cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/mkg3yhtmh7
title: Single-Cell Spatial Transcriptomics Reveals a Dystrophic Trajectory Following a Developmental Bifurcation of FSHD Myoblast Cell Fates

description: Facioscapulohumeral Muscular Dystrophy (FSHD) is linked to abnormal de-repression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single cell analysis. However, single cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use MERFISH (Multiplexed Error Robust Fluorescent In Situ Hybridization) spatial transcriptomics that allows profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated control, isogenic D4Z4 contraction mutant and FSHD1 patient myotubes and unfused mononuclear cells (MNCs), as well as the individual nuclei within them. We find myocyte nuclei segregate into 2 clusters defined by expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, while MNCs cluster based on developmental state. Patient/mutant myotubes are found in “FSHD-hi” and “FSHD-lo” states with the former signified by high DUX4 target expression and decreased muscle gene expression. Pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and FSHD-hi myotube branches, with variable numbers of DUX4 target expressing nuclei found in multi-nucleated FSHD-hi myotubes. Gene co-expression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared to control. We also identify distinct sub-pathways within the DUX4 gene network that differentially contribute to the disease phenotype. Taken together, our MERFISH-based study provides effective gene network profiling of multinucleated cells and uniquely identifies FSHD-induced transcriptomic alterations within myoblast differentiation.
DOI: 10.6084/m9.figshare.14709411.v1
title: Supplementary Material for: Epidemiological Risk Factors Associated with Acne Vulgaris Presentation, Severity, and Scarring in a Singapore Chinese Population: A Cross-Sectional Study

description: <b><i>Background:</i></b> Acne vulgaris is classified based on the severity of skin lesions and post-healing scar types of these lesions. Numerous epidemiology studies have investigated the risk factors associated with acne presentation and severity, but studies for acne scarring are lacking. <b><i>Objective:</i></b> To investigate the prevalence of acne, severity, and scarring grades and their associated risk factors among Singapore Chinese. <b><i>Methods:</i></b> A total of 3,888 subjects (2,090 cases/1,798 controls; median age = 21 ± 4.589; range 17–71) completed an investigator-administered questionnaire as part of a cross-sectional study, which included sociodemographics, familial medical history, lifestyle factors, dietary habits, and acne history. Acne cases were further evaluated for their severity (<i>n</i> = 991) and scarring (<i>n</i> = 988) grades by a trained personnel. <b><i>Results:</i></b> The majority of the acne cases had mild acne/grade 1 scarring, while less than 1% had severe acne/grade 4 scarring. Parental acne was significantly associated with acne presentation and moderate/severe acne, while sibling acne was significantly associated with grade 3/4 scarring. Gender and age affected acne severity and scarring but not acne presentation, while tertiary maternal education level and the possession of ≥3 siblings were particularly associated with acne scarring. Underweight BMI was protective against acne presentation, while atopic diseases (asthma, allergic rhinitis, eczema) were its predisposing factors. Of the evaluated lifestyle factors, computer/TV usage had significant association with acne presentation, while alcohol consumption was significantly associated with acne severity. Frequent milk consumption was associated with a protective effect for moderate-severe acne, while frequent butter consumption had a detrimental effect on acne scarring extent. <b><i>Conclusion:</i></b> Positive familial history is a strong predisposing factor in determining acne presentation, severity, and scarring. Demographic factors (gender, age) and sedentary lifestyle (increased computer/TV usage) influence acne presentation, while dietary habits (milk and butter consumption) influence acne severity and scarring. The predisposing factors revealed in this study could help us to gain insights into acne pathophysiology and hence develop interventions especially targeting modifiable risk factors.
DOI: 10.17632/mdrn2wbn2h
title: Sustainable Transportation Strategies in Business: An Systematic Review Examining Innovative Practices, Environmental Impact, and Economic Wellfare Data

description: Sustainable Transportation Strategies in Business: An Systematic Review Examining Innovative Practices, Environmental Impact, and Economic Wellfare Data
DOI: 10.17632/p77mry4m4y
title: Pig. 2. Indonesia - Eastern Africa total trade volume (2010 – 2022)

