bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional stemness-related genes revealed by single-cell profiling of naïve and stimulated human CD34 + cells from CB and mPB
Authors: Dong Guoyi , Xu Xiaojing , Li Yue , Ouyang Wenjie , Zhao Weihua , Gu Ying , Li Jie , Liu Tianbin , Zeng Xinru , Zou Huilin , Wang Shuguang , Liu Sixi , Sun Hai-Xi , Liu Chao 
Published: April 2022

Abstract
Hematopoietic stem cells (HSCs) from different sources show varied repopulating capacity, and HSCs lose their stemness after long-time ex vivo culture. However, the underlying mechanisms of the stemness differences because of the cell sources and the culture stimulation are not fully understood. Here, we applied single-cell RNA-seq (scRNA-seq) to analyze the naïve and stimulated human CD34+ cells from cord blood (CB) and (mPB). We collected over 16,000 single-cell data to construct a comprehensive trajectory inference map and characterized the HSC population on the hierarchy top, which is under quiescent state. Then we compared HSCs in CB to those in mPB and HSCs of naïve samples to those of cultured samples, and identified stemness-related genes (SRGs) associated with culture time (CT-SRGs) and cell source (CS-SRGs), respectively. Interestingly, CT-SRGs and CS-SRGs share genes enriched in the signaling pathways such as mRNA catabolic process, Translational initiation, Ribonucleoprotein complex biogenesis and Cotranslational protein targeting to membrane, suggesting dynamic protein translation and processing may be a common requirement for stemness maintenance. Meanwhile, CT-SRGs are enriched in pathways involved in glucocorticoid and corticosteroid response that affect HSCs homing and engraftment. In contrast, CS-SRGs specifically contain genes related purine and ATP metabolic process which is important to initiate hematopoiesis. Finally, we presented an application through a small-scale drug screening using Connectivity Map (CMap) against CT-SRGs and found a small molecule cucurbitacin I, targeting STAT3/JAK2, can efficiently expand HSCs ex vivo while maintaining its stemness. These results indicate SRGs revealed by scRNA-seq can provide helpful insights to understand the stemness differences under diverse circumstances, and CT-SRGs can be a valuable database to identify candidates enhancing functional HSC expansion during ex vivo culture.
Top-k Spatial Keyword Query Based on Reachability
Authors: Li Yanhong , Ren Jiayu , Luo Changyin , Feng Yu , Du Xiaokun , Li Jianjun 
Published: April 2022

Abstract
Spatial keyword query (SKQ) is a research hotspot in the field of spatio-temporal databases. The spatial proximity and text similarity between objects and the query are considered during query processing. In order to better meet the personal-ized needs of users and improve the accuracy and real-time of spatial keyword query results, we propose the Top-k spatial keyword query based on reachability (RSKQ). Such query returns the k best objects that satisfy the reachability and query keyword constraints according to a comprehensive score, which considers the spatial proximity, text similarity, and accessibility between the query and the object. Firstly, an efficient index called SRTR-tree is proposed, which can intelligently organize road network structure information, keywords and location information of spatio-textual objects, and vehicle trajectory information. Moreover , several pruning techniques are designed to prune massive objects irrelevant to the query according to accessibility, spatial proximity, and textual similarity, so as to speed up query processing. Based on the SRTR-tree and pruning strategies, a non-trivial basic algorithm is proposed to process RSKQ queries. In addition, we introduce a more efficient optimized algorithm to improve the efficiency of query processing. Finally, a series of experimental evaluations are carried out to show the effectiveness of our methods.
WITHDRAWN: A prospective study of the use of a reverse puncture device and specimen eversion of the rectum for resection in total laparoscopic low rectal cancer resection
Authors: Qian Long , Huang Xiaoxu , Xu Li , Chen Hao , Cao Tingting , Wang Song , Luo Can , Xia Yabin 
Published: April 2022

Abstract
Purpose: To investigate the safety and efficacy of a reverse puncture device and specimen eversion of the rectum for resection in total laparoscopic proctectomy. Methods: In a prospective study from August 2019 to March 2021, 40 patients underwent a procedure with a reverse puncture device and specimen eversion of the rectum for resection in total laparoscopic low rectal cancer resection, that is, natural orifice specimen extraction surgery (the NOSES group). Forty patients in the control group were treated with conventional laparoscopic radical resection of low rectal cancer (the LAP group).Intraoperative- and postoperative-related indicators, recovery, inflammatory factors, quality of life and mental health were compared. Results: All operations were successfully completed . Compared with the LAP group, the NOSES group had better short-term outcomes, such as eating time, postoperative pain, and especially postoperative incision-related complications. At the same time, postoperative inflammatory factor levels, psychological trauma, life-related anxiety and depression scores, and patient’s quality of life were better than those of the LAP group. Conclusions: The application of a reverse puncture device and specimen eversion of the rectum for resection in total laparoscopic low rectal cancer resection is a technically feasible and safe approach that has a short-term curative effect.Chinese Clinilical Registry:Registration number: ChiCTR2100048061（2021.6.29）
Spatial activation of autophagy in human placenta-related tissue during labor: a possible mechanism for labor onset
Authors: Shang Jing , Wang Zhijian , Huang Yingying , Wu Yuyu , Jin Jin 
Published: April 2022

