bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple pattern speeds and the manifold spirals in a simulation of a barred spiral galaxy
Authors: Zouloumi K , Harsoula M , Efthymiopoulos C 
Published: February 2024

ABSTRACT
Observations of real galaxies as well as N-body simulations often indicate the presence of multiple pattern speeds in the disc of a barred spiral galaxy. In this paper we use an accurate frequency extraction algorithm (NAFF) to determine the pattern speeds in an N-body model simulation of a secularly evolving barred spiral galaxy. Then, we compute the manifold spirals under multiple pattern speeds using the algorithm proposed in a previous paper by Efthymiopoulos et al. Our main new results are: (i) We demonstrate that precise frequency extraction algorithms as NAFF allow for a determination of pattern speeds in time windows of length much shorter than the one required by the traditional time-Fourier spectrum of the m = 2 mode. This is particularly convenient in cases where the pattern speeds slowly change in time due to secular evolution in the disc, and/or, the different modes spatially overlap in the disc. (ii) Once we get the frequencies, we compute the approximate gravitational potential, and the manifolds (iii) We show that the observed structures formed by the spiral arms in the simulation (change of form, formation of ‘bridges’, etc.) can be modelled by manifolds, and that this is consistent with the fact that the bar and spirals have different pattern speeds.
Estimates of Crystallinity Utilizing Differential Scanning Calorimetry: Application to the Kīlauea 2018 Lower East Rift Zone Eruption
Authors: Halverson B A , Emerson A , Hammer J , Lira J , Whittington A 
Published: February 2024

Abstract
Rocks produced by diverse processes, from condensation in space to impacts on planetary surfaces to volcanism, contain both crystals and amorphous material. Crystallinity provides information on the thermal history of the sample and is especially important in characterizing volcanic rocks and pyroclasts because lava rheology is profoundly influenced by the crystal content. Crystallinity is typically quantified via microscopy, using transmitted light or backscattered electrons. However, many samples present visibly ambiguous textures such as intimate intergrowth of crystal phases, and/or crystal sizes extending down to the nanometer scale. Here, we apply calorimetric methods involving heat capacity and enthalpy to assess the crystallinity of a series of volcanic samples. We tested three different approaches, using differential scanning calorimetry, on 30–40 mg aliquots of powdered basalts from the 2018 Kīlauea lower East Rift Zone. The first approach involves determining the magnitude of the increase in heat capacity at the glass transition, which can determine crystallinity to a 1σ precision of ±3%. The second approach is based on the enthalpy of fusion, which requires a longer more complex procedure with results that are typically more uncertain than for the heat capacity method, with a 1σ of ±6%. A final method utilizing differences in enthalpies calculated from the heat capacities required the most complex procedure and has the greatest uncertainty of ±18%. Preliminary results for lavas with microscopically determined crystallinities ranging from 11 to 98% indicate that crystallinity based on calorimetric data can be tens of percent higher than the average value identified using microscopy and petrographic analysis. Image-based methodologies applied to sections of samples reveal spatial heterogeneity and details in texture and crystallinity, whereas calorimetry-based methodologies capture the overall ‘bulk sample’ properties, unbiased by section effects or imaging resolution limits. These techniques are a powerful combination that can present complementary views of crystallinity.
Policing a neurodiverse world: Lessons from the social model of disability
Authors: Thacher David 
Published: February 2024

AbstractPrograms that aim to improve the police response to mental health crises and related incidents have implicitly relied on a medical/individual model of psychiatric disability, which emphasizes efforts to provide mental health treatments to individuals. This paper argues that this perspective has unnecessarily limited the range of options that police might draw from to manage these incidents. Advocates of an alternative, social model of psychiatric disability (as well as the “neurodiversity paradigm” it inspired) argue that we should view disability not as a property of individuals with certain impairments but as a property of the society that has failed to accommodate them. I argue that repeated calls to the police provide important information about the location and character of those failures, and that police have an important role to play in rectifying them. I illustrate how police have already played that role in several cities.
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids
Authors: Haloi Nandan , Huang Shan , Nichols Aaron L , Fine Eve J , Friesenhahn Nicholas J , Marotta Christopher B , Dougherty Dennis A , Lindahl Erik , Howard Rebecca J , Mayo Stephen L , Lester Henry A 
Published: February 2024