description: Pig. 2. Indonesia - Eastern Africa total trade volume (2010 – 2022)
DOI: 10.17632/cr2zg9hg55
title: Raw data for the study NOX4 inhibition with GKT137831 protects against diabetic cardiomyopathy: Insights from functional and transcriptomic analysis

description: The raw data files consists Uncrossed western blot images, Raw histopathological images, DCFDA and DHE images, Heamodynamic parameters and biochemical parameters and TUNEL raw images
DOI: 10.17632/zbk4tn7p9r
title: Commercially available Mfsd2a antibody (Abcam, #ab105399) is non-specific

description: A recent article was published last month in Science Advances by Jia Zhou et al entitled “Zika virus degrades the ω-3 fatty acid transporter Mfsd2a in brain microvascular endothelial cells and impairs lipid homeostasis.” The conclusions that Zika virus infection downregulates Mfsd2a protein levels at the blood-brain barrier rely on the quality of the Mfsd2a antibody that they used, which was purchased from Abcam (#ab105399). The Silver lab discovered the function of Mfsd2a as a lysolipid transporter [1] and have published our findings using our own validated antibodies to Mfsd2a [1-9] that we have provided to other researchers who have confirmed their specificity [10-12]. It is disconcerting that there are more than 10 published articles in the literature that have relied on ab105399 for data generation without proof of validation of specificity. This figure shows a side-by-side test of ab105399 versus our published antibody against Mfsd2a, where we show that ab105399 does not detect Mfsd2a with any specificity. Note: #ab105399 appears to be distributed by Invitrogen (#PA5-21049), Genetex (#GTX85147), ProSci incorporated (#6025), and LSBio (#LS-B5348). References: 1. Nguyen, L.N., et al., Mfsd2a is a transporter for the essential omega-3 fatty acid docosahexaenoic acid. Nature, 2014. 509(7501): p. 503-6. 2. Alakbarzade, V., et al., A partially inactivating mutation in the sodium-dependent lysophosphatidylcholine transporter MFSD2A causes a non-lethal microcephaly syndrome. Nat Genet, 2015. 47(7): p. 814-7. 3. Berger, J.H., M.J. Charron, and D.L. Silver, Major facilitator superfamily domain-containing protein 2a (MFSD2A) has roles in body growth, motor function, and lipid metabolism. PLoS One, 2012. 7(11): p. e50629. 4. Chan, J.P., et al., The lysolipid transporter Mfsd2a regulates lipogenesis in the developing brain. PLoS Biol, 2018. 16(8): p. e2006443. 5. Guemez-Gamboa, A., et al., Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Nat Genet, 2015. 47(7): p. 809-13. 6. Harel, T., et al., Homozygous mutation in MFSD2A, encoding a lysolipid transporter for docosahexanoic acid, is associated with microcephaly and hypomyelination. Neurogenetics, 2018. 19(4): p. 227-235. 7. Piccirillo, A.R., et al., The Lysophosphatidylcholine Transporter MFSD2A Is Essential for CD8(+) Memory T Cell Maintenance and Secondary Response to Infection. J Immunol, 2019. 203(1): p. 117-126. 8. Quek, D.Q., et al., Structural insights into the transport mechanism of the human sodium-dependent lysophosphatidylcholine transporter Mfsd2a. J Biol Chem, 2016. 9. Wong, B.H., et al., Mfsd2a Is a Transporter for the Essential omega-3 Fatty Acid Docosahexaenoic Acid (DHA) in Eye and Is Important for Photoreceptor Cell Development. J Biol Chem, 2016. 291(20): p. 10501-14. 10. Wang, Y., et al., Elife, 2019. 8. 11. Vanlandewijck, M., et al., Nature, 2018. 12. Byrne, L.C., et al., Mol Ther, 2015. 23(2): p. 290-6.
DOI: 10.17632/6pvjy3bwz9
title: MFA Financial Dataset

description: MFA Financial (“MFA”) Series C fixed-to-floating rate cumulative redeemable preferred stock is an attractive short duration fixed income instrument that I expect to generate approximately a 25% IRR and 40% total return over the next year and a half.

