bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpreting declines in HIV test positivity: an analysis of routine data from Zimbabwe's national sex work programme, 2009–2019
Authors: Jones Harriet S. , Hensen Bernadette , Musemburi Sithembile , Chinyanganya Lilian , Takaruza Albert , Chabata Sungai T. , Matambanadzo Primrose , Rice Brian , Cowan Frances M. , Hargreaves James R. 
Published: July 2022

AbstractIntroductionEarly diagnosis of HIV is critical for epidemic control. To achieve this, successful testing programmes are essential and test positivity is often used as a marker of their performance. The aim of this study was to analyse trends and predictors of HIV test positivity over time and explore how an understanding of seroconversion rates could build on our interpretation of this indicator among female sex workers in Zimbabwe.MethodsWe analysed HIV test data from Zimbabwe's nationally scaled sex work programme between 2009 and 2019. We defined test positivity as the proportion of all tests that were HIV positive and measured new diagnoses by estimating seroconversion rates among women with repeat tests, defined as an HIV‐positive test after at least one HIV‐negative test in the programme. We used logistic regression to analyse test positivity over three time‐periods: 2009–2013, 2014–2017 and 2018–2019, adjusting for potential confounding by demographic factors and the mediating effects of time since last HIV test. We calculated the seroconversion rates for the same time‐periods.ResultsDuring the 10‐year study period, 54,503 tests were recorded in 39,462 women. Between 2009 and 2013, 18% of tests were among women who reported testing in the previous 6 months. By 2018–2019, this had increased to 57%. Between 2018 and 2019, test positivity was 9.6%, compared to 47.9% for 2009–2013 (aOR 6.08 95% CI 5.52–6.70) and 18.8% for 2014–2017 (aOR 2.17 95% CI 2.06–2.28). Adjusting for time since last test reduced effect estimates for 2009–2013 (aOR 4.03 95% CI 3.64–4.45) and 2014–2017 (aOR 1.97 95% CI 1.86–2.09) compared to 2018–2019. Among 7573 women with an initial HIV‐negative test in the programme and at least one subsequent test, 464 tested HIV positive at a rate of 3.9 per 100 pyar (95% CI 3.5–4.2).ConclusionsTest positivity decreased among women testing through the programme over time, while seroconversion rates remained high. These declines were partly driven by changes in individual testing history, reflecting comprehensive coverage of testing services and greater knowledge of HIV status, but not necessarily declining rates of seroconversion. Understanding testing history and monitoring new HIV infections from repeat tests could strengthen the interpretation of test positivity and provide a better understanding of programme performance.
PrEP user profiles, dynamics of PrEP use and follow‐up: a cohort analysis at a Belgian HIV centre (2017–2020)
Authors: Rotsaert Anke , Reyniers Thijs , Jacobs Bart K. M. , Vanbaelen Thibaut , Burm Christophe , Kenyon Chris , Vuylsteke Bea , Florence Eric 
Published: July 2022

AbstractIntroductionThe number of individuals initiating antiretroviral pre‐exposure prophylaxis (PrEP) is increasing, but we do not fully understand who is coming forward for PrEP, how they use it and how they are followed‐up. The objective of this study was to examine PrEP user profiles, dynamics in PrEP use and follow‐up over time.MethodsWe conducted a cohort analysis of longitudinally collected clinical record and questionnaire data among PrEP users at an HIV centre in Antwerp, Belgium, between June 2017 and March 2020. PrEP follow‐up and user profiles were examined using descriptive analyses and bivariate logistic regression. We compared early adopting PrEP users (started before June 2018) with late users. We also calculated the probabilities of switching between daily and on‐demand PrEP, and interruption, using a naïve estimator.Results and discussionWe included 1347 PrEP users in the analysis. After 12 months, retention in care was 72.3%. Median time between PrEP visits was 98 days (IQR 85–119 days). At screening visit, early adopting PrEP users (starting June 2017–May 2018) were significantly more likely to report one or more sexually transmitted infection in the prior 12 months, having used drugs during sex, a higher number of sexual partners and a history of paid sex and PrEP use prior to initiation, compared with PrEP users who initiated later (starting June 2018–February 2020). When taking PrEP daily, the probability of staying on daily PrEP at the next visit was 76%, while this was 73% when taking PrEP on‐demand. Those using on‐demand PrEP had a higher probability (13%) of interrupting PrEP care than daily PrEP users (7%), whereas those returning to PrEP care would mostly re‐start with on‐demand (35% vs. 13% for daily).ConclusionsThe majority of PrEP users in this sample remained in care after 12 months. The probability of remaining on the same PrEP regimen at the subsequent visit was high. Though, we observed a diversity of transitions between regimens and interruptions in between visits. Our findings reaffirm the need to provide tailored PrEP services, counselling PrEP users across their life course.
Ginsenoside Rg1 ameliorates sepsis-induced acute kidney injury by inhibiting ferroptosis in renal tubular epithelial cells
Authors: Guo Jun , Wang Rong , Min Fei 
Published: July 2022

