bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abnormal changes of IL3/IL3R and its downstream signaling pathways in the prion infected cell line and in the brains of scrapie infected rodents
Authors: Jia Xiao-Xi , Chen Cao , Hu Chao , Chao Zhi-Yue , Zhang Wei-Wei , Wu Yue-Zhang , Fan Qin , A Ru-Han , Liu Xin , Xiao Kang , Shi Qi , Dong Xiao-Ping 
Published: March 2023

Abstract
Interleukin 3 (IL-3) plays an important role in hematopoiesis and immune regulation, brain IL-3/IL-3R signaling has been shown to involve in the physiological and pathological processes of a variety of neurodegenerative diseases, but its role in prion diseases is rarely described. Here, the changes of IL-3/IL-3R and its downstream signaling pathways in a scrapie infected cell line and in the brains of several scrapie infected rodent models were evaluated by various methods. Markedly decreased IL-3Rα were observed in the brains of scrapie infected rodents at terminal stage and in the prion infected cell model, which showed increased in the brain samples collected at early and middle stage of infection. The IL-3 levels were almost unchanged in the brains of scrapie infected mice and in the prion infected cell line. Morphological assays identified close co-localization of the increased IL-3Rα signals with NeuN- and Iba1-positive cells, whereas co-localization of IL-3 signals with NeuN- and GFAP-positive cells in the scrapie infected brain tissues. Some downstream components of IL-3/IL-3R pathways, including JAK2-STAT5 and PI3K/AKT/mTOR pathways, were downregulated in the brains of scrapie infected rodents at terminal stage and in the prion infected cells. Stimulation of recombinant IL-3 on the cultured cells showed prion that the prion infected cells displayed markedly more reluctant responses of JAK2-STAT5 and PI3K/AKT/mTOR pathways than the normal partner cells. These data suggest that although prion infection or PrPSc accumulation in brain tissues does not affect IL-3 expression, it significantly downregulates IL-3R levels, thereby inhibiting the downstream pathways of IL-3/IL-3R and blocking the neuroregulatory and neuroprotective activities of IL-3.
An efficient and simple catalytic method for the synthesis of pyrimido[1,2- a]benzimidazole and 1‐ (benzothiazolylamino) methyl‐ 2‐ naphthol derivatives using ZnO@SO 3 H@Tropine
Authors: Rahimizadeh Fatemeh , Mazloumi Masoumeh , Shirini Farhad 
Published: March 2023

Abstract
In this research, a simple, efficient and green method for the one-pot three-component synthesis of pyrimido[1,2-a]benzimidazole and 1‐ (benzothiazolylamino) methyl‐ 2‐ naphthol derivatives is reported using a new nanoporous catalyst formulated as ZnO@SO3H@Tropine. Further analysis of the catalyst for its characterization has been performed using thermal gravimetric analysis (TGA), field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), and fourier-transform infrared spectroscopy (FT-IR). Among the advantages of the current method are: high yields, reusability of the catalyst, ease of operation, clean reaction profiles, ease of separation and simple work-up.
Genotypic variation in deep roots: implications for nitrogen uptake and drought tolerance in winter wheat
Authors: Odone Arnesta , Popovic Olga , Thorup-Kristensen Kristian 
Published: March 2023

Abstract
Background and Aims

Deep roots are needed to allow uptake of N and water available in the deeper soil layers, to help tolerate increasingly extreme climates. Yet few studies in the field have been able to identify genetic differences in deep roots and how this relates to N and water uptake. This study aimed to identify the relationship between deep roots and tolerance to drought, how this varies by genotype and with differing N fertilization.

Methods

We grew 14 diverse genotypes of winter wheat in a semi-field facility in Denmark, in 2019 and 2020, with a soil depth gradient and a rain-out shelter to create a water stress. We used minirhizotron tubes reaching to 2.5m depth to quantify differences in deep roots. We applied isotope tracers (15N and 2H labelled water) at 1.6-1.8m at anthesis to assess differences in root function. 13C in grain and straw was used to assess drought stress.

Results

We found differences in deep roots between genotypes, and slightly less deep root growth when more N was applied. Deep roots were correlated with grain yield, uptake of deep-placed tracers of water and N, and tolerance to drought. Genotypes with deeper roots had the biggest decrease in water stress and increase in grain yield, when their roots had access to deeper soil.

