bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Cell-Free DNA from Blood Serum of Mice with Metastatic Melanoma on Enhancement of Oncogenic Properties of Melanoma Cells
Authors: Filatova Alina A. , Alekseeva Ludmila A. , Savin Innokenty A. , Sen’kova Aleksandra V. , Zenkova Marina A. , Mironova Nadezhda L. 
Published: July 2023

Abstract
Currently, a significant increase in the levels of circulating cell-free DNA (cfDNA) in the blood of patients is considered as a generally recognized marker of the development of oncological diseases. Although the tumor-associated cfDNA has been well studied, its biological functions remain unclear. In this work, we investigated the effect of cfDNA isolated from the blood serum of the mice with B16-F10 metastatic melanoma on the properties of the B16-F10 melanoma cells in vitro. It was found that the profile of cfDNA isolated from the blood serum of mice with melanoma differs significantly from the cfDNA isolated from the blood serum of healthy mice, and is similar to the genomic DNA of B16 cells with regards to abundance of oncogenes and mobile genetic elements (MGE). It was shown that the cfDNA of mice with melanoma penetrated into B16 cells, resulting in the increase in abundance of oncogenes and MGE fragments, and caused 5-fold increase of the mRNA level of the secreted DNase Dnase1l3 and a slight increase of the mRNA level of the Jun, Fos, Ras, and Myc oncogenes. cfDNA of the healthy mice caused increase of the mRNA level of intracellular regulatory DNase EndoG and 4-fold increase of the mRNA level of Fos and Ras oncogenes, which are well-known triggers of a large number of signal cascades, from apoptosis inhibition to increased tumor cell proliferation. Thus, it is obvious that the circulating cfDNA of tumor origin is able to penetrate into the cells and, despite the fact that no changes were found in the level of viability and migration activity of the tumor cells, cfDNA, even with a single exposure, can cause changes at the cellular level that increase oncogenicity of the recipient cells.
Intrahepatic portosystemic shunts, from prenatal diagnosis to postnatal outcome: a retrospective study
Authors: Steg Saban Or , Weissbach Tal , Achiron Reuven , Pekar Zlotin Marina , Haberman Yael , Anis Heusler Adi , Kassif Eran , Weiss Batia 
Published: July 2023

ObjectiveCongenital intrahepatic portosystemic shunts (IHPSS) are rare vascular malformations resulting in blood bypassing the liver to the systemic circulation. Previous studies included symptomatic patients diagnosed postnatally, but the outcome of IHPSS diagnosed prenatally is rarely reported. We present a cohort of children prenatally diagnosed with IHPSS and report their natural course and outcome.Methods and designThis was a retrospective study of all fetal cases diagnosed by ultrasound with IHPSS between 2006 and 2019 at a single tertiary centre which were prospectively followed up at the paediatric gastroenterology unit. The postnatal outcome was compared between patients with a single versus multiple intrahepatic shunts.ResultsTwenty-six patients (70.3% boys) were included in the study, of them, eight (30.8%) patients had multiple intrahepatic shunts. The median gestational age at diagnosis was 29.5 weeks. Growth restriction affected 77% of the cohort. Postnatally, spontaneous shunt closure occurred in 96% of patients at a median age of 7.5 months (IQR 2.2–20 months). Failure to thrive (FTT) and mild developmental delay were observed in eight (30.8%) and seven (26.9%) patients, respectively. FTT was significantly more prevalent in patients with multiple shunts compared with patients with a single shunt (62.5% vs 16.7%, p=0.02); however, the rate of shunt closure and age at time of closure were similar between these groups. All patients survived with limited to no sequelae.ConclusionsIHPSS usually close spontaneously by 2 years of age. Children with prenatally detected IHPSS may develop FTT and mild developmental delay. Close surveillance at a paediatric gastroenterology unit may be beneficial.
Valued fields with a total residue map
Authors: Kartas Konstantinos 
Published: July 2023

