bluuebunny/crossref_metadata_2025_split huggingface dataset:
An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection
Authors: Mukherji Atish , Jühling Frank , Simanjuntak Yogy , Crouchet Emilie , Del Zompo Fabio , Teraoka Yuji , Haller Alexandre , Baltzinger Philippe , Paritala Soumith , Rasha Fahmida , Fujiwara Naoto , Gadenne Cloé , Slovic Nevena , Oudot Marine A. , Durand Sarah C. , Ponsolles Clara , Schuster Catherine , Zhuang Xiaodong , Holmes Jacinta , Yeh Ming-Lun , Abe-Chayama Hiromi , Heikenwälder Mathias , Sangiovanni Angelo , Iavarone Massimo , Colombo Massimo , Foung Steven K. H. , McKeating Jane A. , Davidson Irwin , Yu Ming-Lung , Chung Raymond T. , Hoshida Yujin , Chayama Kazuaki , Lupberger Joachim , Baumert Thomas F. 
Published: August 2024

AbstractChronic liver disease and cancer are global health challenges. The role of the circadian clock as a regulator of liver physiology and disease is well established in rodents, however, the identity and epigenetic regulation of rhythmically expressed genes in human disease is less well studied. Here we unravel the rhythmic transcriptome and epigenome of human hepatocytes using male human liver chimeric mice. We identify a large number of rhythmically expressed protein coding genes in human hepatocytes of male chimeric mice, which includes key transcription factors, chromatin modifiers, and critical enzymes. We show that hepatitis C virus (HCV) infection, a major cause of liver disease and cancer, perturbs the transcriptome by altering the rhythmicity of the expression of more than 1000 genes, and affects the epigenome, leading to an activation of critical pathways mediating metabolic alterations, fibrosis, and cancer. HCV-perturbed rhythmic pathways remain dysregulated in patients with advanced liver disease. Collectively, these data support a role for virus-induced perturbation of the hepatic rhythmic transcriptome and pathways in cancer development and may provide opportunities for cancer prevention and biomarkers to predict HCC risk.
Climate change will exacerbate land conflict between agriculture and timber production
Authors: Bousfield Christopher G. , Morton Oscar , Edwards David P. 
Published: August 2024

AbstractTimber and agricultural production must both increase throughout this century to meet rising demand. Understanding how climate-induced shifts in agricultural suitability will trigger competition with timber for productive land is crucial. Here, we combine predictions of agricultural suitability under different climate change scenarios (representative concentration pathways RCP 2.6 and RCP 8.5) with timber-production maps to show that 240–320 Mha (20–26%) of current forestry land will become more suitable for agriculture by 2100. Forestry land contributes 21–27% of new agricultural productivity frontiers (67–105 Mha) despite only occupying 10% of the surface of the land. Agricultural frontiers in forestry land occur disproportionately in key timber-producing nations (Russia, the USA, Canada and China) and are closer to population centres and existing cropland than frontiers outside forestry land. To minimize crop expansion into forestry land and prevent shifting timber harvests into old-growth tropical and boreal forests to meet timber demand, emissions must be reduced, agricultural efficiency improved and sustainable intensification invested in.
Evaluation of newly synthesized 2-(thiophen-2-yl)-1H-indole derivatives as anticancer agents against HCT-116 cell proliferation via cell cycle arrest and down regulation of miR-25
Authors: Abdelazeem Nagwa M. , Gouhar Shaimaa A. , Fahmy Cinderella A. , Elshahid Zeinab A. , El-Hussieny Marwa 
Published: August 2024

