bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Dietary Quality on Genital Oncogenic Human Papillomavirus Infection in Women
Authors: Lin Hui-Yi , Fu Qiufan , Tseng Tung-sung , Zhu Xiaodan , Reiss Krzysztof , Joseph Su L , Hagensee Michael E 
Published: May 2023

Abstract

Background
Most cervical cancers are directly linked to oncogenic or high-risk human papillomavirus (HR-HPV) infection. This study evaluates associations between diet quality and genital HPV infection in women.

Methods
This study included 10 543 women from the 2003–2016 National Health and Nutrition Examination Survey. The outcome was the genital HPV infection status (HPV-negative, low-risk [LR] HPV, and HR-HPV). Dietary quality was evaluated using the Healthy Eating Index (HEI), in which a higher score indicates a better diet quality.

Results
Women who did not consume total fruits (15.8%), whole fruits (27.5%), or green vegetables and beans (43%) had a significantly higher risk of HR-HPV infection than women who complied with the Dietary Guidelines for Americans (HR-HPV odds ratio = 1.76, 1.63, and 1.48 for a HEI score of 0 vs 5, respectively) after adjusting confounding factors. Similar results of these food components on LR-HPV infection were found. In addition, intake of whole grains and dairy was inversely associated with LR-HPV infection.

Conclusions
This study showed that women who did not eat fruits, dark-green vegetables, and beans had a higher risk of genital HR-HPV infection. Intake of these food components is suggested for women to prevent HPV carcinogenesis.
Osteopontin Is an Integral Mediator of Cardiac Interstitial Fibrosis in Models of Human Immunodeficiency Virus Infection
Authors: Robinson Jake A , Mahmud Farina J , Greif Elizabeth , Toribio Mabel , Zanni Markella V , Brown Amanda M , Burdo Tricia H 
Published: May 2023

Abstract

Background
People with human immunodeficiency virus (HIV) have heightened incidence/risk of diastolic dysfunction and heart failure. Women with HIV have elevated cardiac fibrosis, and plasma osteopontin (Opn) is correlated to cardiac pathology. Therefore, this study provides mechanistic insight into the relationship between osteopontin and cardiac fibrosis during HIV infection.

Methods
Mouse embryonic fibroblasts (MEFs) modeled cardiac fibroblasts in vitro. Simian immunodeficiency virus (SIV)-infected macaques with or without antiretroviral therapy and HIV-infected humanized mice modeled HIV-associated cardiac fibrosis.

Results
Lipopolysaccharide-stimulated MEFs were myofibroblast-like, secreted cytokines, and produced Opn transcripts. SIV-infected animals had elevated plasma Opn at necropsy, full-length Opn in the ventricle, and ventricular interstitial fibrosis. Regression modeling identified growth differentiation factor 15, CD14+CD16+ monocytes, and CD163 expression on CD14+CD16+ monocytes as independent predictors of plasma Opn during SIV infection. HIV-infected humanized mice showed increased interstitial fibrosis compared to uninfected/untreated animals, and systemic inhibition of osteopontin by RNA aptamer reduced left ventricle fibrosis in HIV-infected humanized mice.

Conclusions
Since Opn is elevated in the plasma and left ventricle during SIV infection and systemic inhibition of Opn reduced cardiac fibrosis in HIV-infected mice, Opn may be a potential target for adjunctive therapies to reduce cardiac fibrosis in people with HIV.
Natural Clearance of Chlamydia trachomatis Infection Is Associated With Distinct Differences in Cervicovaginal Metabolites
Authors: Jordan Stephen J , Wilson Landon , Ren Jie , Gupta Kanupriya , Barnes Stephen , Geisler William M 
Published: May 2023

Abstract

Background
Natural clearance of Chlamydia trachomatis in women occurs in the interval between screening and treatment. In vitro, interferon-γ (IFN-γ)–mediated tryptophan depletion results in C. trachomatis clearance, but whether this mechanism occurs in vivo remains unclear. We previously found that women who naturally cleared C. trachomatis had lower cervicovaginal levels of tryptophan and IFN-γ compared to women with persisting infection, suggesting IFN-γ–independent pathways may promote C. trachomatis clearance.

Methods
Cervicovaginal lavages from 34 women who did (n = 17) or did not (n = 17) naturally clear C. trachomatis were subjected to untargeted high-performance liquid chromatography mass-spectrometry to identify metabolites and metabolic pathways associated with natural clearance.