The opportunity exists because 1.) the interest rate and mortgage spread environment over the last two years has presented a challenging backdrop for levered long fixed income investing strategies, 2.) one mortgage REIT peer took a surprising position with respect to the LIBOR transition, and 3.) preferred instruments broadly have been out of favor.

 

I believe the go forward environment for mortgage REITs is conducive to generating positive economic returns, PMT’s position with respect to LIBOR transition is the exception rather than the rule, and there are early signs of increased investor demand for preferred instruments.

 

MFA Series C preferred will begin paying quarterly dividends at an annual rate of 5.345% over 3-month term SOFR as of March 31, 2025. Mortgage REIT fixed-to-floating rate preferreds that have already reset to floating rate such as AGNC Series C (+5.111%), Annaly Series F (+4.993%) and Annaly Series G (+4.172%) trade at or near par (98% to 101% of par).

 

Assuming MFA Series C preferred trades at 95% of par once the first floating rate dividend is paid in June 2025, this preferred will generate an approximate 25% IRR and 40% total return. Assuming MFA Series C preferred trades at par once the first floating rate dividend is paid, this preferred would generate a 29% IRR and 48% total return.

AGNC on 10/31/2023: “Our outlook for Agency MBS is very favorable. Spreads have decoupled from treasuries and corporates due to supply and demand technical factors that we expect will ease over time…spreads and other fixed income sectors are close to post-GFC long-term averages, which spreads on Agency MBS are in the 95-plus percentile area.”

 

MFA on 11/7/2023: “Mortgage spreads are indeed very wide today, but they were at similar levels in 1986, and ’87, in 1999 and 2000 and in 2008 before the Fed began its first round of QE.”

 

 

The PMT LIBOR transition wrinkle

PennyMac Mortgage Investment Trust (“PMT”) is a mortgage REIT with two series of fixed-to-floating rate preferred stock. On August 25, 2023, PMT issued a press release stating their position that the Federal Reserve’s LIBOR rule would result in PMT’s fixed-to-floating rate preferred not transitioning to a floating reference rate as a result of USD LIBOR being phased out.

 

PMT’s press release can be found here.

 

I believe PMT has taken an aggressive and unique position and am not aware of any other company that has or has indicated an intent to take a similar position. I believe that MFA’s Series C preferred will transition to floating, as scheduled, with the floating benchmark referring to Term SOFR rather than LIBOR for the following reasons:
DOI: 10.17632/858bmcf7j6
title: GeoTaichi: A Taichi-powered high-performance numerical simulator for multiscale geophysical problems

description: This study introduces GeoTaichi, an open-source high-performance numerical simulator designed for addressing multiscale geophysical problems. By leveraging the power of the Taichi parallel language, GeoTaichi maximizes the utilization of modern computer resources on multicore CPU and GPU architectures. It offers robust and reliable modules for the discrete element method (DEM), material point method (MPM), and coupled material point-discrete element method (MPDEM). These modules enable efficient solving of large-scale problems while being implemented in pure Python. The design philosophy of GeoTaichi focuses on creating a framework that is readable, extensible, and user-friendly. This paper highlights the coupling procedure of MPDEM, the code structures, and the most important features of GeoTaichi. Rigorous benchmark tests have been conducted to verify the validity and robustness of GeoTaichi. Additionally, the performance of GeoTaichi is compared with similar software tools in the field, underscoring a notable improvement in both computational efficiency and memory savings when compared to existing alternatives.
DOI: 10.17632/hbs9283b83
title: Data for: Quantitative Analysis of Trans-synaptic Protein Alignment

description: This zip file contains all Matlab scripts involved in the analytical methods in manuscript with a detailed descriptive list in a docx file. It also has a "synapse.txt' file containing all localization coordinates of RIM1/2 and PSD-95 (labeled as 647 and 561, respectively in the channel column) in an example synapse.
DOI: 10.17632/m6772pcxjg
title: Use of NDSS to discriminate between Parmigiano Reggiano and Grana Padano PDO and their ripening times from grated cheese spectra_Experimental design