Abstract
We developed fluorescent protein sensors for nicotine with improved sensitivity. For iNicSnFR12 at pH 7.4, the proportionality constant for ∆F/F0vs [nicotine] (δ-slope, 2.7 μM−1) is 6.1-fold higher than the previously reported iNicSnFR3a. The activated state of iNicSnFR12 has a fluorescence quantum yield of at least 0.6. We measured similar dose-response relations for the nicotine-induced absorbance increase and fluorescence increase, suggesting that the absorbance increase leads to the fluorescence increase via the previously described nicotine-induced conformational change, the ‘candle snuffer’ mechanism. Molecular dynamics (MD) simulations identified a binding pose for nicotine, previously indeterminate from experimental data. MD simulations also showed that Helix 4 of the periplasmic binding protein (PBP) domain appears tilted in iNicSnFR12 relative to iNicSnFR3a, likely altering allosteric network(s) that link the ligand binding site to the fluorophore. In thermal melt experiments, nicotine stabilized the PBP of the tested iNicSnFR variants. iNicSnFR12 resolved nicotine in diluted mouse and human serum at 100 nM, the peak [nicotine] that occurs during smoking or vaping, and possibly at the decreasing levels during intervals between sessions. NicSnFR12 was also partially activated by unidentified endogenous ligand(s) in biofluids. Improved iNicSnFR12 variants could become the molecular sensors in continuous nicotine monitors for animal and human biofluids.
Long non-coding RNA H19X as a regulator of mononuclear cell adhesion to the endothelium in systemic sclerosis
Authors: Tirelli Francesca , Pachera Elena , Gmür Sabrina , Lafyatis Robert , Huang Mengqi , Zulian Francesco , Camarillo Retamosa Eva , Kania Gabriela , Distler Oliver 
Published: February 2024

Abstract

Objective
To define the functional relevance of H19 X-linked (H19X) co-expressed long non-coding RNA (lncRNA) in endothelial cell (EC) activation as a key process in SSc vasculopathy.

Methods
H19X expression in SSc skin biopsies was analysed from single-cell RNA sequencing (scRNA-seq) data. Differential expression and pathway enrichment analysis between cells expressing (H19Xpos) and non-expressing H19X (H19Xneg) cells was performed. H19X function was investigated in human dermal microvascular ECs (HDMECs) by silencing. H19X and EC adhesion molecule levels were analysed by real-time quantitative PCR and western blot after stimulation with pro-inflammatory cytokines. Cytoskeletal rearrangements were analysed by fluorescent staining. Endothelial adhesion was evaluated by co-culture of HDMECs and fluorescent-labelled peripheral blood mononuclear cells (PBMCs). Shedding vascular cell adhesion protein 1 (VCAM1) was evaluated by ELISA on HDMEC supernatant.

Results
The scRNA-seq data showed significant upregulation of H19X in SSc compared with healthy ECs. In HDMECs, H19X was consistently induced by IFN type I and II. H19X knockdown lead to a significant decrease in the mRNA of several adhesion molecules. In particular, VCAM1 was significantly reduced at the protein and mRNA levels. Co-expression analysis of the scRNA-seq data confirmed higher expression of VCAM1 in H19Xpos ECs. ECs were also strongly associated with the ‘cell adhesion molecule’ pathway. Moreover, the VCAM1 downstream pathway displayed less activation following H19X knockdown. Contractility of HDMECs, PBMC adhesion to HDMECs and VCAM1 shedding were also reduced following H19X knockdown.

Conclusions
lncRNA H19X may contribute to EC activation in SSc vasculopathy, acting as a regulator of expression of adhesion molecules in ECs.
Process and Outcomes of Fitting Corneoscleral Profilometry-Driven Scleral Lenses for Patients With Ocular Surface Disease
Authors: Yoon Hannah , Harthan Jennifer S. , Skoog William , Fogt Jennifer S. , Nau Amy , Nau Cherie B. , Schornack Muriel , Shorter Ellen 
Published: February 2024

Objectives:
To assess the feasibility of obtaining cornea scleral profile (CSP) measurements using Scheimpflug imaging and report on the fitting process of free-form custom scleral lenses (SLs) for patients with ocular surface disease (OSD).