Results
In total, 375 positively charged metabolites and 149 negatively charged metabolites were annotated. Compared to women with persisting infection, C. trachomatis natural clearance was associated with increased levels of oligosaccharides trehalose, sucrose, melezitose, and maltotriose, and lower levels of indoline and various amino acids. Metabolites were associated with valine, leucine, and isoleucine biosynthesis pathways.

Conclusions
The cervicovaginal metabolome in women who did or did not naturally clear C. trachomatis is distinct. In women who cleared C. trachomatis, depletion of various amino acids, especially valine, leucine, and isoleucine, suggests that amino acids other than tryptophan impact C. trachomatis survival in vivo.
The scaffold protein PDZK1 governs diurnal localization of CNT2 on the plasma membrane in mouse intestinal epithelial cells
Authors: Jaballah Nour , Tsurudome Yuya , Murakami Chiho , Matsunaga Naoya , Ushijima Kentaro , Koyanagi Satoru , Ohdo Shigehiro 
Published: May 2023

Abstract
Diurnal oscillations in the expression of several types of cell surface transporters have been demonstrated in the intestinal epithelial cells, which are mainly generated at transcriptional or degradation processes. Concentrative nucleoside transporter-2 (CNT2) is expressed at the apical site of intestinal epithelial cells and contributes to the uptake of nucleosides and their analogs from the intestinal lumen into the epithelial cells. In this study, we demonstrated that the localization of CNT2 protein in the plasma membrane of mouse intestinal epithelial cells exhibited a diurnal oscillation without changing its protein level in the whole cell. The scaffold protein PDZK1 interacted with CNT2 and stabilized its plasmalemmal localization. The expression of PDZK1 was under the control of molecular components of the circadian clock. Temporal accumulation of PDZK1 protein in intestinal epithelial cells enhanced the plasmalemmal localization of CNT2 at certain times of the day. The temporal increase in CNT2 protein levels at the plasma membrane also facilitated the uptake of adenosine into the intestinal epithelial cells. These results suggest a novel molecular mechanism for the diurnal localization of cell surface transporters and extend our understanding of the biological clock system that generates apparent physiological rhythms.
How do financialised agri-corporate investors acquire farmland? Analysing land investment in an Australian agricultural region, 2004–2019
Authors: Pritchard Bill , Welch Elen , Restrepo Guillermo Umana , Mitchell Lachlan 
Published: May 2023

Abstract
This article uses a purpose-designed land parcels database covering all rural land transactions over 16 years (2004–2019 inclusive) to document the ways in which financialised agri-corporate investors acquired farmland in a major Australian cropping and grazing region, New England North West (NENW). Framing these investments through the lens of strategic coupling reveals a mix of land acquisition strategies. Almost 200,000 ha of farmland was acquired by financialised agri-corporate investors in NENW during the study period. Approximately one-third was acquired through takeovers of stock market listed agricultural companies or unlisted agricultural asset management companies, another third involved the purchase of farms already packaged into assetised forms by prior rounds of restructuring and the final third involved the purchase and aggregation of family farms. We interpret this mix of entry modes to indicate a flexible and opportunistic set of dynamics in how financialised agri-corporate investors amass their land assets, underlining their reach and scope in the restructuring of regional agricultures.
Macrophage deficiency in CSF1R-knockout rat embryos does not compromise placental or embryo development
Authors: Hume David A , Teakle Ngari , Keshvari Sahar , Irvine Katharine M 
Published: May 2023

Abstract
Macrophages are an abundant cell population in the placenta and developing embryo and appear to be involved in processes of vascularization, morphogenesis, organogenesis, and hematopoiesis. The proliferation, differentiation, and survival are dependent on signals from the macrophage colony-stimulating factor receptor, CSF1R. Aside from the role in macrophages, Csf1r mRNA is highly expressed in placental trophoblasts. To explore the function of macrophages and Csf1r in placental and embryonic development, we analyzed the impact of homozygous Csf1r null mutation (Csf1rko) in the rat. In late gestation, IBA1+ macrophages were abundant in control embryos in all tissues, including the placenta, and greatly reduced in the Csf1rko. CSF1R was also detected in stellate macrophage-like cells and in neurons using anti-CSF1R antibody but was undetectable in trophoblasts. However, the neuronal signal was not abolished in the Csf1rko. CD163 was most abundant in cells forming the center of erythroblastic islands in the liver and was also CSF1R dependent. Despite the substantial reduction in macrophage numbers, we detected no effect of the Csf1rko on development of the placenta or any organs, the relative abundance of vascular elements (CD31 staining), or cell proliferation (Ki67 staining). The loss of CD163+ erythroblastic island macrophages in the liver was not associated with anemia or any reduction in the proliferative activity in the liver, but there was a premature expansion of CD206+ cells, presumptive precursors of liver sinusoidal endothelial cells. We suggest that many functions of macrophages in development of the placenta and embryo can be provided by other cell types in their absence.
ANKRD22 promotes glioma proliferation, migration, invasion, and epithelial-mesenchymal transition by upregulating E2F1-mediated MELK expression
Authors: Liu Xin , Zhao Junling , Wu Qiang , Wang Liqun , Lu Wenpeng , Feng Yan 
Published: May 2023