Conclusion

Deeper roots were related to drought tolerance and increased yields. This suggests that deep rooting should be considered in future breeding efforts for more climate resilient crops.
Ginsenoside Rg1 ameliorates depressive-like behavior by inhibiting NLRP3 inflammasome activation in mice exposed to chronic stress
Authors: He Hui , Xie Xiaofang , Kang Xixi , Zhang Jinqiang , Wang Lu , Hu Nan , Xie Lei , Peng Cheng , You Zili 
Published: March 2023

Abstract
Objectives: Microglia-mediated inflammatory process is recognized as a target in the treatment of depression. Ginsenoside Rg1 (GRg1), the active ingredient of traditional ginseng, regulates microglial phenotypes to resist stress-induced inflammatory responses. Here we used a mouse model of stress-induced depression to investigate the involvement of microglial Nod-like receptor protein 3 (NLRP3) in the antidepressant effects of GRg1.
Methods: Male C57BL/6J mice were exposed to chronic mild stress (CMS) for three weeks, followed by intraperitoneal injection of GRg1 (20 mg/kg) or the antidepressant imipramine (20 mg/kg) for another three weeks. Depressive-like behaviors were assessed by sucrose preference test, forced swimming test, and tail suspension test. Microglial phenotypes were assessed in terms of morphological features and cytokine profiles; inflammasome activity, in terms of levels of complexes containing NLRP3, apoptosis-associated speck-like protein containing CARD (ASC) and caspase-1; and neurogenesis, in terms of numbers of proliferating, differentiating, and mature neurons identified by immunostaining.
Results: GRg1 reduced abnormal animal behaviors caused by CMS, such as anhedonia and desperate behaviors, without affecting locomotor behaviors. GRg1 also reduced the number of ASC-specks, implying inhibition of inflammasome activation, which was associated with weaker activation of pro-inflammatory microglia. At the same time, GRg1 rescued impairment of hippocampal neurogenesis in vivo and in vitro, which correlated with modulation of microglial phenotypes.
Conclusion: GRg1 appears to exert antidepressant effects by preventing stress from activating the NLRP3 inflammasome in microglia, promoting a proneurogenic phenotype and allowing adult hippocampal neurogenesis.
Early detection of Chikungunya virus utilizing the Surface Plasmon Resonance comprising of Silver-Silicon-PtSe 2 Multi-Layer Structure
Authors: Singh Thangjam Iboyaima , Singh Pawan , Karki Bhishma 
Published: March 2023

Abstract
The sensing performance parameters of the SPR sensors are sensitivity, detection accuracy, figure of merit (FOM) and full width half maximum (FWHM), and it has been discussed with Refractive index of analyte 1.33, 1.35, 1.38 and 1.39. In this, we proposed a multilayer structure comprising nano films of Ag, Silicon, PtSe2 for the early diagnosis of chikungunya virus. The suggested sensor structure consists of BK7 (Borosilicate Crown) coupling prism over which the nano film of silver metal is present. The layer thicknesses and the number of PtSe2 sheets are optimized for the high performance. At the operating wavelength of 633 nm, a Kretschmann based SPR sensor has been proposed which gives highest sensitivity of 287.3 Deg/RIU. The principal of attenuated total reflection has been employed for the performance analysis of the sensor.
TNES: Terrain Traversability Mapping, Navigation and Excavation System for Autonomous Excavators on Worksite
Authors: Guan Tianrui , He Zhenpeng , Song Ruitao , Manocha Dinesh , Zhang Liangjun 
Published: March 2023

Abstract
We present a terrain traversability mapping and navigation system (TNS) for autonomous excavator applications in an unstructured environment. We use an efficient approach to extract terrain features from RGB images and 3D point clouds and incorporate them into a global map for planning and navigation. Our system can adapt to changing environments and update the terrain information in real-time. Moreover, we present a novel dataset, the Complex Worksite Terrain (CWT) dataset, which consists of RGB images from construction sites with seven categories based on navigability. Our novel algorithms improve the mapping accuracy over previous methods by 4.17 - 30.48% and reduce MSE on the traversability map by 13.8 - 71.4%. We have combined our mapping approach with planning and control modules in an autonomous excavator navigation system and observe 49.3% improvement in the overall success rate. Based on TNS, we demonstrate the first autonomous excavator that can navigate through unstructured environments consisting of deep pits, steep hills, rock piles, and other complex terrain features. In addition, we combine the proposed TNS with the Autonomous Excavation System (AES), and deploy the new pipeline, TNES, on a more complex construction site. With minimum human intervention, we demonstrate autonomous navigation capability with simple excavation tasks.
Patterns in suicide by marital status in Hong Kong, 2002–2020: Is marriage still a protective factor against suicide?
Authors: Chen Junyou , Lui Ingrid D. , Hsu Yu Cheng , Yip Paul S. F. 
Published: March 2023