Methods:
This prospective study of patients fit with free-form SLs collected data on the following: demographics, indications for wear, corneal and scleral tomography, scan acquisition process, and SL fitting process.

Results:
Cornea scleral profile scans were acquired on 15 eyes of nine patients. Mean scan time for right eyes was 10.7, and 9.7 min for left eyes. A mean of 2.9 follow-up visits were required to complete SL fitting, with a mean of 2.1 lenses ordered. One eye did not tolerate lens wear, and one eye could not be fit using the CSP scan because of insufficient data. The initial lens ordered was dispensed at the first follow-up visit for seven of the remaining 13 eyes, all of which were ultimately fit successfully in free-form lenses.

Conclusions:
In this study of profilometry-guided SL fitting for eyes with OSD and low magnitude corneal astigmatism, the number of lenses and follow-up visits required were similar to outcomes of previous studies that described the diagnostic approach to SL fitting. In addition, imaging technology does not negate the need for skilled clinical observation while fitting SLs.
Dysregulation of the circRNA_0087207/miR-548c-3p/PLSR1-TGFB2 axis in Leber hereditary optic neuropathy in vitro
Authors: Yang Yi-Ping , Chang Yuh-Lih , Chiou Guang-Yuh , Lee Meng-Shiue , Wu You-Ren , Chen Po-Wei , Lin Yi-Ying , Lai Wei-Yi , Liu Yu-Hao , Hwang De-Kuang , Chien Yueh 
Published: February 2024

Background:
Leber hereditary optic neuropathy (LHON) is mainly the degeneration of retinal ganglion cells (RGCs) associated with high apoptosis and reactive oxygen species (ROS) levels, which is accepted to be caused by the mutations in the subunits of complex I of the mitochondrial electron transport chain. The treatment is still infant while efforts of correcting genes or using antioxidants do not bring good and consistent results. Unaffected carrier carries LHON mutation but shows normal phenotype, suggesting that the disease’s pathogenesis is complex, in which secondary factors exist and cooperate with the primary complex I dysfunction.

Methods:
Using LHON patient-specific induced pluripotent stem cells (iPSCs) as the in vitro disease model, we previously demonstrated that circRNA_0087207 had the most significantly higher expression level in the LHON patient-iPSC-derived RGCs compared with the unaffected carrier-iPSC-derived RGCs. To elaborate the underlying pathologies regulated by circRNA_008720 mechanistically, bioinformatics analysis was conducted and elucidated that circRNA_0087207 could act as a sponge of miR-548c-3p and modulate PLSCR1/TGFB2 levels in ND4 mutation-carrying LHON patient-iPSC-derived RGCs.

Results:
Using LHON iPSC-derived RGCs as the disease-based platform, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis on targeted mRNA of miR-548c-3p showed the connection with apoptosis, suggesting downregulation of miR548c-3p contributes to the apoptosis of LHON patient RGCs.

Conclusion:
We showed that the downregulation of miR548c-3p plays a critical role in modulating cellular dysfunction and the apoptotic program of RGCs in LHON.
Policy Challenges and Resiliency Related to Ending the HIV Epidemic in the Southern and Rural United States: A Call to Action
Authors: Moen Marik , Sublette Nina , Alves Justin , Walker Crystal Martin 
Published: February 2024

Abstract
In this commentary, we describe current policy trends and their implications for the health of populations in the Southern and rural United States. We outline policy changes that threaten the prevention, care, and treatment of people at risk for HIV or with HIV and sociopolitical factors contributing to these policy trends. We also issue a call-to-action for individuals with Southern and rural US policy expertise and lived or living experience to collaboratively engage on a systematic policy analysis to thoroughly document relevant policies and deepen our understanding of the influences behind these policies. Finally, we provide examples of individual, community, and national level resiliency and courage—strategies that inspire advocacy and hope in the face of policy setbacks.
Cluster Analysis of World Trade Center Related Lower Airway Diseases
Authors: de la Hoz Rafael E. , Jeon Yunho , Doucette John T. , Reeves Anthony P. , San José Estépar Raúl , Celedón Juan C. 
Published: February 2024