When k is a finite field, [J. Becker, J. Denef and L. Lipshitz, Further remarks on the elementary theory of formal power series rings, in Model Theory of Algebra and Arithmetic, Proceedings Karpacz, Poland, Lecture Notes in Mathematics, Vol. 834 (Springer, Berlin, 1979)] observed that the total residue map [Formula: see text], which picks out the constant term of the Laurent series, is definable in the language of rings with a parameter for t. Driven by this observation, we study the theory [Formula: see text] of valued fields equipped with a linear form [Formula: see text] which restricts to the residue map on the valuation ring. We prove that [Formula: see text] does not admit a model companion. In addition, we show that [Formula: see text] is undecidable whenever k is an infinite field. As a consequence, we get that [Formula: see text] is undecidable, where [Formula: see text] maps f to its complex residue at 0.
Diagnosing Tropical Cyclone Intensity Variations from the Surface Wind Field Evolution
Authors: Vinour Léo , Jullien Swen , Mouche Alexis 
Published: July 2023

Abstract
Tropical cyclone (TC) intensity fluctuations remain a challenge for TC forecasters. Occurring through a wide range of processes, such as vortex contraction, eyewall replacements, or emission of vortex Rossby waves, they are inherently multiscale, transient, and asymmetric. In a recent study, estimates of surface wind field inner-core properties from high-resolution satellite observations were spotted as valuable for the improvement of intensity variations statistical predictability. The present study evaluates how the temporal evolution of the vortex structure, at scales ranging from O(1) km to vortexwide, further provides insights on the modulation of intensity. The study is based on a set of seven realistic TC simulations with 1-km grid spacing. The surface wind field structure is studied through an original set of descriptors that characterize the radial profile, the azimuthal asymmetries, and their spectral distribution. While radial gradients evolve concurrently with intensity, the azimuthal variability of the inner core shows a stronger connection with shorter-scale intensity modulation. The increase of high-wavenumber asymmetries distributed around the ring of maximum winds is shown to precede phases of rapid (re)intensification by 5–6 h, while the concentration of asymmetry in wavenumbers 1 and 2 leads to intensity weakening. A machine learning classification finally highlights that the classification of intensification phases (i.e., intensification or weakening) can be improved by at least 11% (thus reaching ∼75%) when accounting for the evolution of the radial wind gradient and the variance distribution among scales in the ring of maximum wind, relative to the sole use of vortex-averaged parameters.

Significance Statement
The purpose of this study is to relate changes in the surface wind field structure of tropical cyclones to their intensity variations. We design an original set of parameters to characterize the inner- and near-core contraction and asymmetry, and evaluate their connection with TC intensity modulations in a set of realistic high-resolution numerical simulations. The main outcome of our study is that opposite trends in high- and low-wavenumber variance tend to occur prior to intensity changes on short time scales, with more widespread and local-scale asymmetry corresponding to intensification, and vortex-scale polarized asymmetry corresponding to weakening. These diagnoses are shown to improve the classification of intensification and weakening phases. These results advocate for enhancing real-time high-resolution observations of surface wind fields under TCs, and using asymmetry distribution as predictors in statistical forecast models.
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
Authors: Newton Adam J. H. , Chartash David , Kleinstein Steven H. , McDougal Robert A. 
Published: July 2023

Abstract
Background
The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging when the information itself resides beyond titles or abstracts. For emerging science, with a limited set of known papers of interest and an incomplete information model, this is of pressing concern. A timely example in retrospect is the identification of immune signatures (coherent sets of biomarkers) driving differential SARS-CoV-2 infection outcomes.

Implementation
We built a classifier to identify papers containing domain-specific information from the document embeddings of the title and abstract. To train this classifier with limited data, we developed an iterative process leveraging pre-trained SPECTER document embeddings, SVM classifiers and web-enabled expert review to iteratively augment the training set. This training set was then used to create a classifier to identify papers containing domain-specific information. Finally, information was extracted from these papers through a semi-automated system that directly solicited the paper authors to respond via a web-based form.

Results
We demonstrate a classifier that retrieves papers with human COVID-19 immune signatures with a positive predictive value of 86%. The type of immune signature (e.g., gene expression vs. other types of profiling) was also identified with a positive predictive value of 74%. Semi-automated queries to the corresponding authors of these publications requesting signature information achieved a 31% response rate.