Abstract
Purpose:
Marriage has long been considered protective against suicide, but shifting social norms since 2000 in Hong Kong raise doubts regarding whether this is still the case. This study investigates the changing association between suicide and marital status in Hong Kong between 2002 and 2020.
Methods:
Suicide death case reports issued between January 1, 2002 and December 31, 2020 were obtained from the Hong Kong Coroner’s Court. Suicide rates were calculated for each year in the study period by gender, age group, and marital status (married, never-married, widowed, divorced/separated). Suicide risk ratios for each marital status cohort by gender and age group, as well as interactions between year and marital status, were estimated using Poisson regression models.
Results:
Suicide risk decreased significantly over time for men and women of all ages. People who were never-married, or divorced/separated, had significantly higher suicide risks than their married counterparts. Increasing suicide risks over time were observed for never-married men aged between 20 and 49 years, never-married women aged 35–49 years, and divorced/separated men aged 20–34 years. Widowed men and women of any age had higher suicide risks compared with previous studies in Hong Kong.
Conclusion:
Despite rapidly changing social contexts in Hong Kong during the study period, marriage remains a strong protective factor against suicide for men and women of all ages. The protective effect is particularly evident for younger people. Increasing suicide rates for divorced/separated, never-married, or widowed people suggest that they may require more psychosocial support.
Identification and validation of the pyroptosis-related genes signature based on immune microenvironment and molecular heterogeneity in prostate adenocarcinoma
Authors: Liang Linghui , Tao Hengtao , Lu Hongcheng , Wu Qikai , Xu Yuxin , Zhouteng Yihui , Wen Jianxiang , Zhao Yuxin , Cheng Gong , Hua Lixin , Zhao Ruizhe 
Published: March 2023

Abstract
Background: Pyroptosis may affect cancer progression by regulating the tumor microenvironment (TME) and biological function of cancer cells. The relationship between pyroptosis-related genes (PRGs) and prostate adenocarcinoma (PRAD) and its TME is unclear.
Method: In our study, we carried out an overall bioinformatics analysis to build a prognostic PRGs model based on TME and molecular heterogeneity and external validation, then verified the relationship between PRGs and PRAD cells through cell experiments. The relationship between PRGs and tumor-immune cells, immune pathways, immune infiltration, cell-cell communication, genomic alteration tumor mutation burden, microsatellite-instability and drug sensitivity were analyzed.
Results: A total of 36 PRGs were up- or down-regulated in PRAD. Functional enrichment analysis indicated that 33 PRGs were mostly involved in Salmonella infection, apoptosis and some signaling pathways (NOD-like receptor, C-type lectin receptor, AGE-RAGE, Cytosolic DNA-sensing, TNF and p53). We identified five prognostic genes (CHMP4C, PLGG1, TP53, GSDMB and PJVK) and constructed a PRGs model to predict progression free survival (PFS) in PRAD patients with high accuracy. And, it was verified with an external database. We found that there was a marked correlation between prognostic PRGs and immune cells, immune pathway, immune cell infiltration, tumor mutation burden and microsatellite instability. Finally, we increased the level of pyroptosis by LPS and established an RNA interference cell line. It was found that the protein expression of NT-GSDMD decreased. Meanwhile, knocking out the above genes affected their promotion of the proliferation of PRAD cells. The above experiments further showed that the five genes were indeed related to pyroptosis.
Conclusion: We established PRGs signatures based on immune microenvironment and molecular heterogeneity through public data and verified them through external data and cell experiments. Our results might help to better understand the impact of proptosis on the progress of PRAD, and provided a new direction for the treatment of PRAD patients.
A simplified RHSS iteration method for saddle point problems
Authors: bai yuqin 
Published: March 2023