AbstractAcute kidney injury (AKI) represents a prevailing complication of sepsis, and its onset involves ferroptosis. Ginsenoside Rg1 exerts a positive effect on kidney diseases. This study explored the action of ginsenoside Rg1 in sepsis-induced AKI (SI-AKI) by regulating ferroptosis in renal tubular epithelial cells (TECs). Sepsis rat models were established using cecal ligation and puncture (CLP) and cell models were established by treating human renal TECs (HK-2) with LPS to induce ferroptosis. Serum creatinine (SCr) and blood urea nitrogen (BUN) and urine KIM1 contents in rats were determined by ELISA kits. Kidney tissues were subjected to immunohistochemical and H&E stainings. Iron concentration, malondialdehyde (MDA), glutathione (GSH), and ferroptosis-related protein (ferritin light chain [FTL], ferritin heavy chain [FTH], GSH peroxidase 4 [GPX4], and Ferroptosis suppressor protein 1 [FSP1]) levels in kidney tissues and HK-2 cells were measured using ELISA kits and Western blotting. HK-2 cell viability was detected by cell counting kit-8, and cell death was observed via propidium iodide staining. Reactive oxygen species accumulation in cells was detected using C11 BODIPY 581/591 as a molecular probe. In CLP rats, ginsenoside Rg1 reduced SCr, BUN, KIM1, and NGAL levels, thus palliating SI-AKI. Additionally, ginsenoside Rg1 decreased iron content, FTL, FTH, and MDA levels, and elevated GPX4, FSP1, and GSH levels, thereby inhibiting lipid peroxidation and ferroptosis. Moreover, FSP1 knockdown annulled the inhibition of ginsenoside Rg1 on ferroptosis. In vitro experiments, ginsenoside Rg1 raised HK-2 cell viability and lowered iron accumulation and lipid peroxidation during ferroptosis, and its antiferroptosis activity was dependent on FSP1. Ginsenoside Rg1 alleviates SI-AKI, possibly resulting from inhibition of ferroptosis in renal TECs through FSP1.
Time trends, irregularity and multifractal structure on the monthly rainfall regime at Barcelona, NE Spain, years 1786–2019
Authors: Lana Xavier , Casas‐Castillo M. Carmen , Rodríguez‐Solà Raül , Prohom Marc , Serra Carina , Martínez Maria Dolors , Kirchner Ricard 
Published: July 2022

AbstractA long and complete series of monthly rainfall amounts corresponding to Barcelona city (Catalonia, NE Spain), exceeding two centuries (years 1786–2019), is analysed in detail. The obtained results of periodicity (annual scale), time trends (monthly, seasonal and annual scales), statistical distribution (seasonal and annual scale) and fractal/multifractal structures and self‐similarity at monthly scale depict the complex structure of this pluviometric regime, which is characterized by moderate increasing and decreasing trends on rain amounts, varying from +0.08 mm·year−1 (February) to −0.07 mm·year−1 (September) and quite evident changes on the pluviometric trends at annual and seasonal scales when the rainfall data are analysed for segments of 50 years from 1800 up to 2019. A good example could be the relevant change on the annual scale time trend, from +0.77 mm·year−1 (years 1800–1850) to −0.17 mm·year−1 (years 1950–2019). Clear evidences of decreasing pluviometry for spring, summer and autumn for the last segment (1950–2019) in comparison with the other three segments, including years 1800–1950, are also detected. Additionally, increasing rainfall patterns complexity, expected difficulties on monthly rainfall forecasting and the increasing irregularity of monthly amounts is also detected by interpreting fractal and multifractal results. Irregularity increases on the monthly rainfall series and on the rainfall regime complexity derived from multifractal parameters, could be associated with the very notable increase of CO2 emissions into the atmosphere, globally varying from 51.1 × 106 metric tonnes (year 1820) to 36.6 × 109 metric tonnes (year 2019) and the tropospheric concentration increasing from 280.8 ppm (year 1850) to 397.5 ppm (year 2014), being the probable relationship between tropospheric concentrations and changes on rainfall patterns the objective of future researches.
Interface structure of escin at air–water interface probed by sum frequency generation spectroscopy
Authors: Kagiyama Yoshihide , Miyamae Takayuki 
Published: July 2022

