bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in the global exposure, mortality and disability of low bone mineral density between men and women: the underestimated burden in men
Authors: Zhu Binxiang , Hu Shian , Guo Jianfeng , Dong Zijian , Dong Yimin , Li Feng 
Published: December 2022

Abstract
Talking about osteoporosis, we tend to focus on post-menopause women who are at increased risk due to estrogen depletion, while less attention has been paid to the disease in men. Currently, there is a lack of understanding about the difference of osteoporosis incidence and burden by sex. In this study, we used data from the Global Burden of Disease Study 2019 (GBD 2019) to compare the difference in the prevalence and burden of low bone mineral density (LBMD) between men and women, by location, year, age and socio-demographic index. We found the prevalence of LBMD was higher in women than in men. However, the age standardized mortality rate was greatly higher in men than in women. Using disability-adjusted life year (DALY) to measure the burden, we also observed higher age standardized DALY rate in men. Using sociodemographic index (SDI) as the measure of social development level, we found that higher mortality and DALY rates were mainly seen in middle and high SDI countries. Falls were the leading cause for of deaths and disabilities in both men and women with LBMD, followed by transport injuries. Fall-related mortality was higher in women, while transport injuries caused more deaths and disabilities in men. Conclusively, more attention should be paid to osteoporosis in men, and related policies, clinical practices, and guidelines are in need to reduce the burden of LBMD and osteoporosis in men.
SOX17-mediated LPAR4 expression plays a pivotal role in cardiac development and regeneration after myocardial infarction
Authors: Cho Hyun-Jai , Lee Jin-Woo , Lee Choon-Soo , Son HyunJu , Lee Jaewon , Kang Minjun , Chai Jinho , Kim Hyo-Soo 
Published: December 2022

Abstract
Lysophosphatidic acid receptor 4 (LPAR4) exhibits transient expression at the cardiac progenitor stage during pluripotent stem cell (PSC)-derived cardiac differentiation. Using RNA-sequencing, promoter analyses, and a loss-of-function study in human PSCs, we discovered that the SRY-box transcription factor 17 (SOX17) is an essential upstream factor of LPAR4 during cardiac differentiation. We conducted mouse embryo analyses to further verify our human PSC in vitro findings. We confirmed the transient and sequential expression of SOX17 and LPAR4 during in vivo cardiac development. In the adult bone marrow transplantation model using LPAR4 promoter-driven GFP cells, we observed two LPAR4+ cell types in the heart following myocardial infarction (MI). Heart-resident LPAR4+ cells, which are SOX17+, but not bone marrow-derived infiltrated LPAR4+ cells, showed cardiac differentiation potential. Furthermore, we tested various strategies to enhance cardiac repair through the regulation of downstream signals of LPAR4. During the early stage after MI, the downstream inhibition of LPAR4 by a p38 mitogen-activated protein kinase (p38MAPK) blocker improved cardiac function and reduced fibrotic scar, compared with that observed following LPAR4 stimulation. These findings improve our understanding of heart development and suggest novel therapeutic strategies meant to enhance repair and regeneration after injury by modulating the LPAR4 signaling.
The deubiquitinating enzyme MINDY2 promotes pancreatic cancer proliferation and metastasis by stabilizing ACTN4 expression and activating the PI3K/AKT/mTOR signaling pathway
Authors: Liu Peng , Liu Songbai , Zhu Changhao , Li Yongning , Ying Li , Fei Xiaobin , Hou Junyi , Wang Xing , Pan Yaozhen 
Published: December 2022

Abstract
The pathogenic mechanisms of pancreatic cancer (PC) are still not fully understood. Ubiquitination modifications have a crucial role in tumorigenesis and progression. Yet, the role of MINDY2, a member of the motif interacting with Ub-containing novel DUB family (MINDY), as a newly identified deubiquitinating enzyme, in PC is still unclear. In this study, we found that MINDY2 expression is elevated in PC tissue (clinical samples) and was associated with poor prognosis. We also found that MINDY2 is associated with pro-carcinogenic factors such as epithelial-mesenchymal transition (EMT), inflammatory response, and angiogenesis; the ROC curve suggested that MINDY2 has a high diagnostic value in PC. Immunological correlation analysis suggested that MINDY2 is deeply involved in immune cell infiltration in PC and is associated with immune checkpoint-related genes. In vivo and in vitro experiments further suggested that elevated MINDY2 promotes PC proliferation, invasive metastasis, and EMT. Meanwhile, actinin alpha 4 (ACTN4) was identified as a MINDY2-interacting protein by mass spectrometry and other experiments, and ACTN4 protein levels were significantly correlated with MINDY2 expression. The ubiquitination assay confirmed that MINDY2 stabilizes the ACTN4 protein level by deubiquitination. The pro-oncogenic effect of MINDY2 was significantly inhibited by silencing ACTN4. Bioinformatics Analysis and Western blot experiments further confirmed that MINDY2 stabilizes ACTN4 through deubiquitination and thus activates the PI3K/AKT/mTOR signaling pathway. In conclusion, we identified the oncogenic role and mechanism of MINDY2 in PC, suggesting that MINDY2 is a viable candidate gene for PC and may be a therapeutic target and critical prognostic indicator.
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
Authors: Siepel Adam , Zhao Yixin , Liu Lingjie 
Published: December 2022

