bluuebunny/crossref_metadata_2025_split huggingface dataset:
ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction
Authors: Chen Kai , Zhu Xiaodong , Hao Lei , Wang Jiahao , Liu Zhen , Liu Yuanning 
Published: December 2022

Abstract
Background: Although research on non-coding RNAs (ncRNAs) is a hot topic in life sciences, the functions of numerous ncRNAs remain unclear. In recent years,researchers have found that ncRNAs of the same family have similar functions,therefore, it is important to accurately predict ncRNAs families to identify their functions. There are several methods available to solve the prediction problem of ncRNAs family, whose main ideas can be divided into two categories, including prediction based on the secondary structure features of ncRNAs, and prediction according to sequence features of ncRNAs. The first type of prediction method requires a complicated process and has a low accuracy in obtaining the secondary structure of ncRNAs, while the second type of method has a simple prediction process and a high accuracy, but there is still room for improvement. The existing methods for ncRNAs family prediction are associated with problems such ascomplicated prediction processes and low accuracy, in this regard, it is necessary to propose a new method to predict the ncRNAs family more perfectly.
Results: A deep learning model-based method, ncDENSE, was proposed in this study, which predicted ncRNAs families by extracting ncRNAs sequence features.The bases in ncRNAs sequences were encoded by one-hot coding and later fed into an ensemble deep learning model, which contained the dynamic bi-directional gated recurrent unit (Bi-GRU), the dense convolutional network(DenseNet), and the Attention Mechanism (AM). To be specific, dynamic Bi-GRU was used to extract contextual feature information and capture long-term dependencies of ncRNAs sequences. AM was employed to assign different weights to features extracted by Bi-GRU and focused the attention on information with greater weights. Whereas DenseNet was adopted to extract local feature information of ncRNAs sequences and classify them by the full connection layer. According to our results, the ncDENSE method improved the Accuracy, Sensitivity, Precision, F-score, and MCC by 2.08%, 2.33%, 2.14%,2.16%, and 2.39%, respectively, compared with the suboptimal method.
Conclusions: Overall, the ncDENSE method proposed in this paper extracts sequence features of ncRNAs by dynamic Bi-GRU and DenseNet and improves the accuracy in predicting ncRNAs family and other data .
Determinants and Economic Consequences of Self Reported Illness Among Indian Construction Workers – A Multicentre Study
Authors: Soundararajan Soundarya , Viramgami Ankit , Sheth Ankit , Beerappa Ravichandran , Kalahasthi Ravibabu , Sampathraju Raghavan , Venugopal Dhananjayan , Sarkar Kamalesh , Balachandar Rakesh 
Published: December 2022

Abstract
Background
Construction workers have health hazards inherent to the nature of work and at further risk for poverty due to poor living conditions. We investigated perceived illness among workers and family members in the past year and the economic consequences of morbidities in terms of Catastrophic Health Expenditure (CHE).
Methods
In this cross-sectional multicenter study, we recruited construction workers of both sexes from construction sites of two Indian cities. We collected details on illnesses requiring a healthcare visit in the past year, expenditure and related details.
Results
Of 1263 participants recruited, data on illness during the past year were reported by 1110 participants; 37% (n = 302) reported illness among themselves or family members requiring a healthcare visit. We constructed a regression model to ascertain demographic and living condition determinants of illness (R^2 = 54%, p < 0.001). We observed kitchen in the living space (OR = 1.87), and using unhygienic smoky cooking fuels (OR = 1.87) were associated with an increased likelihood of reporting illness. More than a quarter of those who reported illness incurred CHE. Both CHE incurred and non-incurred groups displayed similar trends of health-seeking behaviors.
Conclusion
We conclude that both prevalence of self reported illness and CHE were relatively high, especially among the migratory group. Our results demonstrate that poor living conditions add to the burden of morbidity in construction workers and families. Providing medical coverage for this population vulnerable to economic hardships, engaging and educating about affordable healthcare are important future steps to prevent further economic consequences.
Development and Validation of 105 SNP Markers in Chionodraco rastrospinosus
Authors: Yu Yewei , Wang Congcong , Liu Yang , Zhu Guoping 
Published: December 2022