Abstract
Introduction: Cluster analysis can classify without a priori assumptions the heterogeneous chronic lower airway diseases found in former workers at the World Trade Center (WTC) disaster site. Methods: We selected the first available chest computed tomography scan with quantitative computed tomography measurements on 311 former WTC workers with complete clinical, and spirometric data from their closest surveillance visit. We performed a nonhierarchical iterative algorithm K-prototype cluster analysis, using gap measure. Results: A five-cluster solution was most satisfactory. Cluster 5 had the healthiest individuals. In cluster 4, smoking was most prevalent and intense but there was scant evidence of respiratory disease. Cluster 3 had symptomatic subjects with reduced forced vital capacity impairment (low FVC). Clusters 1 and 2 had less dyspneic subjects, but more functional and quantitative computed tomography evidence of chronic obstructive pulmonary disease (COPD) in cluster 1, or low FVC in cluster 2. Clusters 1 and 4 had the highest proportion of rapid first-second forced expiratory volume decliners. Conclusions: Cluster analysis confirms low FVC and COPD/pre-COPD as distinctive chronic lower airway disease phenotypes on long-term surveillance of the WTC workers.
A case report: intravenous leiomyomatosis extending from the uterus to the right atrium
Authors: Ziani Hicham , El Idrissi Jallal Nora , Lahbabi Yassir , Slaihi Zakariae , Lahbabi Sophia , Oudghiri Nezha , Tachinante Rajae 
Published: February 2024

Introduction and importance:Intra veinous leiomyomatosis (IVL) is one pathology of a known group of ectopic leiomyomatosis that gathers many entities all defined by the presence of benign tumours arising from uterine smooth muscle cells. The authors aim through this case report to address the underdiagnosis of IVL in pre-menopausal women and the potential confusion with other cardiac tumours.Case presentation:A 48-year-old woman initially treated for a suspected intracardiac myxoma underwent two surgeries. Seeking gynaecological care for menometrorrhagia related to a polymyomatous uterus, she was scheduled for radical surgery. Unexpectedly, extended explorations during a hysterectomy revealed a tumour originating from the pelvis, extending to the right atrium and inferior vena cava, indicative of intravascular leiomyomatosis.Clinical discussion:IVL’s diagnosis is often incidental during hysterectomy analysis, with symptoms mimicking uterine fibroids. Treatment involves radical surgery, emphasizing the importance of complete resection to reduce the significant risk of recurrence.Conclusion:Pre-menopausal women with a history of hysterectomy or myomectomy and a detected right chamber mass should be screened for intravascular leiomyomatosis. Diagnosis relies on histological examination, guiding tailored treatment choices such as surgical resection with a focus on bilateral adnexectomy for optimal outcomes.
A Case of Varicella Zoster and Mpox Coinfection in a Patient Living With HIV
Authors: Mazumder Archisman , Lim Lindsay , White Cameron M. , Van Gerwen Olivia T. 
Published: February 2024

Abstract
We present a case of recurrent, cutaneous mpox with coinfection of disseminated varicella zoster in an immunocompromised patient with poorly controlled HIV. This case demonstrates the importance of maintaining a high index of suspicion for mpox despite prior infection and vaccination, as suboptimal immune response is possible in immunocompromised patients, and also noting the potential for coinfection necessitating timely diagnosis and appropriate testing.
Assessing the Impact of COVID-19 on HIV Outcomes in the United States: A Modeling Study
Authors: Viguerie Alex , Jacobson Evin U. , Hicks Katherine A. , Bates Laurel , Carrico Justin , Honeycutt Amanda , Lyles Cindy , Farnham Paul G. 
Published: February 2024

Background
The COVID-19 pandemic impacted sexual behaviors and the HIV continuum of care in the United States, reducing HIV testing and diagnosis, and use of preexposure prophylaxis and antiretroviral therapy. We aimed to understand the future implications of these effects through a modeling study.