Abstract
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions, leading to a complex dynamic equilibrium in RNAP occupancy of the ∼100 bp immediately downstream of the transcription start site. In this article, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations over a broad range of parameters, we show that this model enables accurate estimation of initiation and pause-escape rates even in the presence of collisions between RNAPs and variable elongation rates. Furthermore, we show by simulation and analysis of data for human cell lines that pause-escape is often more strongly rate-limiting than conventional “pausing indices” would suggest, that occupancy of the pause site is elevated at many genes, and that steric hindrance of initiation can lead to a pronounced reduction in apparent initiation rates. Our modeling framework is generally applicable for all types of nascent RNA sequencing data and can be applied to a variety of inference problems. Our software for estimation and simulation is publicly available.
Abnormal thickness-dependent magneto-transport properties of vdW magnetic semiconductor Cr2Si2Te6
Authors: Karel Julie , Li Yun , Chen Zheng , Wang Jie , Li Teng , Tian Mingliang , Suzuki Kiyonori 
Published: December 2022

Abstract
Cr2Si2Te6 (CST) is a van der Waals (vdW) ferromagnetic semiconductor. The unique Ising spin model and temperature-dependent magnetic ordering of CST provide opportunities for the next generation of two-dimensional (2D) spintronic devices. Here, abnormal magneto-transport properties are found in CST nanoflakes with variations of thickness. Interestingly, the thickness-dependent magnetoresistance (MR) effect exhibits a nonlinear change as a function of the magnetic field, temperature, and thickness. At a certain temperature below Curie temperature (Tc), a sign reversal of MR ratio from positive to negative can be even detected with thickness reduction. At the temperature range from Tc to 60 K, the Hall effect also presents a transformation from nonlinear behavior in thick layer CST to linear behavior in thin layer CST. These distinctive magneto-transport properties are attributed to the variation of spin correlation with thickness in CST nanoflakes. These findings probe the unique magneto-transport properties of CST and associate it with ferromagnetic correlation, which provides a basis for subsequent spintronics device design based on this material. This work also offers new insights into the relationship between sample thickness, transport properties, and spin correlation of other vdW ferromagnets. It lays a foundation for future vdW magnets-based device fabrication and possible spintronic applications.
Mechanistic Manifold in a Hemoprotein-Catalyzed Cyclopropanation Reaction with Diazoketone
Authors: Nam Donggeon , Bacik John-Paul , Khade Rahul , Aguileraa Maria Camila , Wei Yang , Neidig Michael , Zhang Yong , Ando Nozomi , Fasan Rudi 
Published: December 2022

Abstract
Hemoproteins have recently emerged as a promising class of biological catalysts for promoting carbene transfer reactions not found in nature. Despite this progress, our mechanistic understanding of the interplay between productive and unproductive pathways in these reactions is limited. Using a combination of spectroscopic, structural, and computational methods, we have investigated the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. Our studies shed light into the nature and kinetics of key catalytic steps in this reaction, including formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the mechanism of the cyclopropanation step. Importantly, our studies reveal the existence of a complex mechanistic manifold behind this hemoprotein-catalyzed cyclopropanation, wherein the cyclopropanation pathway competes with alternative pathways, including formation of an N-bound carbene adduct of the protein heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species is able to regenerate the active biocatalyst, thus constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings improve our understanding of biocatalytic cyclopropanations and the ensuing mechanistic picture is expected to offer a blueprint for both the mechanistic analysis of other hemoprotein-catalyzed carbene transfer reactions and the design and engineering of carbene transferases.
Research paper: Water Resources Management

Small reservoir water dynamics modeling
Authors: Rodrigues Alisson , Rodrigues Lineu Neiva , Marques Guilherme Fernandes , Villa Pedro Manuel 
Published: December 2022