Abstract
Introduction: The study aimed to explore the mechanism of labor onset via investigation on autophagy in placental tissues of normal pregnant women. Methods: Placentas at the first, second, and third months of gestation and membrane samples from uniparous women without signs of uterine contractions (gestation group) were collected as well as placentas and membranes from uniparous women (parturition group) who underwent vaginal delivery (parturition-initiation group; PI group) or cesarean sections (parturition-non-initiation group; PNI group) without any medical complications. Autophagosomes were observed by transmission electron microscopy (TEM). Immunofluorescence and western blotting (WB) were used to quantify the protein levels of autophagy markers LC3A and LC3B in placenta and fetal membrane. TEM, immunohistochemistry (IHC) and WB were used to compare the autophagy in different parts of placenta and fetal membrane in the PI and PNI groups. Results: TEM and IHC results showed that the number of autophagosomes and autophagolysosomes increased in the gestation group, and WB results suggested increased LC3B/A ratio between the placenta and the fetal membrane in gestation group. Autophagy in the maternal side of placenta in PI group was significantly increased, and the autophagy level in the placenta and fetal membrane near rupture became higher in both PI and PNI groups. Discussion: Autophagy can occur in placenta and fetal membrane, with its activity higher in the initiation of labor, indicating its role during labor.
Nischarin expression may have differing roles in male and female melanoma patients
Authors: Ostojić Marija , Jevrić Marko , Mitrović-Ajtić Olivera , Tanić Miljana , Čavić Milena , Milovanović Zorka , Srdić-Ra Tatjana , Grahovac Jelena 
Published: April 2022

Abstract
PurposeMelanoma is the deadliest form of skin cancer. Despite the advancements in targeted and immunotherapies, metastatic melanoma patients still have poor prognosis, and there is an urgent need for novel treatment modalities. Nischarin (NISCH) is a druggable scaffolding protein shown to be a tumor suppressor in breast cancer through regulation of cancer cell survival, motility and invasion. The aim of this study was to determine NISCH expression, prognostic value, and potential role in melanoma progression.MethodsNISCH expression and regulation mechanisms were examined in publicly available data sets and on a retrospective cohort of melanoma patient tissue samples from our institution using RT-qPCR and MSP. Gene set enrichment analysis (GSEA) was used to examine the potential role of NISCH in melanoma. Tumor immune profiles were investigated using TIMER2.0 website.ResultsNISCH was expressed at both mRNA and protein level, and its expression was decreased in tumors compared to skin and nevi. Lower expression could be attributed to the presence of microdeletions and hyper-methylation of the NISCH promoter in the tumor tissue. NISCH expression in primary melanoma had favorable prognostic value for females, but high NISCH expression meant worse prognosis for males. GSEA indicated significant sex-related disparities in predicted NISCH-associated signaling pathways in melanoma. High NISCH expression in males was associated with higher content of B cells in primary tumors. ConclusionsOur data indicate that levels of NISCH expression may have an impact on melanoma progression, but that its function is different in male and female patients. Since NISCH was previously investigated only in female cancers, our findings open up a new avenue of investigation.
Effectiveness of pembrolizumab in trial-ineligible patients with metastatic urothelial carcinoma
Authors: Fukuokaya Wataru , Yanagisawa Takafumi , Hashimoto Masaki , Yamamoto Shutaro , Koike Yuhei , Imai Yu , Iwatani Kosuke , Onuma Hajime , Ito Kagenori , Urabe Fumihiko , Tsuzuki Shunsuke , Kimura Shoji , Miki Jun , Oyama Yu , Abe Hirokazu , Kimura Takahiro 
Published: April 2022