AbstractIn the present study, we prepared new sixteen different derivatives. The first series were prepared (methylene)bis(2-(thiophen-2-yl)-1H-indole) derivatives which have (indole and thiophene rings) by excellent yield from the reaction (2 mmol) 2-(thiophen-2-yl)-1H-indole and (1 mmol) from aldehyde. The second series were synthesized (2-(thiophen-2-yl)-1H-indol-3-yl) methyl) aniline derivatives at a relatively low yield from multicomponent reaction of three components 2-(thiophen-2-yl)-1H-indole, N-methylaniline and desired aldehydes. The anticancer effect of the newly synthesized derivatives was determined against different cancers, colon, lung, breast and skin. The counter screening was done against normal Epithelial cells (RPE-1). The effect on cell cycle and mechanisms underlying of the antitumor effect were also studied. All new compounds were initially tested at a single dose of 100 μg/ml against this panel of 5 human tumor cell lines indicated that the compounds under investigation exhibit selective cytotoxicity against HCT-116 cell line and compounds (4g, 4a, 4c) showed potent anticancer activity against HCT-116 cell line with the inhibitory concentration IC50 values were, 7.1±0.07, 10.5± 0.07 and 11.9± 0.05 μΜ/ml respectively. Also, the active derivatives caused cell cycle arrest at the S and G2/M phase with significant(p < 0.0001) increase in the expression levels of tumor suppressors miR-30C, and miR-107 and a tremendous decrease in oncogenic miR-25, IL-6 and C-Myc levels. It is to conclude that the anticancer activity could be through direct interaction with tumor cell DNA like S-phase-dependent chemotherapy drugs. Which can interact with DNA or block DNA synthesis such as doxorubicin, cisplatin, or 5-fluorouracil and which were highly effective in killing the cancer cells. This data ensures the efficiency of the 3 analogues on inducing cell cycle arrest and preventing cancer cell growth. The altered expressions explained the molecular mechanisms through which the newly synthesized analogues exert their anticancer action.
An experimental approach on dynamic occlusal fingerprint analysis to simulate use-wear localisation and development on stone tools
Authors: Rausch Hannah , Marreiros João , Kullmer Ottmar , Schunk Lisa , Gneisinger Walter , Calandra Ivan 
Published: August 2024

AbstractInformation about the use of stone tools in the past is encoded in the wear patterns left on their surface; however, post-depositional processes can modify and obstruct these traces. One aim in the field of lithic functional analysis is to develop methods to detect and quantify these traces on stone tools. The occlusal fingerprint analysis (OFA) is a well-established method in dental wear studies to virtually simulate dental occlusal (contact between teeth) stroke movements and thus locate and quantify the sequential contact between opposing tooth crowns. Reaching across disciplines, we conducted controlled experiments to test the applicability of the OFA method on stone tools to address the challenge of use-wear quantification and localisation, and therefore the identification of post-depositional wear. Our findings reveal a clear overlap between zones of experimentally produced use-wear and OFA-calculated contact areas. We demonstrate OFA as a potential method to generate models of multiscale use-wear that can be used as references on experimental tools to identify post-depositional surface modifications on stone tool artefacts.
Understanding period product use among young women in rural and urban India from a geospatial perspective
Authors: Biswas Sourav , Alam Asraful , Islam Nazrul , Roy Ranjan , Satpati Lakshminarayan 
Published: August 2024

AbstractEnsuring proper menstrual hygiene management remains a significant challenge for young women in India. The term "exclusive use of hygienic period products during menstruation" refers to relying solely on period products like sanitary pads, tampons, or menstrual cups. Poor menstrual hygiene practices not only increase the risk of reproductive tract infections but also lead to various negative health outcomes, including discomfort and potential complications. This study explores factors associated with the exclusive use of period products during menstruation aged 15–24, investigates geographic disparities, examines rural–urban gaps, and assesses inequality in India. Utilizing data from the fifth National Family Health Survey (NFHS-5), responses from 2,41,180 women aged 15 to 24 were analysed using logistic regression and multivariate decomposition analyses to explore socioeconomic predictors. Moran's I statistics also assessed spatial dependency, while Lorenz curves and Gini coefficients measured inequality. Quintile and LISA maps visualized regional disparities. The study found that 76.15% of women in India reported exclusive use of hygienic period products during menstruation. Rural areas reported a lower percentage of exclusive use of hygienic period products (72.32%) during menstruation compared to urban areas (89.37%). Key factors associated with the exclusive use of hygienic period products among 15–24-year-old women in India include age, education, place of residence, wealth, access to media, and healthcare discussions. Geographically, central districts exhibited the lowest coverage (< 65%), while the Southern region reported the highest (> 85). The GINI coefficient of 0.39 highlighted moderate inequality in distribution. Decomposition analysis revealed that household wealth contributed 49.25% to rural–urban differences, followed by education (13.41%), media access (7.97%), and region (4.97%). This study highlights significant regional disparities and low utilization of hygienic period products among young women in India, particularly in central districts. Policymakers should prioritize interventions targeting these regions, addressing socio-economic disparities. Strategies to promote education, improve media access, and enhance household wealth can facilitate menstrual hygiene adoption. Initiatives to reduce sanitary napkin costs and increase accessibility, particularly in rural areas, are crucial to mitigating geographical disparities nationwide.
Exploring the neuroprotective potential of Nrf2-pathway activators against annonacin toxicity
Authors: Costa Márcia F. D. , Rösler Thomas W. , Höglinger Günter U. 
Published: August 2024