Conclusions
Our results demonstrate the efficacy of using a SVM classifier with document embeddings of the title and abstract, to retrieve papers with domain-specific information, even when that information is rarely present in the abstract. Targeted author engagement based on classifier predictions offers a promising pathway to build a semi-structured representation of such information. Through this approach, partially automated literature mining can help rapidly create semi-structured knowledge repositories for automatic analysis of emerging health threats.
Transcriptomic regulations of heat stress response in the liver of lactating dairy cows
Authors: Li Guangsheng , Yu Xingtan , Portela Fontoura Ananda B. , Javaid Awais , de la Maza-Escolà Víctor Sáinz , Salandy Nia S. , Fubini Susan L. , Grilli Ester , McFadden Joseph. W. , Duan Jingyue Ellie 
Published: July 2023

Abstract
Background
The global dairy industry is currently facing the challenge of heat stress (HS). Despite the implementation of various measures to mitigate the negative impact of HS on milk production, the cellular response of dairy cows to HS is still not well understood. Our study aims to analyze transcriptomic dynamics and functional changes in the liver of cows subjected to heat stress (HS). To achieve this, a total of 9 Holstein dairy cows were randomly selected from three environmental conditions - heat stress (HS), pair-fed (PF), and thermoneutral (TN) groups - and liver biopsies were obtained for transcriptome analysis.

Results
Both the dry matter intake (DMI) and milk yield of cows in the HS group exhibited significant reduction compared to the TN group. Through liver transcriptomic analysis, 483 differentially expressed genes (DEGs) were identified among three experimental groups. Especially, we found all the protein coding genes in mitochondria were significantly downregulated under HS and 6 heat shock proteins were significant upregulated after HS exposure, indicating HS may affect mitochondria integrity and jeopardize the metabolic homeostasis in liver. Furthermore, Gene ontology (GO) enrichment of DEGs revealed that the protein folding pathway was upregulated while oxidative phosphorylation was downregulated in the HS group, corresponding to impaired energy production caused by mitochondria dysfunction.

Conclusions
The liver transcriptome analysis generated a comprehensive gene expression regulation network upon HS in lactating dairy cows. Overall, this study provides novel insights into molecular and metabolic changes of cows conditioned under HS. The key genes and pathways identified in this study provided further understanding of transcriptome regulation of HS response and could serve as vital references to mitigate the HS effects on dairy cow health and productivity.
Relationship between depressive symptoms and sleep quality and cognitive inhibition ability in prenatal pregnant women
Authors: Bao Ciqing , Wang Yali , Le Tao , Xu Ling , Tang Weina , Zou Wanyun , Bao Yin , Xu Dongwu , Zhao Ke 
Published: July 2023

AbstractBackgroundSleep problems and cognitive changes are typical in pregnant women with depressive symptoms. However, the relationship between sleep quality and executive dysfunction remains unclear. This study aims to explore the differences in sleep quality and cognitive inhibition between pregnant women with and without depressive symptoms in the third trimester of pregnancy and investigate the correlations between sleep quality, cognitive inhibition and depressive symptoms.MethodsIn the third trimester, 169 women without depressive symptoms and 88 women with depressive symptoms participated in the study. Edinburgh Postpartum Depression Questionnaire (EPDS) was used to assess depressive symptoms, and Pittsburgh Standard Sleep Quality Index Questionnaire (PSQI) was used to investigate sleep quality. The color-word Stroop task is used to evaluate cognitive inhibition.ResultsCompared with women without depressive symptoms, pregnant women with depressive symptoms showed worse sleep quality and Stroop task performances (response speed and accuracy). In addition, the speed of cognitive inhibition plays a mediating role in the relationship between sleep quality and prenatal depressive symptoms.ConclusionThis research emphasizes the importance of sleep quality screening and cognitive training for depression during pregnancy and childbirth in ensuring women’s mental health during pregnancy and childbirth.
A coupled experimental and statistical approach for an assessment of SARS-CoV-2 infection risk at indoor event locations
Authors: Siebler Lukas , Rathje Torben , Calandri Maurizio , Stergiaropoulos Konstantinos , Donker Tjibbe , Richter Bernhard , Spahn Claudia , Nusseck Manfred 
Published: July 2023