AbstractSaponins are natural amphiphilic surfactants with high surface activity and unique surface properties at the air–water interfaces. We have applied sum frequency generation (SFG) vibrational spectroscopy to study escin, a kind of saponins that is extracted from chestnut (Aesculus hippocastanum), which adsorbed at water surfaces as a function of the solution concentrations, and have characterized the net orientation of the hydrophobic aglycone moieties at the water interfaces by varying the solution concentration of the escin. SFG results of escin adsorbed water surfaces demonstrate that the hydrophobic aglycone moieties show nearly standing‐up configuration above the critical micelle concentration (cmc), while its preferred orientation is nearly parallel to the surface below cmc. In addition to the changes in the CH stretching band intensities from the escin adsorbed interfaces, we found that the structural arrangement of the escin molecules at the air–water interface is also a function of solution pH and clarified the correlation between the ionic state of the solution and the structure.
Mannosylerythritol lipids as green pesticides and plant biostimulants
Authors: Matosinhos Renato Dias , Cesca Karina , Carciofi Bruno Augusto Mattar , de Oliveira Débora , de Andrade Cristiano José 
Published: July 2022

AbstractBiosurfactants can be applied in the formulation of personal care products, as food additives, and as biocontrol agents in the agricultural sector. Glycolipids and lipopeptides represent an important group of microbial‐based biosurfactants with biostimulating properties. Among them, the mannosylerythritol lipids also presented antimicrobial activity, mostly against Gram‐positive bacteria and phytopathogenic fungi. In this sense, mannosylerythritol lipids are a potential safer green alternative for partially replacing synthetic pesticides. This review aimed to critically discuss the current state of the art and future trends of mannosylerythritol lipids as green pesticides and biostimulants for seed germination and plant growth. Due to their chemical structure, mannosylerythritol lipids are likely related to energy pathways such as glycolysis and Krebs cycle, i.e. a direct cellular biostimulant potential. In this case, experimental evidence from other glycolipids indicated that structural and chemical changes as a potential drug vehicle due to morphological changes caused by biosurfactant–membrane interaction. In addition, like other biosurfactants, mannosylerythritol lipids can trigger self‐defense mechanisms, leading to a lower frequency of phytopathogen infections. Therefore, mannosylerythritol lipids have the potential for biostimulation and antiphytopathogenic action, despite that to date no data are available on mannosylerythritol lipids as biostimulants and green pesticides simultaneously. Based on the current state of the art, mannosylerythritol lipids have great potential for a biotechnological advance toward more sustainable agriculture. © 2022 Society of Chemical Industry.
Publication practices during the COVID‐19 pandemic: Expedited publishing or simply an early bird effect?
Authors: Sevryugina Yulia V. , Dicks Andrew J. 
Published: July 2022

AbstractThis study explores the evolution of publication practices associated with the SARS‐CoV‐2 research papers, namely, peer‐reviewed journal and review articles indexed in PubMed and their associated preprints posted on bioRxiv and medRxiv servers: a total of 4,031 journal article‐preprint pairs. Our assessment of various publication delays during the January 2020 to March 2021 period revealed the early bird effect that lies beyond the involvement of any publisher policy action and is directly linked to the emerging nature of new and ‘hot’ scientific topics. We found that when the early bird effect and data incompleteness are taken into account, COVID‐19 related research papers show only a moderately expedited speed of dissemination as compared with the pre‐pandemic era. Medians for peer‐review and production stage delays were 66 and 15 days, respectively, and the entire conversion process from a preprint to its peer‐reviewed journal article version took 109.5 days. The early bird effect produced an ephemeral perception of a global rush in scientific publishing during the early days of the coronavirus pandemic. We emphasize the importance of considering the early bird effect in interpreting publication data collected at the outset of a newly emerging event.
Quantum Magnetometer with Dual‐Coupling Optomechanics
Authors: Zhu Gui‐Lei , Liu Jing , Wu Ying , Lü Xin‐You 
Published: July 2022