Abstract
Ankyrin repeat domain protein 22 (ANKRD22) has been implicated in various types of cancers but its expression and potential functions have not been investigated in gliomas. In this study, the high expression of ANKRD22 in gliomas and its correlation with survival were identified based on the Cancer Genome Atlas database. Similar expression trends were observed in glioma tissues and cell lines. Functionally, the loss of ANKRD22 suppressed glioma cell proliferation, migration, and invasion and cell cycle progression in vitro and tumor growth in vivo. Mechanistically, ANKRD22 interacted with the E2F transcription factor 1 (E2F1), thereby upregulating maternal embryonic leucine zipper kinase (MELK) protein expression. Moreover, E2F1 overexpression partly restored ANKRD22 silence-mediated tumor suppressive effects in glioma cells. In conclusion, our data highlight the oncogenic role of ANKRD22 in gliomas via E2F1/MELK signaling, which may serve as a promising target for glioma treatment.
The impact of pharmacist-guided inhaler technique education on chronic obstructive pulmonary disease and asthma patients
Authors: Cohen Jacob , Rosenbaum Iris , Oberman Bernice , Katz Irit , Sharabi Naama , Shlomi Dekel 
Published: May 2023

Abstract

Objective
The core treatment for asthma and chronic obstructive pulmonary disease (COPD) is inhalers. Today, there are many types of pressurized metered-dose inhalers (pMDIs) and dry powdered inhalers (DPIs). Each inhaler requires special sequential manoeuvres and coordination. It is well-known from previous studies that most patients perform at least one mistake using their inhaler which may lead to ineffective drug delivery and poor disease control. The aim of this study is to measure the proportion of patients who used the inhalers in a fully effective way before and after the pharmacist’s guidance.

Methods
Patients prescribed inhalers for asthma and COPD, were offered by the local pharmacist to personally assess and correct their inhaler use technique over two visits. At each visit, before any pharmacist correction of technique, a general score for inhaler technique was given and 16 types of mistakes were assessed. Comparisons of inhaler technique were made between the two visits.

Key findings
Sixty patients aged 21–91 (median 69; IQR 48–78) participated in the initial session of which 35 (58%) were females using 81 inhalers (DPI-60, pMDI-21). A fully effective inhaler technique was found in nine patients (15%) using 13 inhalers (16%) while 22 inhalers (27%) were used fully ineffectively (there were no statistically significant differences between DPIs and pMDIs). Twenty-three patients using 24 inhalers returned for a second visit in which 12 patients (52%, P = 0.0014 between the visits) used 12 inhalers (50%) fully effectively and only three inhalers (12.5%) were used fully ineffectively (P = 0.0045 between the visits). The odds for using the inhaler fully effectively were 5.2 (95% CI, 1.9 to 14.2; P = 0.0011) times higher on the second visit.

Conclusions
Personal pharmacist guidance can improve inhaler technique in a low socio-economic neighbourhood. However, larger multicentre studies that will also examine clinical outcomes are needed.
Mapping the X-ray variability of GRS 1915 + 105 with machine learning
Authors: Ricketts Benjamin J , Steiner James F , Garraffo Cecilia , Remillard Ronald A , Huppenkothen Daniela 
Published: May 2023