Abstract
Ocellated icefish (Chionodraco rastrospinosus, C. rastrospinosu), is played an essential role in the Antarctic food web, which is mainly distributed in the deep waters of the Southern Ocean. The abundance of this species has been drastically reduced due to various impacts, including overfishing and climate change. Therefore, in order to sustainably exploit and protect this species, it is urgent to understand the state of its population resources. However, the population genetics and effective molecular markers of this species have not been reported. In this study, 105 novel single nucleotide polymorphism (SNP) markers were developed using double digest restriction site-associated DNA sequencing (ddRAD-Seq). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0 to 1 and 0.2188 to 0.5, respectively. The polymorphism information content (PIC) value ranged from 0.194824 to 0.375. After Bonferroni correction, none of the loci deviated significantly from Hardy-Weinberg equilibrium (p ＞0.05). The development of these SNP markers will be useful for the genetic analysis and scientific management of C. rastrospinosus.
Effect of deep gray matter atrophy on information processing speed in early relapsing- remitting multiple sclerosis
Authors: Naghavi Saba , Ashtari Fereshteh , Adibi Iman , Shaygannejad Vahid , Ramezani Neda , Pourmohammadi Ahmad , Davanian Fariba , Karimi Zahra , Khaligh-Razavi Seyed-Mahdi , Sanayei Mehdi 
Published: December 2022

Abstract
Background. Cognitive dysfunction, including Information processing speed (IPS), is relatively common in multiple sclerosis(MS). IPS deficits have profound effects on several aspects of patients’ life. Previous studies showed that deep gray matter atrophy is highly correlated with overall cognitive impairment in MS. However, the effect of deep gray matter atrophy on IPS deficits is not well understood. In this study, we evaluated the effects of deep gray matter volume changes on IPS in early relapse-remitting MS (RRMS) patients compared to healthy control.
Methods. In this case-control study, we enrolled 63 RRMS patients and 36 healthy controls. All patients were diagnosed within 6 years. IPS was evaluated using the Integrated Cognitive Assessment (ICA) test. We also performed a 1.5T MRI to evaluate deep gray matter structures.
Results. RRMS patients had lower accuracy in the ICA test (p = .01). However, the reaction time did not significantly differ between RRMS and control groups (p = .6). Thalamus volume was significantly lower in the RRMS group with impaired IPS compared to the RRMS with normal IPS and control groups (p < 10-4). Other deep gray matter structures were not significantly different between the RRMS with impaired IPS group and the RRMS with normal IPS group.
Conclusion. MS patients are impaired in IPS even in the early stages of the disease. Thalamic atrophy affected IPS in these patients, however atrophy in other deep gray matter structures, including caudate, putamen, globus pallidus, hippocampus, amygdala, accumbens, and cerebellum, were not significantly correlated with IPS impairment in early RRMS.
Changes in maternal heart rate in delayed post-partum preeclampsia
Authors: Ravid Dorit , Ovadia Michal , Asali Aula , Nisim Shlomo , Gershnabel Sivan Farladansky , Biron-Shental Tal , Weitzner Omer 
Published: December 2022

Abstract
Background
To investigate the difference of maternal heart rate in women with delayed onset postpartum preeclampsia as compared to healthy controls.
Methods
The medical files of all women who were readmitted with delayed onset postpartum preeclampsia during 2014–2020 were reviewed. Data on maternal physiological characteristics were compared to healthy control group of women at the same post-partum day, with uncomplicated pregnancies.
Results
Included 45 women with the diagnosis of delayed onset of preeclampsia at 6.3 ± 2.86 post-partum day. As compared to controls (n = 49), women with delayed post-partum were older, 34.6 ± 5.4 vs. 32.3 ± 4.7 years, p = 0.003. There were no differences between groups regarding maternal gravidity, parity, BMI (kg/m2) or Hb level at delivery day. Women with delayed post-partum preeclampsia had lower mean pulse rate as compared to controls, 58 ± 15 bpm vs. 83 ± 11.6 bpm, respectively, P < 0.0001. Only 17% of the women in the delayed onset group had pulse rate above 70 bpm as compared to 83% in the control group.
Conclusions
Maternal low heart rate in cases with delayed onset of post-partum preeclampsia is an important clinical characteristic that may reflect baroreceptors response to maternal hypertension.
Activation-induced cytidine deaminase, an antibody diversification enzyme, interacts with chromatin modifier UBN1 in B-cells
Authors: Jaiswal Ankit , Roy Rajarshi , Tamarkar Anubhav , Singh Amit Kumar , Kar Parimal , Kodgire Prashant 
Published: December 2022