AbstractIndoor event locations are particularly affected by the SARS-CoV-2 pandemic. At large venues, only incomplete risk assessments exist, whereby no suitable measures can be derived. In this study, a physical and data-driven statistical model for a comprehensive infection risk assessment has been developed. At venues displacement ventilation concepts are often implemented. Here simplified theoretical assumptions fail for the prediction of relevant airflows for airborne transmission processes. Thus, with locally resolving trace gas measurements infection risks are computed more detailed. Coupled with epidemiological data such as incidences, vaccination rates, test sensitivities, and audience characteristics such as masks and age distribution, predictions of new infections (mean), situational R-values (mean), and individual risks on- and off-seat can be achieved for the first time. Using the Stuttgart State Opera as an example, the functioning of the model and its plausibility are tested and a sensitivity analysis is performed with regard to masks and tests. Besides a reference scenario on 2022-11-29, a maximum safety scenario with an obligation of FFP2 masks and rapid antigen tests as well as a minimum safety scenario without masks and tests are investigated. For these scenarios the new infections (mean) are 10.6, 0.25 and 13.0, respectively. The situational R-values (mean) – number of new infections caused by a single infectious person in a certain situation – are 2.75, 0.32 and 3.39, respectively. Besides these results a clustered consideration divided by age, masks and whether infections occur on-seat or off-seat are presented. In conclusion this provides an instrument that can enable policymakers and operators to take appropriate measures to control pandemics despite ongoing mass gathering events.
Temporal trend analysis of the HIV/AIDS burden before and after the implementation of antiretroviral therapy at the population level from 1990 to 2020 in Ghana
Authors: Boah Michael , Yeboah Daudi , Kpordoxah Mary Rachael , Issah Abdul-Nasir , Adokiya Martin Nyaaba 
Published: July 2023

Abstract
Background
Antiretroviral therapy (ART) has helped reduce the burden of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) in the majority of countries. Its contribution to the HIV/AIDS burden in Ghana is still understudied. This study examined HIV/AIDS trends in Ghana before (1990–2004) and after (2004–2020) the implementation and expansion of ART.

Methods
We obtained HIV/AIDS epidemiology and treatment data for the years 1990–2020 from the United Nations Programme on HIV/AIDS. We investigated the impact of the ART rollout on HIV/AIDS in Ghana using Joinpoint regression models.

Results
The HIV incidence, prevalence, and AIDS-related deaths decreased significantly after 2004, as ART coverage increased from 1% to 2004 to 60% in 2020. The HIV incidence decreased by approximately 3% (AAPC = -2.6%; 95% CI: -3.2, -1.9) per year from 1990 to 2004 and approximately 5% (AAPC = -4.5%; 95% CI: -4.9, -4.2) per year from 2004 to 2020. Between 1990 and 2004, the HIV prevalence increased by approximately 5% (AAPC = 4.7%; 95% CI: 3.6, 5.8) per year but decreased by 2% (AAPC = -1.9%; 95% CI: -2.1, -1.6) per year between 2004 and 2020. Between 1990 and 2004, the annual increase in AIDS-related mortality was 14% (AAPC = 13.8%; 95% CI: 12.6, 15.0), but between 2004 and 2020, it decreased at nearly a 4% (AAPC= -3.6%; 95% CI: -4.7, -2.5) annual rate.

Conclusions
We found trends indicating progress in Ghana’s fight against HIV/AIDS. However, the most significant declines occurred after the introduction of ART, suggesting that the scale-up of ART may have contributed to the decline in HIV/AIDS in Ghana. We advocate for the rapid expansion of ART in Ghana.
Efficient production of bacterial antibiotics aminoriboflavin and roseoflavin in eukaryotic microorganisms, yeasts
Authors: Dmytruk Kostyantyn V. , Ruchala Justyna , Fayura Liubov R. , Chrzanowski Grzegorz , Dmytruk Olena V. , Tsyrulnyk Andriy O. , Andreieva Yuliia A. , Fedorovych Daria V. , Motyka Olena I. , Mattanovich Diethard , Marx Hans , Sibirny Andriy A. 
Published: July 2023

Abstract
Background
Actinomycetes Streptomyces davaonensis and Streptomyces cinnabarinus synthesize a promising broad-spectrum antibiotic roseoflavin, with its synthesis starting from flavin mononucleotide and proceeding through an immediate precursor, aminoriboflavin, that also has antibiotic properties. Roseoflavin accumulation by the natural producers is rather low, whereas aminoriboflavin accumulation is negligible. Yeasts have many advantages as biotechnological producers relative to bacteria, however, no recombinant producers of bacterial antibiotics in yeasts are known.