Abstract
BackgroundThe KEYNOTE-045 trial showed that pembrolizumab therapy improved the survival of patients with advanced urothelial carcinoma (UC). However, its effectiveness in trial-ineligible patients remains unclear.Materials and MethodsWe conducted a multicenter retrospective study to evaluate the effectiveness of pembrolizumab in patients with metastatic UC who were trial-ineligible. The data of 222 consecutive patients with platinum-treated metastatic UC who received pembrolizumab as second-line therapy were analyzed. Trial eligibility was assessed using the KEYNOTE-045 criteria. Inverse probability weighting (IPW) was used to balance patient characteristics. Overall survival (OS) and progression-free survival (PFS) were examined using the IPW-adjusted Kaplan-Meier method. IPW-adjusted restricted mean survival times (RMSTs) were compared between trial-ineligible and trial-eligible patients.ResultsOne hundred thirty-three patients (59.9%) were classified as trial-ineligible according to the KEYNOTE-045 criteria. Patients who did not develop progression following chemotherapy were the most common reason for trial protocol violation (N = 58 [26.1%]). The trial-ineligible patients showed similar RMST for PFS (difference: 2.4 months, 95% CI: -3.2 to 8.0, P = 0.40) and OS (difference: 1.7 months, 95% CI: -8.3 to 4.9, P = 0.60) compared with the trial-eligible patients. Furthermore, patients who were trial-ineligible because of comorbidities, poor performance status, or impaired liver or kidney function also had similar RMST for PFS and OS compared with those who were trial-eligible.ConclusionsThis study suggests that the effectiveness of pembrolizumab may be retained in trial-ineligible patients with platinum-treated metastatic UC. Expanding trial eligibility criteria for these patients may be beneficial.
Livelihood zone-based perception and adaptation strategies of rural households’ to rainfall and temperature variability in the Northeastern Highlands of Ethiopia
Authors: Mekonen Abebe Arega 
Published: April 2022

Abstract
BackgroundAppraising of rural households’ perception and observed rainfall and temperature variability is a vital stage in devising operational adaptation strategies. Therefore, this study aims to examine the rural households’ perception and adaptation strategies to climate variability induced vulnerability in Northeastern Highlands of Ethiopia across the livelihood zones. A total of 361 sample households were selected using proportional probability sampling techniques. Data sources such as survey questionnaire, interview and focus group discussion were used to collect the necessary information. Historical rainfall and temperature data from CenTrends Great Horn of Africa v1 and CRU_TS 4.0 were also used. Precipitation Concentration Index (PCI) and Standardized Anomaly Index (SAI) model were employed to analyze the data. Descriptive statistical tools for frequency and percentage were also used. ResultsThe result showed that rainfall and temperature variability induced vulnerability were well perceived by rural households’ though varied across the livelihood zones. This was also similarly shown by Precipitation concentration index and standardized anomaly index at the annual, Kiremt and Belg seasons in the observed rainfall and temperature information. In response to rainfall and temperature variability induced vulnerability, rural households have engaged in a range of adaptation measures. These include the different biophysical soil and water conservation measures; crop and livestock diversification by planting and rearing variety of crop and livestock; changing crop planting and harvesting dates according to the changing pattern of rainfall. However, the executed adaptation strategies are insufficient as compared to the imposed vulnerability challenges by climate variability. There is also a great gap between rural households’ climate variability perception and level of actual adaptation response measures. Because the result revealed that the presence of various impediments deterred the available and implemented adaptation response measures to climate variability induced vulnerability. ConclusionEven if rural households perceiving and practicing adaptation measures to climate variability induced vulnerability, still different impediments weaken the actual adaptation responses. Therefore, these demands the government, communities, and other stakeholders at different level in designing integrated and distinct livelihood zone-based adaptation strategies to reduce households’ crop-livestock mixed agriculture from climate calamity vulnerability.
Genome-wide integrated analyses of DNA methylation and gene expression of rainbow trout muscle under variable ploidy and muscle atrophy conditions
Authors: Salem Mohamed , Al-Tobasei Rafet , Ali Ali , Kenney Brett 
Published: April 2022

Abstract
BackgroundRainbow trout is an important cool, freshwater aquaculture species used as a model for biological research. However, the genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. ResultsMethyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1,206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. ConclusionsThis study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates.
On the Seismic Design and Behavior of Automated Rack Supported Warehouses
Authors: Natali Agnese , Morelli Francesco , Salvatore Walter 
Published: April 2022

Abstract
Automated Rack Supported Warehouses (ARSWs), consisting in huge steel buildings offering optimized storage solutions, have been facing a huge diffusion in the last decade, mainly due to the necessity of having bigger and more efficient places to stock and handle goods through automated systems. However, there is not a specific regulatory framework for them, and they are currently being designed adopting the approach used for traditional steel racks. Even if traditional steel racks and ARSWs have several common aspects, there are relevant differences that do not allow to adopt the same design approach, especially for seismic actions. With the aim of highlighting the factors and parameters currently influencing the seismic design and the behaviour of these constructions, and the consequent need of a different design approach, the present paper presents a critical analysis of the seismic design approach currently adopted by technicians and designers. Then, a set of 5 structures designed by 5 of the major European companies specialized in this field is used to perform both the critical analysis of the different design approaches adopted and the assessment of the seismic performance. The results of the seismic assessment highlight the main typical criticalities and the necessity of a novel proper design approach.
Exploring the lncRNA localization landscape within the retinal pigment epithelium under normal and stress conditions
Authors: Kaczynski Tadeusz J. , Au Elizabeth D. , Farkas Michael H. 
Published: April 2022