Abstract

Small reservoirs play a key role in agricultural development in the Brazilian Savannah (Cerrado) region. They contribute to diminish rural communities’ vulnerability to drought and improve the livelihood of rural populations. Thousands of small reservoirs have been built in the last few decades in the Cerrado, but efficient water management and sound planning are hindered by inadequate knowledge of their water dynamics. Studies related to small reservoir water dynamics are generally scarce in the world hydrological literature. The main objective of this study was to develop a dynamic simulation model based on the system dynamics model to evaluate the water dynamics in small reservoirs over time, and the risk of not meeting the predicted water demand. Daily data on reservoir inflows were obtained for the period from October 2009 to September 2011, and extended to June 2015 through modeling. The developed model was calibrated and validated with historical data. The main variables which have impact on the water volume were evaluated through sensitivity analysis. The results indicated that reservoir inflow was the variable which had the highest impact on water volume in the reservoir, followed by the reservoir surface area and by evaporation and infiltration, which together represented 14.4% of reservoir inflow. The risk assessment of not meeting the predicted water demand showed that the water in the reservoir was above the critical level 85.9% of the time and that 81.6% of the reservoir water was available to meet water demand. Small dams pose a risk of not meeting the community’s water demand at least 18% of the time.
Cross-sectional correlation network analysis identifies plasma proteins and metabolites associated with the pathogenesis and treatment of acute promyelocytic leukemia
Authors: Qiao Niu , Liu Feng , Lyu Yizhu , Zhang Yuliang , Ma Xiaolin , Lin Xiaojing , Wang Junyu , Xie Yinyin , Zhang Ruihong , Qiao Jing , Zhu Hongming , Chen Li , Yin Tong , Fang Hai , Tian Qiang , Chen Zhu , Chen Sai-Juan 
Published: December 2022

Abstract
The treatment of PML/RARA+ acute promyelocytic leukemia (APL) with all-trans retinoic acid and arsenic trioxide (ATRA/ATO) has been recognized as a model for translational medicine research. Though an altered microenvironment is a general cancer hallmark, whether and how APL blasts shape their plasma microenvironment is poorly understood. Here we reported a cross-sectional correlation network framework that was successfully applied to interpret multi-layered datasets on clinical laboratory tests, proteomes, and metabolomes of paired plasma samples from APL patients before or after ATRA/ATO remission induction therapy. Our study identified an untreated APL plasma network, revealing two prominent features: one characterized by altered secretory protein and metabolite profiles, indicative of heightened proliferative and energy consumption states of APL blasts; the other featuring APL plasma-enriched proteins, or enzymes catalyzing the metabolism of plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA, suggesting a possible involvement of APL blasts in modulating their plasma microenvironment. Our study further identified a plasma network at the hematological complete remission stage, in which above-normal levels of intracellular proteins might be attributed to therapy-induced cell death, with enhanced interferon-gamma signaling activity likely explaining a tumor-suppressing function of the immune system. This work sheds new light into the pathophysiology and treatment of APL and provides an information-rich reference data cohort for exploratory and translational study of leukemia microenvironment.
Practical Black Box Hamiltonian Learning
Authors: Gu Andi , Cincio Lukasz , Coles Patrick 
Published: December 2022

Abstract
We study the problem of learning the parameters for the Hamiltonian of a quantum many-body system, given limited access to the system.
In this work, we build upon recent approaches to Hamiltonian learning via derivative estimation. We propose a protocol that improves the scaling dependence of prior works, particularly with respect to parameters relating to the structure of the Hamiltonian (e.g., its locality k). Furthermore, by deriving exact bounds on the performance of our protocol, we are able to provide a precise numerical prescription for theoretically optimal settings of hyperparameters in our learning protocol, such as the maximum evolution time (when learning with unitary dynamics) or minimum temperature (when learning with Gibbs states). Thanks to these improvements, our protocol is practical for large problems: we demonstrate this with a numerical simulation of our protocol on an 80-qubit system.
Monitoring treatment of industrial wastewater using conventional methods and Impedance spectroscopy
Authors: Hafidi El Mokhtar El , Mortadi Abdelhadi , Graich Abderrazzak , Chahid El Ghaouti , Laasri Said , Moznine Reddad El , Monkade Mohammed 
Published: December 2022

Abstract
In this work, we treated wastewater from the detergent manufacturing industry on natural carriers and by-products from a coal-fired thermal power plant. The filtration was carried out by infiltration- percolation using a vertical cylindrical column manufactured in our laboratory. The main parameters analyzed before and after treatment are: suspended matter (SM), chemical oxygen demand (COD), biochemical oxygen demand (BOD5) and pH. This treatment system achieved a reduction of 89% COD, 73% BOD5, 54% SS and (66-99%) heavy metals. The COD/BOD5 rejection ratio before treatment, which was greater than 4.24, has become less than 1.73. Thus, impedance measurements of the wastewater before and after treatment were carried out. The results of the electrical parameters deduced from the impedance spectra show a good correlation with the parameters obtained by the classical methods.
Experimental study on the Hydraulic Performance of Porous Broad-Crested Weirs with Sloping Crests
Authors: Doustkam Mehrdad , Rahmanshahi Mostafa , Fathi-Moghadam Manoochehr , Keramat Alireza , Duan Huan-Feng 
Published: December 2022