AbstractAn experimentally feasible magnetometer based on a dual‐coupling optomechanical system is proposed, where the radiation‐pressure coupling transduces the magnetic signal to the optical phase, and the quadratic optomechanical interaction induces a periodic squeezing effect. The latter not only amplifies the signal to be measured, but also accelerates the signal transducing rate characterized by an experimentally observable phase accumulation efficiency. In the vicinity of opto‐mechanical decoupled time, the ultimate bound to the estimability of magnetic signal is proportional to , and then the optimized accuracy of estimation can be enhanced nearly three orders with a controllable squeezing parameter . Moreover, this proposal is robust against the mechanical thermal noise, and the sensitivity of a specific measurement can reach to the order of in the presence of dissipations and without ground state cooling of mechanical oscillator. The proposal fundamentally broadens the fields of quantum metrology and cavity optomechanics, with the potential application for on‐chip magnetic detection with high precision.
Further delineation of SLC9A3‐related congenital sodium diarrhea
Authors: Bogdanic Ema , Müller Thomas , Heinz‐Erian Peter , Garczarczyk‐Asim Dorota , Janecke Andreas R. , Rückel Aline 
Published: July 2022

AbstractBackgroundCongenital sodium diarrhea (CSD) is a rare enteropathy displaying both broad variability in clinical severity and genetic locus and allelic heterogeneity. Eleven CSD patients were reported so far with SLC9A3 variants that impair the function of the encoded intestinal sodium‐proton exchanger 3 (NHE3).MethodsWe report a 4‐year‐old patient, born prematurely in the 35th week of gestation, with antenatal polyhydramnios and dilated intestinal loops, and with diarrhea of congenital onset, 2–6 times a day, and with polydipsia. She thrived age‐appropriately under a normal family diet. Serum sodium levels were repeatedly normal but urinary sodium excretion was low. Exome sequencing revealed compound heterozygous variants in SLC9A3 as the likely cause of the congenital diarrhea.ResultsWhile exome sequencing did not reveal pathogenic or likely pathogenic variants in other genes that cause syndromic or non‐syndromic forms of congenital and intractable diarrheas, we identified novel compound heterozygous variants in SLC9A3, a complex allele with two missense changes, NP_004165.2:p.[Ser331Leu;Val449Ile] and in‐trans the missense variant p.(Phe451Ser).ConclusionThe clinical phenotype here appears to localize to the milder end of the known CSD spectrum, and the identified variants suggest that this is the twelfth patient reported to date with CSD due to mutations in SLC9A3.
The Relevance of Goodness‐of‐fit, Robustness and Prediction Validation Categories of OECD‐QSAR Principles with Respect to Sample Size and Model Type
Authors: Király Péter , Kiss Ramóna , Kovács Dániel , Ballaj Amine , Tóth Gergely 
Published: July 2022

AbstractWe investigated the relevance of the validation principles on the Quantitative Structure Activity Relationship models issued by Organization for Economic and Co‐operation and Development. We checked the goodness‐of‐fit, robustness and predictivity categories in linear and nonlinear models using benchmark datasets. Most of our conclusions are drawn using the sample size dependence of the different validation parameters. We found that the goodness‐of‐fit parameters misleadingly overestimate the models on small samples. In the case of neural network and support vector models, the feasibility of the goodness‐of‐fit parameters often might be questioned. We propose to use the simplest y‐scrambling method to estimate chance correlation. We found that the leave‐one‐out and leave‐many‐out cross‐validation parameters can be rescaled to each other in all models and the computationally feasible method should be chosen depending on the model type. We assessed the interdependence of the validation parameters by calculating their rank correlations. Goodness of fit and robustness correlate quite well over a sample size for linear models and one of the approaches might be redundant. In the rank correlation between internal and external validation parameters, we found that the assignment of good and bad modellable data to the training or the test causes negative correlations.
Cardio‐respiratory motion‐corrected 3D cardiac water‐fat MRI using model‐based image reconstruction
Authors: Mayer Johannes , Blaszczyk Edyta , Cipriani Alberto , Ferrazzi Giulio , Schulz‐Menger Jeanette , Schaeffter Tobias , Kolbitsch Christoph 
Published: July 2022