ABSTRACT
Black hole X-ray binary systems (BHBs) contain a close companion star accreting onto a stellar-mass black hole. A typical BHB undergoes transient outbursts during which it exhibits a sequence of long-lived spectral states, each of which is relatively stable. GRS 1915 + 105 is a unique BHB that exhibits an unequaled number and variety of distinct variability patterns in X-rays. Many of these patterns contain unusual behaviour not seen in other sources. These variability patterns have been sorted into different classes based on count rate and colour characteristics by previous work. In order to remove human decision-making from the pattern-recognition process, we employ an unsupervised machine learning algorithm called an auto-encoder to learn what classifications are naturally distinct by allowing the algorithm to cluster observations. We focus on observations taken by the Rossi X-ray Timing Explorer’s Proportional Counter Array. We find that the auto-encoder closely groups observations together that are classified as similar by previous work, but that there is reasonable grounds for defining each class as made up of components from three groups of distinct behaviour.
JWST NIRCam + NIRSpec: interstellar medium and stellar populations of young galaxies with rising star formation and evolving gas reservoirs
Authors: Tacchella Sandro , Johnson Benjamin D , Robertson Brant E , Carniani Stefano , D’Eugenio Francesco , Kumari Nimisha , Maiolino Roberto , Nelson Erica J , Suess Katherine A , Übler Hannah , Williams Christina C , Adebusola Alabi , Alberts Stacey , Arribas Santiago , Bhatawdekar Rachana , Bonaventura Nina , Bowler Rebecca A A , Bunker Andrew J , Cameron Alex J , Curti Mirko , Egami Eiichi , Eisenstein Daniel J , Frye Brenda , Hainline Kevin , Helton Jakob M , Ji Zhiyuan , Looser Tobias J , Lyu Jianwei , Perna Michele , Rawle Timothy , Rieke George , Rieke Marcia , Saxena Aayush , Sandles Lester , Shivaei Irene , Simmonds Charlotte , Sun Fengwu , Willmer Christopher N A , Willott Chris J , Witstok Joris 
Published: May 2023

ABSTRACT
We present an interstellar medium and stellar population analysis of three spectroscopically confirmed z &gt; 7 galaxies in the Early Release Observations JWST/NIRCam and JWST/NIRSpec data of the SMACS J0723.3−7327 cluster. We use the Bayesian spectral energy distribution-fitting code prospector with a flexible star formation history (SFH), a variable dust attenuation law, and a self-consistent model of nebular emission (continuum and emission lines). Importantly, we self-consistently fit both the emission line fluxes from JWST/NIRSpec and the broad-band photometry from JWST/NIRCam, taking into account slit-loss effects. We find that these three z=7.6–8.5 galaxies (M⋆ ≈ 108 M⊙) are young with rising SFHs and mass-weighted ages of 3–4 Myr, though we find indications for underlying older stellar populations. The inferred gas-phase metallicities broadly agree with the direct metallicity estimates from the auroral lines. The galaxy with the lowest gas-phase metallicity (Zgas= 0.06 Z⊙) has a steeply rising SFH, is very compact (&lt;0.2 kpc), and has a high star formation rate surface density (ΣSFR ≈ 22 M⊙ yr−1 kpc−2), consistent with rapid gas accretion. The two other objects with higher gas-phase metallicities show more complex multicomponent morphologies on kpc scales, indicating that their recent increase in star formation rate is driven by mergers or internal, gravitational instabilities. We discuss effects of assuming different SFH priors or only fitting the photometric data. Our analysis highlights the strength and importance of combining JWST imaging and spectroscopy for fully assessing the nature of galaxies at the earliest epochs.
Revealing the intrinsic X-ray reverberation lags in IRAS 13224−3809 through the Granger causality test
Authors: Chainakun P , Nakhonthong N , Luangtip W , Young A J 
Published: May 2023

ABSTRACT
The Granger causality is an econometric test for determining whether one time series is useful for forecasting another one with a certain Granger lag. Here, the light curves in the 0.3–1 keV (reflection dominated, soft) and 1.2–5 keV (continuum dominated, hard) bands of active galactic nuclei are produced, and the Granger lags are estimated and compared to the traditional lag–frequency spectra. We find that the light curves in the hard band Granger-cause (lead) those in the soft band, whereas the obtained Granger lags could be interpreted as the intrinsic reverberation lags. Then, we extract the Granger-lag profiles from 14 XMM–Newton observations of IRAS 13224−3809, and find that the lags are significant in 12 observations. The majority of the obtained Granger (intrinsic) lags are ∼200–500 s. With the IRAS 13224−3809 mass of 2 × 106 M⊙, these lags correspond to the true light travel distance of ∼20–50 rg. Hence, by assuming a lamp-post geometry and a face-on disc, this places the corona at ∼10–25 rg above the central black hole. Moreover, multiple Granger lags consisting of the small and large lags of &lt;500 s and &gt;1000 s are detected in four observations. This means that the corona height can significantly evolve from ∼10–25 rg to ∼55rg, or vice versa, towards the end of the observation. Granger lags are a promising way to measure the intrinsic lags, and provide evidence of coronal height variability within each individual observation.
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction
Authors: Wang Yunxia , Chen Zhen , Pan Ziqi , Huang Shijie , Liu Jin , Xia Weiqi , Zhang Hongning , Zheng Mingyue , Li Honglin , Hou Tingjun , Zhu Feng 
Published: May 2023