Abstract
Background:Long noncoding RNAs (lncRNAs) are emerging as a class of genes whose importance has yet to be fully realized. It is becoming clear that the primary function of lncRNAs is to regulate gene expression, and they do so through a variety of mechanisms that are critically tied to their subcellular localization. Although most lncRNAs are poorly understood, mapping lncRNA subcellular localization can provide a foundation for understanding these mechanisms. Results:Here, we present an initial step toward uncovering the localization landscape of lncRNAs in the human retinal pigment epithelium (RPE) using high throughput RNA-Sequencing (RNA-Seq). To do this, we differentiated human induced pluripotent stem cells (iPSCs) into RPE, isolated RNA from nuclear and cytoplasmic fractions, and performed RNA-Seq on both. Furthermore, we investigated lncRNA localization changes that occur in response to oxidative stress. We discovered that, under normal conditions, most lncRNAs are seen in both the nucleus and the cytoplasm to a similar degree, but of the transcripts that are highly enriched in one compartment, far more are nuclear than cytoplasmic. Interestingly, under oxidative stress conditions, we observed an increase in lncRNA localization in both nuclear and cytoplasmic fractions. In addition, we found that nuclear localization was partially attributable to the presence of previously described nuclear retention motifs, while adenosine to inosine (A-to-I) RNA editing appeared to play a very minimal role. Conclusions:Our findings map lncRNA localization in the RPE and provide two avenues for future research: 1) how lncRNAs function in the RPE, and 2) how one environmental factor, in isolation, may alter lncRNA localization and play a potential role in retinal disease pathogenesis.
Learning two-phase microstructure evolution using neural operators and autoencoder architectures
Authors: Karniadakis George , Oommen Vivek , Shukla Khemraj , Goswami Somdatta , Dingreville Remi 
Published: April 2022

Abstract
Phase-field modeling is an effective but computationally expensive method for capturing the mesoscale morphological and microstructure evolution in materials. Hence, fast and generalizable surrogate models are needed to alleviate the cost in computationally taxing processes such as in optimization and design of materials. The intrinsic discontinuous nature of the physical phenomena incurred by the presence of sharp phase boundaries makes the training of the surrogate model cumbersome. We develop a framework that integrates a convolutional autoencoder architecture with a deep neural operator (DeepONet) to learn the dynamic evolution of a two-phase mixture. We utilize the convolutional autoencoder to provide a compact representation of the microstructure data in a low-dimensional latent space. DeepONet, which consists of two sub-networks, one for encoding the input function at a fixed number of sensors locations (branch net) and another for encoding the locations for the output functions (trunk net), learns the mesoscale dynamics of the microstructure evolution from the autoencoder latent space. The decoder part of the convolutional autoencoder then reconstructs the time-evolved microstructure from the DeepONet predictions. The result is an efficient and accurate accelerated phase-field framework that is robust to noisy inputs.
Optimization of hot-air drying process parameters of wheat by the response surface method combined with NSGA-Ⅱ algorithm
Authors: Sun Tongsheng , Ling Feng 
Published: April 2022

Abstract
In order to reduce the energy consumption and accelerate the drying rate in the process of hot-air drying wheat, and provide a theoretical basis for the wheat drying equipment and process. This paper designed hot-air drying experiments with hot air temperature, hot air speed and loading capacity as the influencing factors and drying rate and energy consumption as the targets according to Box-Behnken response surface design theory. The factors in the experiments were analyzed by a comprehensive scoring model. The effects of hot air temperature, hot air speed and loading quantity on drying rate, energy consumption and comprehensive score were investigated by using grey relation analysis theory. The multiple non-linear regression method was used to fit the functional relationships between the influencing factors and the targets. The NSGA-Ⅱ algorithm was used for multi-objective optimization of the targets to obtain the best hot-air drying conditions. The results demonstrated that the three factors that determine the drying rate and energy consumption are in order: hot air temperature, hot air speed, and loading capacity. The optimal process parameters for hot-air drying wheat are: hot air temperature 53.4°C, hot air speed 1.80 m/s, loading capacity 1.40 kg/m2.