Abstract
Activation-induced cytidine deaminase (AID) is the key mediator of antibody diversification in activated B-cells by the process of somatic hypermutation (SHM) and class switch recombination (CSR). Targeting of AID to the Ig genes requires transcription (initiation and elongation), and enhancers as well as its interaction with numerous factors. Furthermore, the HIRA chaperone complex, a regulator of chromatin architecture, is indispensable for SHM. The HIRA chaperone complex consists of UBN1, ASF1a, HIRA, and CABIN1 that deposit H3.3 onto the DNA, which is a hallmark of SHM. We explored whether UBN1 interacts with AID using computational as well as in-vitro experiments. Interestingly, our in-silico studies, such as molecular docking and molecular dynamics simulation results, predict that AID interacts with UBN1. Subsequent co-immunoprecipitation experiments established interactions between UBN1 and AID inside B-cells. Additionally, a double immunofluorescence assay confirmed that AID and UBN1 were co-localized in the human as well as chicken B-cell lines. Moreover, proximity ligation assay studies validated that AID interacts with UBN1. Ours is the first report on the interaction of genome mutator enzyme AID with UBN1. Nevertheless, the fate of interaction between UBN1 and AID is yet to be explored in the context of SHM or CSR.
Macrophage-derived MMP-9/MMP-2 are closely related to the rupture of the fibrous capsule of hepatocellular carcinoma leading to tumor invasion
Authors: Cui Quanwei , Wang Xuben , Zhang Yongwei , Shen Yiqing , Qian Yeben 
Published: December 2022

Abstract
Background
Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor clinical prognosis. Rupture of the fibrous capsule (FC) is a very important clinical phenomenon in the invasion and metastasis of HCC. FC is mainly composed of type I collagen (COL1A1). However, it is not clear what caused the FC rupture. In this study, we aimed to determine whether the rupture of FC in HCC patients was related to macrophage-derived MMP-9/MMP-2, and their clinical diagnostic value for FC rupture.
Results
By performing immunohistochemical and immunofluorescence staining of ruptured FC and intact FC, the results showed that the ruptured area of FC aggregated a large number of macrophages with MMP-9/MMP-2. Western blot analysis and Quantitative real-time PCR were used to assess the expression of MMP-9/MMP-2 in the ruptured and relatively intact area of FC in ruptured FC patients, and the results revealed a significantly different expression of MMP-9/MMP-2. ELISA experiments show that we could discriminate effectively between ruptured FC and intact FC by MMP-9/MMP-2.
Conclusions
Taken together, macrophage-derived MMP-9/MMP-2 were closely related to the rupture of the FC of HCC and subsequently led to the migration and invasion of the tumor cells into the ruptured area of FC to the para cancer. it is suggested that when performing surgical resection, it is necessary to expand the range of tumor resection for patients with ruptured FC and hence reduce the possibility of recurrence and metastasis in HCC patients.
A study on the spatiotemporal differentiation of typical ecosystem services and influencing factors in the Dongjiang River Basin from 2000 to 2019
Authors: Liu Jie , Chen Dequan , Wu Hui , Liang Xiaojin , Chen XiaoHui , Wang Yingying 
Published: December 2022

Abstract
Monitoring changes in watershed ecosystem services is an important aspect of watershed ecological security assessment and the anchor point for research on watershed ecological protection and economic development. Current research has focused on the assessment of typical ecosystem service functions in watersheds, with relatively little research on influencing factors and their spatio-temporal change impact mechanisms. This paper presents a comprehensive analysis of the spatio-temporal variation mechanisms of ecosystem services and influencing factors in the Dongjiang River Basin(DRB) in China from 2000 to 2019. The results show that the land use structure of DRB has been stable and typical ecosystem services such as water retention, soil and water conservation, and carbon storage are slightly reduced in the past 20 years. The typical ecosystem services of the study area are influenced by topographic factors, climatic factors, and natural socio-economic factors, and are significantly related to precipitation, temperature, elevation, slope, GDP, population, and NDVI. From 2000 to 2019, the influence factors have obvious spatial and temporal heterogeneity, with the largest positive influence factor of NDVI and slope showing a diffusion enhancement trend, and the largest negative influence factor of population density showing the same trend. The overall ecosystem service function has remained stable, and the coordination between economic development and ecological protection has been good. Future regional development needs to further implement the ecological protection development strategy, focus on and implement measures to improve the ecological service function of key areas, and reduce the negative impact of population.
Effect of spray cryotherapy on respiratory function in canine models of chronic bronchitis
Authors: Liang Long , Duan Hongxia , Li Xuan , Wang Changhui , Xie Shuanshuan 
Published: December 2022