description: Diagram for the description of the experimental design used for the work entitled: Use of NDSS to discriminate between Parmigiano Reggiano and Grana Padano PDO and their ripening times from grated cheese spectra
DOI: 10.17632/4r3frnc9yw
title: Windshield recycling PATSTAT data

description: The dataset includes several Excel sheets, each listing the records obtained from Patstat online database (https://data.epo.org/expert-services/index.html) by means of SQL queries run in Patstat online (Autumn 2017 ed.). Such investigation is aimed at retrieving patent documents data including in particular: • the individual patent application identification code (appln_id attribute in the table), • the application authorities (i.e. the patent offices to whom the patent applications are filed), • the earliest filing year, • the docdb_family_id code univocally identifying a single patent family (a.k.a. DOCDB family), • the patent applications titles and abstracts, • the classification codes (IPC and CPC, respectively) assigned to each patent application, • the patent publication authority, • the patent publication number, • the patent publication kind, • the denomination of each assignee/applicant (psn_name) and • the type of applicant (psn_sector allowing for distinguishing companies, universities, individuals etc. among applicants/assignees). PDF files (named as the corresponding Excel) may be present. Each provides lists of the documents downloadable from PATSTAT online. The number of documents corresponds to the amount of non-duplicated appln_id values (eg. 1125 for PHASE A in the pdf, as arguable from the PHASE A Excel file). URLs are provided for each record to link to Espacenet (https://worldwide.espacenet.com/) • PHASE A TABLE concern a broad search regarding glass recycling. • PHASE B concerns a more specific search, based on keywords AND IPC/CPC codes, regarding recycling of laminated glass by means of mechanical comminution. Data rather based on keywords are argued from PHASE B_query A. Records selected by means of cpc code Y02W30/521 are included in PHASE B Query B TABLE. • PHASE C Query C1 TABLE concerns recycling of glass with poly-vinyl-butyral interlayer (PVB) • PHASE C Query C2’ TABLE concerns recycling of glass with ethyl-vinyl-acetate interlayer (EVA) • PHASE C Query C2’’ TABLE concerns recycling of glass with (thermoplastic) poly-urethane interlayer (TPU). One file with SQL scripts not detailed in other publications is included (PATSTAT SCRIPTS). The file contains two scripts to be run with Patstat: the former is aimed at ranking the patent families depending on the co-occurrence of IPC classification codes, while the latter is aimed at ranking the granted patents depending on the number of annual fee payments and the date of patent validity expiration. SQL scripts are included in a manuscript submitted to Data in Brief journal, accompanying the manuscript submitted to World Patent Information for review (WPI_2018_95 _R1).
DOI: 10.17632/5cdygw94rn
title: Research on low-power destruction-resistant routing protocol assisted by intelligent reflective surface based on spatiotemporal reinforcement learning

description: Research on low-power destruction-resistant routing protocol assisted by intelligent reflective surface based on spatiotemporal reinforcement learning
DOI: 10.17632/mjbgkg63m2
title: Efficacy and safety of anti-CD45-saporin as conditioning agent for RAG deficiency

description: TITLE: Efficacy and safety of anti-CD45–saporin as conditioning agent for RAG deficiency 

Maria Carmina Castiello, Marita Bosticardo, Nicolò Sacchetti, Enrica Calzoni, Elena Fontana, Yasuhiro Yamazaki, Elena Draghici, Cristina Corsino , Ileana Bortolomai, Lucia Sereni, Hsin-Hui Yu, Paolo Uva, Rahul Palchaudhuri, David T. Scadden, Anna Villa, Luigi D. Notarangelo.