AbstractModulation of the Nrf2 pathway, a master regulator of the antioxidant response and cellular metabolism, has been suggested as a promising therapeutic strategy in tauopathies, a heterogeneous group of neurodegenerative disorders characterized by intracellular proteinaceous inclusions of abnormally phosphorylated tau. Here, we explored the neuroprotective potential of different Nrf2-pathway activators in human immortalized dopaminergic neurons against annonacin-induced toxicity, a mitochondrial inhibitor associated with a PSP-like syndrome and capable of mimicking tauopathy-like features. Interestingly, we observed heterogenous and compound-dependent neuroprotective effects among the different Nrf2-pathway activators. With the exception of Fyn inhibitors, all the selected Nrf2-pathway activators improved cell viability and the oxidative status, and reduced the annonacin-induced tau hyperphosphorylation and neurite degeneration, particularly the p62-activators. However, improvement of the impaired mitochondrial function was only observed by the Bach-1 inhibitor. Surprisingly, we found evidence that ezetimibe, an approved drug for hypercholesterolemia, prevents the transcriptional upregulation of 4R-tau triggered by annonacin insult. Overall, our results suggest that the neuroprotective effects of the Nrf2-pathway activators against annonacin toxicity may rely on the specific mechanism of action, intrinsic to each compound, and possibly on the concomitant modulation of additional signaling pathways. Further research will be needed to fully understand how synergistic modulation of metabolic adaptation and cell survival can be exploit to develop new therapeutical strategies for tauopathies and eventually other neurodegenerative diseases.
Enhancement of rider comfort by magnetorheological elastomer based damping treatment at strategic locations of an electric two wheeler
Authors: Krishna Keerthan , Mahesha G. T. , Hegde Sriharsha , Shenoy B. Satish 
Published: August 2024

AbstractThe vibrations generated in the two-wheeled vehicles like motorcycles due to road irregularities such as cracks, potholes, and bumps on the road cause discomfort for the rider as well as the pillion. These vibrations are reported to cause lower back pains, musculoskeletal effects, fatigue, and long-term health issues. Particularly, electric two-wheelers are more susceptible to these vibrations caused by the road and need attention. This paper presents an innovative technique for the reduction of vibrations at prominent locations in the electric two-wheeler to improve the rider’s comfort. All measured accelerations are about vertical direction (along z-axis as per ISO 2631-1 standard). Passive and Semi-active damping treatments namely, Room temperature vulcanizing Silicone rubber and Magnetorheological elastomer (MRE) were applied on the test vehicle at strategic locations of vibration. Both were compared for their effectiveness in reducing the vibrations. Results showed that MRE based damping technique proved better vibration isolation at the strategic locations. The weighted root mean square acceleration as well as vibration dose values were found to decrease with the help of damping treatments thus improving the rider’s overall comfort level.
Quantifying thoracolumbar fascia deformation to discriminate acute low back pain patients and healthy individuals using ultrasound
Authors: Brandl Andreas , Wilke Jan , Horstmann Thomas , Reer Rüdiger , Egner Christoph , Schmidt Tobias , Schleip Robert 
Published: August 2024