Abstract
Objective: Our aim was to explore whether SCT is effective in improving respiratory function in a canine model of chronic bronchitis and to further elucidate the associated biological mechanisms.
Methods: A total of ten experimental dogs were recruited for this study, eight of which were exposed to sulfur dioxide (SO2) for 6 months as a model group and the other two as healthy controls. We analyzed and compared the differences of respiratory function, airway morphology and inflammatory cell infiltration at 1-, 3- and 6-month intervals after SCT treatment and further explored the intrinsic correlations.
Results: Respiratory function was significantly reduced after six months of SO2 exposure compared to healthy controls. PIF and PEF significantly decreased by 30.64% and 18.35%, respectively. Other respiratory function indicators such as TV, tI, tE, MV, EIP, EF25%, EF50%, EF75%, IF25%, IF50%, IF75%, FIaV, FEaV and CI also showed a significant downward trend (P<0.05). Respiratory function and airway morphometry were significantly improved at 1-, 3-, and 6- month intervals after SCT compared to chronic bronchitis group. The number of infiltrated neutrophils and macrophages per unit area of airway epithelium was negatively correlated with respiratory function, implying that decreased respiratory function was accompanied by more infiltration of neutrophils and macrophages.
Conclusions: SCT significantly improved respiratory function, airway morphometry and infiltrated inflammatory cell count in a canine model of chronic bronchitis for at least six months. Our study identifies the relevant biological mechanisms by which infiltrating neutrophil and macrophage counts can have a critical impact on respiratory function.
ChemR23 activation attenuates cognitive impairment in chronic cerebral hypoperfusion via inhibiting NLRP3 inflammasome-induced neuronal pyroptosis
Authors: Zhang Yaxuan , Zhang Jiawei , Zhao Yao , Zhang Yueqi , Liu Lan , Xu Xiaofeng , Wang Xiuzhe , Fu Jianliang 
Published: December 2022

AbstractBackgroundNeuroinflammation plays critical roles in vascular dementia (VaD), the second leading cause of dementia which can be induced by chronic cerebral hypoperfusion (CCH). NLRP3 inflammasome-induced pyroptosis, the inflammatory programmed cell death has been reported to contribute to the development of VaD [1]. ChemR23 is a G protein coupled receptor that has emerging roles in regulating inflammation. However, the role of ChemR23 signaling in NLRP3 inflammasome-induced pyroptosis in CCH remains elusive.MethodsPermanent bilateral common carotid artery occlusion (BCCAO) surgery was performed in rats to establish the CCH model. Eight weeks after the surgery, the rats were intraperitoneally injected with Resolvin E1 (RvE1) or chemerin-9 (C-9) every other day for 4 weeks. Besides, SH-SY5Y cells with hypoglycemic and hypoxic stimulation were adopted to mimic CCH injury in vitro. Behavioral test was applied to access cognitive impairment. Histological and immunofluorescent staining, RNA sequencing analysis, western blot, enzyme-linked immunosorbent assay, transmission electron microscope, LDH activity assay, flow cytometry and scanning electron microscope were conducted to evaluate neuronal damage and explore the possible mechanisms in vivo and in vitro.Results:Here, we found that the levels of ChemR23 expression were decreased from the 8th week after BCCAO, accompanied by significant cognitive impairment. Further analysis revealed that CCH induced neuronal damage, synaptic injury and NLRP3-related pyroptosis activation in hippocampal neurons. However, pharmacologic activation of ChemR23 with RvE1 or C-9 counteracted these changes. Moreover, In vitro experiments showed that manipulating ChemR23 expression markedly regulated NLRP3 inflammasome-induced neuronal pyroptosis through PI3K/AKT/Nrf2 signaling in SH-SY5Y cells under hypoglycemic and hypoxic condition.ConclusionsOur data demonstrated that ChemR23 activation inhibits NLRP3 inflammasome-induced neuronal pyroptosis and improves the cognitive function via PI3K/AKT/Nrf2 signaling pathway in CCH models. ChemR23 may serve as a potential novel therapeutic target to treat CCH-induced cognitive impairment.
Dataset on infant mortality rates in Brazil
Authors: Souto Gabriel , Miloski Matheus , Cardoso Carlos Leonardo Souza , Kreischer Vinicius , Paixão Balthazar , Ribeiro Victor de Paula Dornellas , Gritz Raquel , Carraro Lucas , Cruz Sérgio Ricardo de Borba , Bonifácio Carmen Lúcia Corrêa , Saldanha Raphael de Freitas , Zirondi Leandro , Alencar Gizelton Pereira , Alves Ariane Camilo Pinheiro , Neto Nelson Niero , Salles Rebecca , Lima Jefferson da Costa , Pedroso Marcel 
Published: December 2022