Abstract
Recently, Bai and Benzi [Regularized HSS iteration methods for saddlepoint linear systems, Bit Numer. Math., 57 (2017) 287-311] have presented a class of regularized Hermitian and skew-Hermitian splitting methods to solve saddle point problems. In this paper, we establish a simplified RHSS (SRHSS) preconditioner which is much closer to the saddle point matrix than the RHSS preconditioner. We prove the convergence of the proposed method (SRHSS) under suitable restrictions on the iteration parameters. We also study the spectral properties of the preconditioned matrix and eigenvector distribution. Lastly, numerical experiments are carried out and experimental results show that the proposed SRHSS preconditoner method is feasible and effective.
AMSC : 65F10; 65F15; 65F50
Human Germ Cell Specification via Combinatorial Expression of Prioritized Transcription Factors
Authors: Kramme Christian , Smela Merrick , Wolf Bennett , Fortuna Patrick , Brixi Garyk , Zang Tian-Lai , Vincoff Sophia , Palepu Kalyan , Koseki Sabrina , Bhat Suhaas , Dong Edward , Adams Jessica , Kohman Richie , Liu Songlei , Kobayashi Mutsumi , Shioda Toshihiro , Church George , Chatterjee Pranam 
Published: March 2023

Abstract
The generation of germline cell types from human induced pluripotent stem cells (hiPSCs) represents a key milestone toward in vitro gametogenesis, which has the potential to transform reproductive medicine. Methods to recapitulate germline cell specification in vitro have relied on extensive, long term culture methods, the most notable of which is a four-month culture protocol employing xenogeneic reconstituted ovaries with mouse embryonic ovarian somatic cells. Recently, transcription factor (TF)-based methods have demonstrated the feasibility of exogenous factor expression to directly differentiate hiPSCs into cell types of interest, including various ovarian cell types. The protocols leveraged in these studies, however, utilize more local methods of factor selection, such as basic differential gene expression analysis, and lower-throughput screening strategies via iterative testing of a small set of TFs. In this work, we integrate our recently-described, more globally-representative graph theory and highly-parallelized screening protocols to globally identify and screen 46 oogenesis-regulating TFs for their role in human germline formation. We identify DLX5, HHEX, and FIGLA whose individual overexpression enhances hPGCLC formation from hiPSCs, as well as an additional set of three TFs, ZNF281, LHX8, and SOHLH1, whose combinatorial overexpression drives DDX4+ germ cell formation from hiPSCs. In contrast to previous methods, our protocol employs a simple four-day, feeder-free monolayer culture condition. We characterize these TF-based germ cells via gene expression analyses, and demonstrate their broad similarity to in vivo and in vitro-derived germ cells. Together, these results identify new regulatory factors that enhance in vitro human germ cell specification and further establish unique computational and experimental tools for human in vitro oogenesis research.
Full Band Incorporation in Ab-initio Simulations of Two-dimensional Semiconductor Based Devices
Authors: Duflou Rutger , Houssa Michel , Afzalian Aryan 
Published: March 2023

Abstract
Quantum transport simulations based on the Non-Equilibrium Green’s Function formalism require accurate integration of the charges in the system. We demonstrate our implementation of a full-band integration scheme, which automatically incorporates electronic screening effects and is predicted to incorporate interface charges more correctly than the simpler excess charge approach. We show that for single doping type purely semiconducting devices, the two approaches are equivalent. We also highlight the influence of using the full-band approach for devices containing metals.
Exploring Perspectives on Agroecological Transition in Scotland with Critical Systems Heuristics
Authors: Hutcheson Matthew , Morton Alec , Blair Shona 
Published: March 2023

Abstract
Critical systems heuristics (CSH) is a framework that facilitates reflective practice in exploring and solving complex management problems. Despite its versatility, CSH has so far been under-utilised in addressing problems concerning the environment and sustainability. We apply CSH to explore perspectives on agroecological transition in Scotland. In interviews with 10 farmers, agricultural professionals, and researchers, we demonstrate the utility of boundary critique as a practice for unpacking the judgements that underpin perspectives on Scottish farming. Moreover, we derive a series of practical insights and recommendations to progress agroecological transition in Scotland, including: support for a greater diversity of farming systems; action across the entire food system to avoid ‘lock-ins’; improved tools to measure farming outcomes; and nuanced and precise conversations regarding the nature and purpose of agroecological farming. In doing so, we demonstrate that in the context of sustainable transitions, CSH need not be limited to a retrospective analytical framework, but may guide reflective practice throughout the entire research process.
New analytical wave solutions to the M-fractional Kuralay-II equations based on three distinct schemes
Authors: Raheel M. , Zafar Asim , Ali M. R. , Myrzakulova Zhaidary , Bekir Ahmet , Myrzakulov Ratbay 
Published: March 2023