Results
Roseoflavin biosynthesis genes have been expressed in riboflavin- or FMN-overproducing yeast strains of Candida famata and Komagataella phaffii. Both these strains accumulated aminoriboflavin, whereas only the latter produced roseoflavin. Aminoriboflavin isolated from the culture liquid of C. famata strain inhibited the growth of Staphylococcus aureus (including MRSA) and Listeria monocytogenes. Maximal accumulation of aminoriboflavin in shake-flasks reached 1.5 mg L− 1 (C. famata), and that of roseoflavin was 5 mg L− 1 (K. phaffii). Accumulation of aminoriboflavin and roseoflavin by K. phaffii recombinant strain in a bioreactor reached 22 and 130 mg L− 1, respectively. For comparison, recombinant strains of the native bacterial producer S. davaonensis accumulated near one-order less of roseoflavin while no recombinant producers of aminoriboflavin was reported at all.

Conclusions
Yeast recombinant producers of bacterial antibiotics aminoriboflavin and roseoflavin were constructed and evaluated.
L-carnitine promotes liver regeneration after hepatectomy by enhancing lipid metabolism
Authors: Zhou Xi , Huang Guobin , Wang Lu , Zhao Yuanyuan , Li Junbo , Chen Dong , Wei Lai , Chen Zhishui , Yang Bo 
Published: July 2023

Abstract
Background
Lipid metabolism plays an important role in liver regeneration, but its regulation still requires further research. In this study, lipid metabolites involved in mouse liver regeneration at different time points were sequenced and analyzed to study their influence on liver regeneration and its mechanism.

Methods
Our experiment was divided into two parts. The first part examined lipid metabolites during liver regeneration in mice. In this part, lipid metabolites were sequentially analyzed in the livers of 70% mouse hepatectomy models at 0, 1, 3and 7 days after operation to find the changes of lipid metabolites in the process of liver regeneration. We screened L-carnitine as our research object through metabolite detection. Therefore, in the second part, we analyzed the effects of carnitine on mouse liver regeneration and lipid metabolism during liver regeneration. We divided the mouse into four groups: control group (70% hepatectomy group); L-carnitine group (before operation) (L-carnitine were given before operation); L-carnitine group (after operation)(L-carnitine were given after operation) and L-carnitine + perhexiline maleate (before operation) group. Weighing was performed at 24 h, 36 and 48 h in each group, and oil red staining, HE staining and MPO staining were performed. Tunnel fluorescence staining, Ki67 staining and serological examination.

Results
Sequencing analysis of lipid metabolites in 70% of mouse livers at different time points after hepatectomy showed significant changes in carnitine metabolites. The results showed that, compared with the control group the mouse in L-carnitine group (before operation) at 3 time points, the number of fat drops in oil red staining was decreased, the number of Ki67 positive cells was increased, the number of MPO positive cells was decreased, the number of Tunnel fluorescence positive cells was decreased, and the liver weight was increased. Serum enzymes were decreased. Compared with control group, L-carnitine group (after operation) showed similar trends in all indexes at 36 and 48 h as L-carnitine group (before operation). L-carnitine + perhexiline maleate (before operation) group compared with control group, the number of fat drops increased, the number of Ki67 positive cells decreased, and the number of MPO positive cells increased at 3 time points. The number of Tunnel fluorescent positive cells increased and serum enzyme increased. However, both liver weights increased.

Conclusion
L-carnitine can promote liver cell regeneration by promoting lipid metabolism and reduce aseptic inflammation caused by excessive lipid accumulation.