Abstract
Objectives: Surveillance of infant and fetal deaths is of paramount importance inthinking about government strategies to reduce these rates, provide greatervisibility of these mortality figures in the country, enable the adoption ofprevention measures, as well as contribute to a better record of deaths.
Data description: The dataset comprises fetal, neonatal, early neonatal, lateneonatal, and perinatal Mortality Rates of Brazilian municipalities with theirrespective information, between 2010 to 2020, aggregated by epidemiologicalweek.
Genetic etiology and clinical outcomes of fetuses with duodenal obstruction detected using chromosomal microarray analysis
Authors: Wang You , Fu Fang , Zhou Hang , Ma Chunling , Cheng Ken , Huang Ruibin , Liao Can 
Published: December 2022

Abstract
Objective:
To assess the value of chromosomal microarray analysis (CMA) in fetuses with duodenal obstruction (DO) and to evaluate the associated prenatal findings and pregnancy outcomes.
Methods:
The study included 428 fetuses with duodenal obstruction (DO) identified in prenatal diagnostic centers between January 2015 and May 2022, of which 103 fetuses underwent invasive prenatal diagnosis. The fetuses were classified into non-isolated and isolated groups based on prenatal ultrasound DO with or without other structural abnormalities. Quantitative fluorescence polymerase chain reaction (QF-PCR) and chromosome microarray analysis (CMA) were applied as first-line techniques for detection and analysis, pregnancy outcome was recorded in all cases, and newborns were followed up to 2.5 years of age.
Results:
Among 103 fetuses, Overall, the CMA identified clinically significant copy number variations (CNVs) in 9/103 (8.74%) fetuses and variants of unknown significance (VOUS) in 7/103 (6.80%). 9 cases of pathogenic CNVs were 1 case of 15q25.2 deletion, 2 cases of 17q12 microduplication syndrome, 2 cases of 13q21.2q31.1 deletion, 1 case of 13q21.33q31.1 deletion, 1 case of 7q11.23 microdeletion, 1 case of 1q41q44 duplication and 1 case of 16q23.3q24.1 deletion. The EDNRB gene in the 13q region and the HNF1B gene in the 17q12 region are candidate genes for the pathogenicity of fetal duodenal obstruction. The difference in the detection rate of pathogenic CNVs between the isolated group and the non-isolated group is statistically significant (5.75%, 5/87, and 25.00%, 4/16, p=0.031). Among 103 fetuses, 77 were live births, 2 were stillborn, 2 died after birth, and 22 cases of induced labor.
Conclusions:
This study highlights the value of CMA of variants in unbalanced genomes of DO fetuses, especially non-isolated DO fetuses. Adverse pregnancy outcomes in DO fetuses are influenced by several factors, including maternal age (MA), gestational age (GA), and Polyhydramnios.
Geometry-Inference based Clustering-Heuristic: An empirical method for kmeans optimal clusters determination
Authors: Khattabi Mohammed Zakariae El , Jai Mostapha El , Akhrif Iatimad , Lahmadi Youssef , Oughdir Lahcen 
Published: December 2022

Abstract
Kmeans is one of the most algorithms that are utilized in data clustering. Number of metrics is coupled with kmeans in order cluster data targeting the enhancement of both locally clusters compactness and the globally clusters separation. Then, before the ultimate data assignment to their corresponding clusters, the selection of the optimal number of clusters should constitute a crucial step in the clustering process. The present work aims to build up a new clustering metric/heuristic that takes into account both space dispersion and inferential characteristics of the data to be clustered. Hence, in this paper, a Geometry-Inference based Clustering (GIC) heuristic is proposed for selecting the optimal numbers of clusters. The conceptual approach proposes the “Initial speed rate” as the main geometric parameter to be inferentially studied. After, the corresponding histograms are fitted by means of classical distributions. A clear linear behaviour regarding the distributions’ parameters was detected according to the number of optimal clusters k* for each of the 14 datasets adopted in this work. Finally, for each dataset, the optimal k* is observed to match with the change-points assigned as the intersection of two clearly salient lines. All fittings are tested using Khi2 tests showing excellent fitting in terms of p-values, and R² also for linear fittings. Then, a change-point algorithm is launched to select k*. To sum up, the GIC heuristic shows a full quantitative aspect, and is fully automated; no qualitative index or graphical techniques are used herein.