PMID: 32387109 


Background: Mutations in the recombinase-activating genes cause severe immunodeficiency, with a spectrum of phenotypes ranging from severe combined immunodeficiency to immune dysregulation. Hematopoietic stem cell transplantation is the only curative option, but a high risk of graft failure and poor immune reconstitution have been observed in the absence of myeloablation.
Objectives: Our aim was to improve multilineage engraftment; we tested nongenotoxic conditioning with anti-CD45 mAbs conjugated with saporin CD45 (CD45-SAP).
Methods: Rag1-KO and Rag1-F971L mice, which represent models of severe combined immune deficiency and combined immune deficiency with immune dysregulation, respectively, were conditioned with CD45-SAP, CD45-SAP plus 2 Gy of total body irradiation (TBI), 2 Gy of TBI, 8 Gy of TBI, or no conditioning and treated by using transplantation with lineage-negative bone marrow cells from wild-type mice. Flow cytometry and immunohistochemistry were used to assess engraftment and immune reconstitution. Antibody responses to 2,4,6-trinitrophenyl-conjugated keyhole limpet hemocyanin were measured by ELISA, and presence of autoantibody was detected by microarray.
Results: Conditioning with CD45-SAP enabled high levels of multilineage engraftment in both Rag1 mutant models, allowed overcoming of B- and T-cell differentiation blocks and thymic epithelial cell defects, and induced robust cellular and humoral immunity in the periphery.
Conclusions: Conditioning with CD45-SAP allows multilineage engraftment and robust immune reconstitution in mice with either null or hypomorphic Rag mutations while preserving thymic epithelial cell homeostasis.
DOI: 10.6084/m9.figshare.27332292.v1
title: 原始data.xlsx

description: Changes in 24-hour urine output and renal function in patients.
DOI: 10.17632/jf6k3vmrg6
title: Frequency and attitudes of purchasing medications online in the Visegrad Countries Europe after the pandemic - 2022 survey data

description: Evidently, the e-pharmacy market has been accelerated by the pandemic and has made pharmacy e-commerce integral to healthcare delivery, as commerce and healthcare has shifted to the digital environment. Therefore, the aim of provided research was to assess the frequency and attitudes of patients purchasing medications online before and after the COVID-19 pandemic in the Visegrad Group countries (Czech Republic, Hungary, Poland and Slovakia) following a similar path regarding the regulatory environment of internet pharmacies and distant sale of pharmaceuticals.
An online descriptive cross-sectional study was conducted in four central European countries (Czech Republic, Hungary, Poland and Slovakia) representing 12.5% of EU-28, to measure the prevalence and attitudes towards purchasing medications and health products from the internet, further, to evaluate the change of such purchases before and after the outbreak of the coronavirus disease in March 2020. These countries have similar indicators regarding socio-demographic characteristics, economic and cultural background. Respondents were approached via the most popular social media platforms in the region (Facebook and Instagram) with the questionnaire formatted into the Google forms, further, surveyed through the Pollfish survey research platform between May and August 2022.  
The 25-item questionnaire included single choice and 5-point Likert scale answers. It consisted of an introductory paragraph on the purpose of the survey, information on confidentiality, and anonymity followed by four main sections: Questions related to drug procurement (n=3); Attitudes towards online drug purchases (n=4); Internet usage habits including medicines and health product purchases (n=13); Sociodemographic data (n=5). The first section is preceded by four screening questions to increase consciousness regarding the attributes of medicines for participants to be able to differentiate medicines from health products (e.g., dietary supplements or herbals) in the later sections of the survey. Participation was voluntarily and anonymous. We have not directly collected data on health status, however, respondents had to select if they were taking medications for chronic conditions and they had the opportunity to name the products purchased online and the website they have used for the purchase.
DOI: 10.17632/x45h92cygc
title: Robustness_Results

description: The results of difference-in-differences analysis robustness checks conducted to measure causal effects of the hurricanes, for each value of geographical extent, timing, and duration, and for each control group matching criteria, as discussed in Section 4.1, are attached.
DOI: 10.17632/bf58fznfx2
title: Vaughnetal2023_IntegrOrganBiol_PodarcisMorphologyPerformance

description: Data and analysis code associated with Vaughn et al. 2023, "Climbing and clinging of urban lizards are differentially affected by morphology, temperature, and substrate" published in the journal Integrative Organismal Biology.