AbstractReduced shear strain and deformability of the thoracolumbar fascia has been linked to low back pain. A number of ultrasound examination methods have been developed for laboratory rather than clinical practice. The aim of this study was to examine the reliability and discriminative validity (patients vs. healthy individuals) of an ultrasound (US) measurement method for the quantification of thoracolumbar fascia deformation (TLFD). A cross-sectional study with US assessment and rater blinding was conducted in a manual therapy clinic and a university laboratory. 16 acute low back pain (aLBP) patients and 15 healthy individuals performed a standardized trunk extension task. US measurements of TLFD were carried out independently by two raters by imaging the TLF in the starting and ending positions of the movement. Intra-rater and inter-rater reliability were calculated using intraclass correlation coefficients (ICCs) and minimal detectable changes (MDC) were calculated. Receiver operating characteristic (ROC) curve analysis was used to determine the cut-off for TLFD to discriminate the study groups. Kappa statistics were performed to assess rater agreement in discrimination. Intra-rater reliability was excellent (ICC: .92, MDC: 5.54 mm, p < .001) and inter-rater reliability was good (ICC: .78, MDC: 8.70 mm, p < .001). The cut-off for TLFD was 6 mm with a sensitivity of 100% and a specificity of 93.75% and the raters agreed moderately (κ = 0.74, p < .001) when distinguishing patients and controls. The reliability of the US method for assessing TLFD is moderate to excellent, and the ability to discriminate aLBP patients from healthy individuals is moderate. The method could be used to capture an additional parameter in morphological aLBP screenings.
Physics-Informed Masked Autoencoder for active sparse imaging
Authors: McEvoy Luke , Tafone Daniel , Sua Yong Meng , Huang Yuping 
Published: August 2024

AbstractImaging technology based on detecting individual photons has seen tremendous progress in recent years, with broad applications in autonomous driving, biomedical imaging, astronomical observation, and more. Comparing with conventional methods, however, it takes much longer time and relies on sparse and noisy photon-counting data to form an image. Here we introduce Physics-Informed Masked Autoencoder (PI-MAE) as a fast and efficient approach for data acquisition and image reconstruction through hardware implementation of the MAE (Masked Autoencoder). We examine its performance on a single-photon LiDAR system when trained on digitally masked MNIST data. Our results show that, with $$1.8\times 10^{-6}$$

1.8
×

10

-
6

or less detected photons per pulse and down to 9 detected photons per pixel, it achieves high-quality image reconstruction on unseen object classes with 90% physical masking. Our results highlight PI-MAE as a viable hardware accelerator for significantly improving the performance of single-photon imaging systems in photon-starving applications.
SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling
Authors: Tuomivaara Sami T. , Teo Chin Fen , Jan Yuh Nung , Wiita Arun P. , Jan Lily Y. 
Published: August 2024

AbstractTo facilitate our understanding of proteome dynamics during signaling events, robust workflows affording fast time resolution without confounding factors are essential. We present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT) to label extracellularly exposed proteins in a rapid, specific, and sensitive manner. Simple and flexible SLAPSHOT utilizes recombinant soluble APEX2 protein applied to cells, thus circumventing the engineering of tools and cells, biological perturbations, and labeling biases. We applied SLAPSHOT and quantitative proteomics to examine the TMEM16F-dependent plasma membrane remodeling in WT and TMEM16F KO cells. Time-course data ranging from 1 to 30 min of calcium stimulation revealed co-regulation of known protein families, including the integrin and ICAM families, and identified proteins known to reside in intracellular organelles as occupants of the freshly deposited extracellularly exposed membrane. Our data provide the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome.
Efflux pump-mediated resistance to new beta lactam antibiotics in multidrug-resistant gram-negative bacteria
Authors: Dulanto Chiang Augusto , Dekker John P. 
Published: August 2024

AbstractThe emergence and spread of bacteria resistant to commonly used antibiotics poses a critical threat to modern medical practice. Multiple classes of bacterial efflux pump systems play various roles in antibiotic resistance, and members of the resistance-nodulation-division (RND) transporter superfamily are among the most important determinants of efflux-mediated resistance in gram-negative bacteria. RND pumps demonstrate broad substrate specificities, facilitating extrusion of multiple chemical classes of antibiotics from the bacterial cell. Several newer beta-lactams and beta-lactam/beta-lactamase inhibitor combinations (BL/BLI) have been developed to treat infections caused by multidrug resistant bacteria. Here we review recent studies that suggest RND efflux pumps in clinically relevant gram-negative bacteria may play critical but underappreciated roles in the development of resistance to beta-lactams and novel BL/BLI combinations. Improved understanding of the genetic and structural basis of RND efflux pump-mediated resistance may identify new antibiotic targets as well as strategies to minimize the emergence of resistance.
HR-GO
Authors: Sitnova T. M. , Yuan Z. , Matsuno T. , Mashonkina L. I. , Alexeeva S. A. , Holmbeck E. , Sestito F. , Lombardo L. , Banerjee P. , Martin N. F. , Jiang F. 
Published: August 2024