Abstract
Due to the high technical and hydraulic performance and negligible environmental adverse impact of a porous weir, this structure is a reasonable substitute for conventional impermeable solid weirs in water transmission and distribution systems. This research focused on the hydraulic performance of porous broad-crested weirs (PBCWs) with sloping crests. To this end, 30 PBCWs models in free and submerged flow conditions were designed and examined under different operation conditions. In particular, a comparative study was performed between PBCWs with and without sloping crests, the performance of which were then compared with a solid broad-crested weir (SBCW) model. Based on the results and analysis, the PBCWs with sloping crests have a more significant discharge coefficient than common PBCWs (without sloping crests), and the upstream slope has a more significant impact on the discharge coefficient than the downstream slope. In addition, the PBCWs with sloping crests are more sensitive to tailwater than common PBCWs, and thus the discharge reduction factor of the weir with the upstream crest slope is lower than that of the downstream. Finally, based on the extensive experimental results, both nonlinear multi-variable regression and gene-expression programming approaches were applied to extract empirical equations for expressing the free flow discharge coefficient and submerged flow discharge reduction factor.
Modelling of flow through naturally fractured geothermal reservoirs, Taupo Volcanic Zone, New Zealand
Authors: Kissling Warwick , Massiot Cecile 
Published: December 2022

Abstract
Background: Numerous fractures are observed in fractured geothermal reservoirs on borehole images in the Taupō Volcanic Zone (TVZ), Aotearoa New Zealand. These fractures are necessary to explain the sustained reservoir permeabilities despite the low matrix porosity. However, conventional continuum models do not adequately represent fluid flow through these fractured rocks.
Method: We present new Discrete Fracture Network (DFN) codes that model fractures and associated fluid flow in 2-D at reservoir scales to represent typical rock types found in TVZ reservoirs. Input parameters are derived from interpretations of borehole images at the Rotokawa and Wairakei geothermal fields where fractures have high dip magnitudes (>60°-70°). This paper focuses on the effect of fracture density along virtual boreholes (P10), that is in average 0.6 m-1 in sheet-like andesites; 0.8 m-1 in ignimbrites and 1.7 m-1 in rhyolite lavas.
Results: The number of fractures in the models scale linearly with the input P10 in virtual boreholes. The percolation threshold, where the backbone of fractures is connected across the entire model domain, is reached for P10 > 0.2 m-1. Above this threshold, mean flow measured along the mean fracture direction scales linearly with P10. For P10 > 0.4 m-1 the permeability anisotropy lies in the interval 13 ± 3, with the scatter decreasing as P10 increases. The pressure distributions in individual DFN realisations are highly variable, but averages of 50 realisations converge towards those given by equivalent continuum models. Probability density functions resulting from DFN realisations can therefore be used to constrain continuum models. Tracing of fluid particles through the DFN shows that particles can take numerous pathways to define a swath of paths. The travel time of particles over 1 km follows a distribution similar to real tracer tests, with arrivals peaking at 1-2 days and a long tail stretching to over 200 days.
Conclusions: The new codes, calibrated to real measurements of fracture geometries in borehole images of the TVZ, reproduce patterns of flows in fractured geothermal systems. Mean flows and permeability anisotropies derived from the DFNs can be used to improve modelling of flows through fractured geothermal reservoirs using continuum models at a limited computational cost.
“I get higher marks via BYOD“ - a descriptive qualitative study on student experiences using BYOD e-assessments to enhance the dimensions of administration and support for learning excellence.
Authors: As Janus van , Brits Kanita Elizabeth 
Published: December 2022

Abstract
Bring Your Own Device (BYOD) e-assessment is a strategy that allows students to use their own devices for conducting digital assessments without the need for specialised facilities. This can enhance learning excellenceas it improves the administration and support of the student experience. BYOD e-assessment is not a widely used strategy, yet it has multiple benefits. Therefore this study explores the use of BYOD for high stakes e-assessment and was conducted at a Faculty of Medicine and Health Science. Since 2014, over 14 000 exams have been conducted using this approach. This study evaluates students' perceptions of BYOD e-assessment and was conducted through survey research with open-ended questions. The following themes were identified; technical and ICT barriers (technical challenges for student devices, technical challenges with infrastructure, type of device determines user-experience) and student experience (safety and familiarity with own device, convenience, supporting environment, autonomy, digital abilities, better quality assessments, and feedback). The findings showed that for most students using their devices provides them with a feeling of safety due to the familiarity with their own devices. Being able to write in a familiar more pleasant environment reduces stress. However, students with older devices might stress about using their own devices and students should feel comfortable with using technology. BYOD for e-assessment is a good solution to enhance the student experience and reduce administration. However, it is not a one size fits-all solution and requires multiple interventions such as faculty development, support, training of students and a good strategy before implementation.