dimensional Tooth Segmentation via Deep Learning
Creators: name: Hao, J.
name: Liao, W.
name: Zhang, Y.L.
name: Peng, J.
name: Zhao, Z.
name: Chen, Z.
name: Zhou, B.W.
name: Feng, Y.
name: Fang, B.
name: Liu, Z.Z.
name: Zhao, Z.H.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110599 Dentistry not elsewhere classified
subject: FOS: Clinical medicine
subject: 91299 Materials Engineering not elsewhere classified
subject: FOS: Materials engineering

description: Supplemental material, sj-docx-1-jdr-10.1177_00220345211040459 for Toward Clinically Applicable 3-Dimensional Tooth Segmentation via Deep Learning by J. Hao, W. Liao, Y.L. Zhang, J. Peng, Z. Zhao, Z. Chen, B.W. Zhou, Y. Feng, B. Fang, Z.Z. Liu and Z.H. Zhao in Journal of Dental Research
Molecular modeling of novel 2-aminopyridine derivatives as potential JAK2 inhibitors: a rational strategy for promising anticancer agents
Creators: name: Munir, Nadia
name: Chohan, Tahir Ali
name: Qayyum, Aisha
name: Chohan, Talha Ali
name: Batool, Fakhra
name: Mustafa, Mian Waqar
name: Anwar, Sirajudheen
name: Alheibshy, Fawaz
name: Hussein, Weiam
name: Alafnan, Ahmed
name: Khurshid, Umair
name: Khursheed, Anjum
name: Saleem, Hammad
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biophysics
Biochemistry
Medicine
Molecular Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Janus kinase 2(JAK2) is a potential target for anticancer drugs in the treatment of numerous myeloproliferative diseases due to its central role in the JAK/STAT signaling cascade. In this study, the binding behavior of 2 amino-pyridine derivatives as JAK2 inhibitors was investigated by using multifaceted strategies including 3D-QSAR, molecular docking, Fingerprint analysis, MD simulations, and MM-PBSA calculations. A credible COMFA (q2 = 0.606 and r2 = 0.919) and COMSIA (q2 = 0.641 and r2 = 0.992) model was developed, where the internal and external validation revealed that the obtained 3D-QSAR models could be capable of predicting bioactivities of JAK2 inhibitors. The structural criteria provided by the contour maps of model were used to computationally develop more potent 100 new JAK2 inhibitors. Docking studies were conducted on the model data set and newly developed compounds (in-house library) to demonstrate their binding mechanism and highlight the key interacting residues within JAK2 active site. The selected docked complexes underwent MD simulation (100 ns), which contributed in the further study of the binding interactions. Binding free energy analyses (MMGB/PBSA) revealed that key residues such as Glu930, Leu932 (hinge region), Asp939 (solvent accessible region), Arg980, Asn981and Asp994 (catalytic site) have a significantly facilitate ligand-protein interactions through H-bonding and van der Waals interactions. The preliminary in-silico ADMET evaluation revealed encouraging results for all the modeled and in-house library compounds. The findings of this research have the potential to offer valuable recommendations for the advancement of novel, potent, and efficacious JAK2 inhibitors. Overall, this work has successfully employed a wide range of computer-based methodologies to understand the interaction dynamics between 2-amino-pyridine derivatives and the JAK2 enzyme, which is a crucial target in myeloproliferative disorders.
sj-pdf-1-jbr-10.1177_07487304211054408 – Supplemental material for Nitecap: An Exploratory Circadian Analysis Web Application
Creators: name: Brooks, Thomas G.
name: Mrčela, Antonijo
name: Lahens, Nicholas F.
name: Paschos, Georgios K.
name: Grosser, Tilo
name: Skarke, Carsten
name: FitzGerald, Garret A.
name: Grant, Gregory R.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Neuroscience

description: Supplemental material, sj-pdf-1-jbr-10.1177_07487304211054408 for Nitecap: An Exploratory Circadian Analysis Web Application by Thomas G. Brooks, Antonijo Mrčela, Nicholas F. Lahens, Georgios K. Paschos, Tilo Grosser, Carsten Skarke, Garret A. FitzGerald and Gregory R. Grant in Journal of Biological Rhythms
sj-docx-1-jva-10.1177_11297298211054621 – Supplemental material for Ultrasound-guided access to the axillary vein for implantation of cardiac implantable electronic devices: A systematic review and meta-analysis
Creators: name: D’Arrigo, Sonia
name: Perna, Francesco
name: Annetta, Maria Giuseppina
name: Pittiruti, Mauro
Publisher: name: SAGE Journals
Year: 2021
Subjects: Cardiology

description: Supplemental material, sj-docx-1-jva-10.1177_11297298211054621 for Ultrasound-guided access to the axillary vein for implantation of cardiac implantable electronic devices: A systematic review and meta-analysis by Sonia D’Arrigo, Francesco Perna, Maria Giuseppina Annetta and Mauro Pittiruti in The Journal of Vascular Access