PurposeMyocardial fat infiltrations are associated with a range of cardiomyopathies. The purpose of this study was to perform cardio‐respiratory motion‐correction for model‐based water‐fat separation to image fatty infiltrations of the heart in a free‐breathing, non‐cardiac‐triggered high‐resolution 3D MRI acquisition.MethodsData were acquired in nine patients using a free‐breathing, non‐cardiac‐triggered high‐resolution 3D Dixon gradient‐echo sequence and radial phase encoding trajectory. Motion correction was combined with a model‐based water‐fat reconstruction approach. Respiratory and cardiac motion models were estimated using a dual‐mode registration algorithm incorporating both motion‐resolved water and fat information. Qualitative comparisons of fat structures were made between 2D clinical routine reference scans and reformatted 3D motion‐corrected images. To evaluate the effect of motion correction the local sharpness of epicardial fat structures was analyzed for motion‐averaged and motion‐corrected fat images.ResultsThe reformatted 3D motion‐corrected reconstructions yielded qualitatively comparable fat structures and fat structure sharpness in the heart as the standard 2D breath‐hold. Respiratory motion correction improved the local sharpness on average by 32% ± 24% with maximum improvements of 81% and cardiac motion correction increased the sharpness further by another 15% ± 11% with maximum increases of 31%. One patient showed a fat infiltration in the myocardium and cardio‐respiratory motion correction was able to improve its visualization in 3D.ConclusionThe 3D water‐fat separated cardiac images were acquired during free‐breathing and in a clinically feasible and predictable scan time. Compared to a motion‐averaged reconstruction an increase in sharpness of fat structures by 51% ± 27% using the presented motion correction approach was observed for nine patients.
MRSCloud: A cloud‐basedMRStool for basis set simulation
Authors: Hui Steve C. N. , Saleh Muhammad G. , Zöllner Helge J. , Oeltzschner Georg , Fan Hongli , Li Yue , Song Yulu , Jiang Hangyi , Near Jamie , Lu Hanzhang , Mori Susumu , Edden Richard A. E. 
Published: July 2022

PurposeThe purpose of this study is to present a cloud‐based spectral simulation tool “MRSCloud,” which allows MRS users to simulate a vendor‐specific and sequence‐specific basis set online in a convenient and time‐efficient manner. This tool can simulate basis sets for GE, Philips, and Siemens MR scanners, including conventional acquisitions and spectral editing schemes with PRESS and semi‐LASER localization at 3 T.MethodsThe MRSCloud tool was built on the spectral simulation functionality in the FID‐A software package. We added three extensions to accelerate computation (ie, one‐dimensional projection method, coherence pathways filters, and precalculation of propagators). The RF waveforms were generated based on vendors' generic pulse shapes and timings. Simulations were compared within MRSCloud using different numbers of spatial resolution (21 × 21, 41 × 41, and 101 × 101). Simulated metabolite basis functions from MRSCloud were compared with those generated by the generic FID‐A and MARSS, and a phantom‐acquired basis set from LCModel. Intraclass correlation coefficients were calculated to measure the agreement between individual metabolite basis functions. Statistical analysis was performed using R in RStudio.ResultsSimulation time for a full PRESS basis set is approximately 11 min on the server. The interclass correlation coefficients ICCs were at least 0.98 between MRSCloud and FID‐A and were at least 0.96 between MRSCloud and MARSS. The interclass correlation coefficients between simulated MRSCloud basis spectra and acquired LCModel basis spectra were lowest for glutamine at 0.68 and highest for N‐acetylaspartate at 0.96.ConclusionsSubstantial reductions in runtime have been achieved. High ICC values indicated that the accelerating features are running correctly and produce comparable and accurate basis sets.