Context. Dwarf galaxy streams encode vast amounts of information essential to understanding early galaxy formation and nucleosynthesis channels. Due to the variation in the timescales of star formation history in their progenitors, stellar streams serve as ‘snapshots’ that record different stages of galactic chemical evolution.
Aims. This study focusses on the Cetus stream, stripped from a low-mass dwarf galaxy. We aim to uncover its chemical evolution history as well as the different channels of its element production from detailed elemental abundances.
Methods. We carried out a comprehensive analysis of the chemical composition of 22 member stars based on their high-resolution spectra. We derived abundances for up to 28 chemical species from C to Dy and, for 20 of them, we account for the departures from local thermodynamic equilibrium (NLTE effects).
Results. We confirm that the Cetus stream has a mean metallicity of [Fe/H] = −2.11 ± 0.21. All observed Cetus stars are α enhanced with [α/Fe] ≃ 0.3. The absence of the α-‘knee’ implies that star formation stopped before iron production in type Ia supernovae (SNe Ia) became substantial. Neutron capture element abundances suggest that both the rapid (r-) and the main slow (s-) processes contributed to their origin. The decrease in [Eu/Ba] from a typical r-process value of [Eu/Ba] = 0.7–0.3 with increasing [Ba/H] indicates a distinct contribution of the r- and s-processes to the chemical composition of different Cetus stars. For barium, the r-process contribution varies from 100 to 20% in different sample stars, with an average value of 50%.
Conclusions. Our abundance analysis indicates that the star formation in the Cetus progenitor ceased after the onset of the main s-process in low- to intermediate-mass asymptotic giant branch stars but before SNe Ia played an important role. A distinct evolution scenario is revealed by comparing the abundances in the Ursa Minor dwarf spheroidal galaxy, showing the diversity in – and uniqueness of – the chemical evolution of low-mass dwarf galaxies.
Sulfur monoxide (SO) as a shock tracer in protoplanetary disks: Case of AB Aurigae
Authors: Dutrey A. , Chapillon E. , Guilloteau S. , Tang Y. W. , Boccaletti A. , Bouscasse L. , Collin-Dufresne T. , Di Folco E. , Fuente A. , Piétu V. , Rivière-Marichalar P. , Semenov D. 
Published: August 2024

Context. Sulfur monoxide (SO) is known to be a good shock tracer in molecular clouds and protostar environments, but its abundance is difficult to reproduce, even with state-of-the-art astrochemical models.
Aims. We investigate the properties of the observed SO emission in the protoplanetary disk of AB Auriga, a Herbig Ae star of 2.4 M⊙ in mass, located at 156 pc. The AB Aur system is unique because it exhibits a dust trap and at least one young putative planet orbiting at about 30 au from the central star.
Methods. We reduced ALMA archival data (projects 2019.1.00579.S, 2021.1.00690.S, and 2021.1.01216.S) and analyzed the three detected SO lines (SO 65 − 54, 67 − 56 and 56 − 45). We also used C17O and C18O 2–1 data to complement the interpretation of the SO data.
Results. For the three SO lines, the maximum SO emission in the ring is not located in the dust trap. Moreover, the inner radius of the SO ring is significantly larger than the CO emission inner radius, ∼160 au versus ∼90 au. The SO emission traces gas located in part beyond the dust ring. This emission likely originates from shocks at the interface of the outer spirals, observed in CO and scattered light emission, as well as those in the molecular and dust ring. Also, SO is detected within the cavity, at a radius of ∼20 − 30 au and with a rotation velocity compatible with the protoplanet P1. We speculate that this SO emission originates from accretion shocks onto the circumplanetary disk of the putative protoplanet P1.
Conclusions. These observations confirm that SO is a good tracer of shocks in protoplanetary disks and could serve as a powerful new tool for detecting embedded (proto)planets.