Abstract
This article is about, the new analytical wave solutions of Kuralay-II equations (K-IIAE and K-IIBE) along new definition of derivative have been explored. For this purpose, expa function, extended sinh-Gordon equation expansion scheme and generalized Kudryashov schemes have been utilized. The resulting solutions are dark, bright, dark-bright, periodic, singular and other kinds of solitons. These results are obtained and also verified by Mathematica tool. Our gained solutions are newer than the present solutions in the literature. The gained results can also be fruitful for the development of model in future. The schemes used in this research are effective, easy and reliable to handle the other fractional non-linear partial differential equations (FNLPDEs).
Novel Scheme for Defining the Clinical Implications of TP53 Mutations in Myeloid Neoplasia
Authors: Bahaj Waled , Kewan Tariq , Gurnari Carmelo , Durmaz Arda , Ponvilawan Ben , Pandit Ishani , Kubota Yasuo , Ogbue Olisaemeka D. , Zawit Misam , Madanat Yazan , Bat Taha , Balasubramanian Suresh K. , Awada Hussein , Ahmed Ramsha , Mori Minako , Meggendorfer Manja , Haferlach Torsten , Visconte Valeria , Maciejewski Jaroslaw P. 
Published: March 2023

Abstract
Background: TP53 mutations (TP53MT) occur in diverse genomic configurations. Particularly, biallelic inactivation is associated with poor overall survival in cancer. Lesions affecting only one allele might not be directly leukemogenic, questioning the presence of cryptic biallelic subclones in cases with dismal prognosis.
Methods: We have collected clinical and molecular data of 7400 patients with myeloid neoplasms and applied a novel model to properly resolve the allelic configuration of TP53MT and assess prognosis more precisely.
Results: Overall, TP53MT were found in 1010 patients. Following the traditional criteria, 36% of cases were classified as single hits while 64% exhibited double hits genomic configuration. Using a newly developed molecular algorithm, we found that 579 (57%) patients had unequivocally biallelic, 239 (24%) likely contained biallelic, and 192 (19%) had most likely monoallelic TP53MT. Such classification was further substantiated by a survival-based model built after re-categorization. Among cases traditionally considered monoallelic, the overall survival of those with probable monoallelic mutations was similar to the one of wild-type patients and was better than that of patients with a biallelic configuration. As a result, patients with certain biallelic hits, regardless of the disease subtype (AML or MDS), had a similar prognosis. Similar results were observed when the model was applied to an external cohort. These results were recapitulated by single-cell DNA studies, which unveiled the biallelic nature of previously considered monoallelic cases.
Conclusion: Our novel approach more accurately resolves TP53 genomic configuration and uncovers genetic mosaicism for the use in the clinical setting to improve prognostic evaluation.
Personalization of Industrial Human-Robot Communication through Domain Adaptation based on User Feedback
Authors: Mukherjee Debasmita , Hong Jayden , Vats Haripriya , Bae Sooyeon , Najjaran Homayoun 
Published: March 2023

Abstract
Achieving safe collaboration between humans and robots in an industrial work-cell requires effective communication. This can be achieved through a robot perception system developed using data-driven machine learning. The challenge for human-robot communication is the availability of extensive, labelled datasets for training. Due to the variations in human behaviour and the impact of environmental conditions on the performance of perception models, models trained on standard, publicly available datasets fail to generalize well to domain and application-specific scenarios. Thus, model personalization involving the adaptation of such models to the individual humans involved in the task in the given environment would lead to better model performance. A novel framework is presented that leverages robust modes of communication and gathers feedback from the human partner to auto-label the mode with the sparse dataset. The strength of the contribution lies in using in-commensurable multimodes of inputs for personalizing models with user-specific data. The personalization through feedback-enabled human-robot communication (PF-HRCom) framework is implemented on the use of facial expression recognition as a safety feature to ensure that the human partner is engaged in the collaborative task with the robot. Additionally, PF-HRCom has been applied to a real-time human-robot handover task with a robotic manipulator. The perception module of the manipulator adapts to the user's facial expressions and personalizes the model using feedback. Having said that, the framework is applicable to other combinations of multimodal inputs in human-robot collaboration applications.