Methods
We first ran our compartmental model of HIV transmission in the United States accounting for pandemic-related short-term changes in transmission behavior and HIV prevention and care provision in 2020 to 2021 only. We then ran a comparison scenario that did not apply pandemic effects but assumed a continuation of past HIV prevention and care trends. We compared results from the 2 scenarios through 2024.

Results
HIV incidence was 4·4% lower in 2020 to 2021 for the pandemic scenario compared with the no-pandemic scenario because of reduced levels of transmission behavior, despite reductions in HIV prevention and care caused by the pandemic. However, reduced care led to less viral load suppression among people with HIV in 2020, and in turn, our model resulted in a slightly greater incidence of 2·0% from 2022 to 2024 in the COVID-19 scenario, as compared with the non-COVID scenario.

Discussion
Disruptions in HIV prevention and care services during COVID-19 may lead to somewhat higher postpandemic HIV incidence than assuming prepandemic trends in HIV care and prevention continued. These results underscore the importance of continuing to increase HIV prevention and care efforts in the coming years.
Implementation of Point of Care Sexually Transmitted Infections Testing in a Community Clinic Setting
Authors: Toma Emily , Malyuta Yelena , Salhaney Peter , Nunn Amy , Maynard Michaela , Tao Jun , Sutten Coats Cassie , Chan Philip A. 
Published: February 2024

Abstract
The rates of sexually transmitted infections (STIs) in the United States, including chlamydia and gonorrhea, are rising. Point-of-care (POC) testing could increase access to testing and treatment. This evaluation found POC STI testing to be concordant with the results of traditional laboratory testing for 100% of patients who were tested. Ninety-five percent of the patients reported being satisfied with the experience, and 66% preferred it to traditional laboratory testing. The most commonly reported reason for preferring the test was the short amount of time it took to receive results. However, insurance reimbursed less than 30% of what was billed for the POC tests. Low insurance reimbursement rates could be a barrier to implementation long-term financial sustainability of POC STI testing.
Al18F-NOTA-Octreotide PET/CT and 18F-FDG PET/CT for Detecting Cerebellar Hemangioblastoma in a Patient With Von Hippel-Lindau Disease
Authors: Hou Guozhu , Cheng Xin , Chi Yihebali , Wang Xuejuan , Zheng Rong 
Published: February 2024

Abstract
Von Hippel-Lindau disease is a hereditary syndrome associated with various benign and malignant tumors, including hemangioblastomas. A 42-year-old man with a history of Von Hippel-Lindau disease underwent surgery for pancreatic neuroendocrine tumor and renal clear cell carcinoma and was recommended to undergo Al18F-NOTA-octreotide and 18F-FDG PETCT examination to assess potential metastases. 18F-FDG PET/CT showed low uptake in the right cerebellum, which demonstrated increased Al18F-NOTA-octreotide activity. Cerebellar mass resection surgery was performed. Pathological result was consistent with hemangioblastoma. This case report indicates the significant role of Al18F-NOTA-octreotide in the diagnosis of hemangioblastoma.
LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins
Authors: Sobala Łukasz F. 
Published: February 2024

AbstractThe origins and early evolution of animals is a subject with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from non-bilaterians. Publicly available data is plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic and metagenomic studies and is an extension of EukProt (Richter et al., 2022,Peer Community Journal,2, e56). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections and major updates will synchronize LukProt to each new version of EukProt and releases are permanently stored on Zenodo. A BLAST server to search the database is available athttps://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database can be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.Graphical abstractSignificance statementLukProt is a sequence database aiming to accelerate the research on the evolution of animals by cutting the time-consuming step of assembling sequences from disparate sources. Non-bilaterians are currently not well covered by general purpose databases, despite plentiful, public sequencing data. These data were integrated into a consistently curated database, presented here. It can be downloaded and used locally or used via a public BLAST search server. A clear taxonomic framework is also introduced, as well as scripts to aid local data analyses. LukProt will be publicly available on Zenodo, kept up to date and synchronized with each new version of its parent database, EukProt.