Abstract
Ribonucleic acids (RNAs) involve in various physiological/pathological processes by interacting with proteins, compounds, and other RNAs. A variety of powerful computational methods have been developed to predict such valuable interactions. However, all these methods rely heavily on the ‘digitalization’ (also known as ‘encoding’) of RNA-associated interacting pairs into a computer-recognizable descriptor. In other words, it is urgently needed to have a powerful tool that can not only represent each interacting partner but also integrate both partners into a computer-recognizable interaction. Herein, RNAincoder (deep learning-based encoder for RNA-associated interactions) was therefore proposed to (a) provide a comprehensive collection of RNA encoding features, (b) realize the representation of any RNA-associated interaction based on a well-established deep learning-based embedding strategy and (c) enable large-scale scanning of all possible feature combinations to identify the one of optimal performance in RNA-associated interaction prediction. The effectiveness of RNAincoder was extensively validated by case studies on benchmark datasets. All in all, RNAincoder is distinguished for its capability in providing a more accurate representation of RNA-associated interactions, which makes it an indispensable complement to other available tools. RNAincoder can be accessed at https://idrblab.org/rnaincoder/
Management of antineutrophil cytoplasmic antibody–associated vasculitis with glomerulonephritis as proposed by the ACR 2021, EULAR 2022 and KDIGO 2021 guidelines/recommendations
Authors: Casal Moura Marta , Gauckler Philipp , Anders Hans-Joachim , Bruchfeld Annette , Fernandez-Juarez Gema M , Floege Jürgen , Frangou Eleni , Goumenos Dimitrios , Segelmark Marten , Turkmen Kultigin , van Kooten Cees , Tesar Vladimir , Geetha Duvuru , Fervenza Fernando C , Jayne David R W , Stevens Kate I , Kronbichler Andreas 
Published: May 2023

ABSTRACT
Updated guidelines on the management of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) were released in 2021 by the American College of Rheumatology jointly with the Vasculitis Foundation and, subsequently, in 2022 by the European Alliance of Associations for Rheumatology. In addition, in 2021, the Kidney Disease: Improving Global Outcomes had released updated recommendations on the treatment of AAV with glomerulonephritis (AAV-GN). Kidney involvement is particularly relevant in microscopic polyangiitis and granulomatosis with polyangiitis, but is less frequent in eosinophilic granulomatosis with polyangiitis. The management of AAV-GN has been a focus for drug development and change over the past 10 years. Avoidance of progression to end-stage kidney disease (ESKD) or kidney failure is one of the main unmet needs in the management of AAV, with ESKD having a major impact on morbidity, health costs and mortality risk. Relevant changes in AAV-GN management are related to remission-induction treatment of patients with severe kidney disease, the use of glucocorticoids and avacopan, and remission-maintenance treatment. All the documents provide guidance in accordance with the evidence-based standard of care available at the time of their release. With our work we aim to (i) show the progress made and identify the differences between guidelines and recommendations, (ii) discuss the supporting rationale for those, and (iii) identify gaps in knowledge that could benefit from additional research and should be revised in subsequent updates.
Troubleshooting Violence: An Evaluation of Ghost Guns, Firearm-Related Violence, and Law Enforcement Policy in a Bay Area city
Authors: Jackson Summer M , Rippy Michelle , Chaplin Toney 
Published: May 2023

Abstract
Similar to many cities across the nation, Hayward, CA, is experiencing an uptick in gun-related violence. From 2015 to 2021, the City of Hayward experienced a 147% increase in assaults with a firearm and a 106% increase in firearm discharges. Gun crimes continue to threaten the safety of the community and its first responders. Likewise, technological advancements and the availability of non-serialized firearms, such as ghost guns, are becoming an increasing threat to community members. Through an evaluation of firearm-related criminal cases from 2015 to 2021, researchers seek to understand the extent and nature of gun violence in the City of Hayward, crime control efforts, and how firearm-related crimes have changed over time. The goal is to analyse trends in gun-related incidents to help shape future policies, data collection, and responses to gun-related calls for service.