bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron Therapy-Induced Leukopenia in Arab Female Population, an experience in Qatar
Authors: Almasri Hussam , Soliman Ashraf , Desanctis Vincenzo , Alsaud Arwa , Alhashimy Roua , Babikr Mona , Ahmad Rita , Aldwairi Majd , Kloub Mohammad , Ahmed Shaima , Al-Tikrity Mustafa , Eisa Mahmoud , Yassin Mohamed 
Published: May 2021

Abstract
IntroductionIron deficiency anemia (IDA) is the most common cause of anemia in both developed and developing countries. Leukopenia is an infrequent side effect of iron therapy reported in the literature as sporadic cases. We conducted a study to clarify this issue and to check its consequences in a big cohort of patients with IDA.ObjectiveTo assess the relationship between iron therapy (intravenous) and leukopenia, neutropenia or lymphocytopenia, and its clinical impact, if any, on patients.Materials and Methodsthis is a retrospective study conducted in Hamad Medical Corporation, Doha/Qatar. the clinical and biochemical data of 1567 females with IDA who attended the hematology clinic and were treated with intravenous iron therapy were collected and analysed. Complete and differential blood counts and iron profile were studied before and after iron treatment. In addition, cases who developed infections during the time of leukopenia were noted and checked for possible complications.ResultsAfter iron therapy, out of 1567 case of iron deficiency anemia, 30 cases (1.914%) developed leukopenia,15 cases (0.957%) developed neutropenia and 12 cases (0.765%) developed lymphocytopenia. All had normal WBC counts before treatment. 2 patients (6.66%) had infection, 1 had upper respiratory tract infection and 1 urinary tract infection, the latter was treated with antibiotics. There were no reported infections during or after iron therapy.ConclusionsLeukopenia in form of neutropenia or lymphocytopenia may occur as a side effect of IV iron therapy, however, its clinical significance appeared to be limited.
A nationwide study of adolescent psychosocial well-being one year after the outbreak of the COVID-19 pandemic
Authors: von Soest Tilmann , Kozák Michal , Rodriguez-Cano Ruben , Fluit Sam , Cortés-García Laura , Ulseth Vidar , Haghish E. F. , Bakken Anders 
Published: May 2021

Abstract
]The COVID-19 pandemic has dramatically restricted adolescents’ lives. We used nationwide Norwegian survey data collected from 2014–2021 (N = 227,258; ages 13–18) to address three essential questions: What are the psychosocial consequences of the pandemic? Are disadvantaged adolescents disproportionally affected by the pandemic? Do pandemic effects vary with geographical variations in infection rates and restrictions? Multilevel models revealed higher depressive symptoms and lower optimism during the pandemic than before the pandemic, even when accounting for the measures’ time trends. Further, alcohol and cannabis use decreased, and screen time increased. Social relationships and conduct problems remained stable. Girls, younger adolescents, and adolescents from low socioeconomic backgrounds were disproportionally affected by the pandemic. The pandemic’s effects varied little with municipality infection rates and restrictions. These findings can inform means and interventions to reduce negative pandemic effects and identify groups that need particular attention during and after the pandemic.
RAISING: a high-performance method for identifying random transgene integration sites
Authors: Wada Yusaku , Sato Tomoo , Hasegawa Hiroo , Matsudaira Takahiro , Nao Naganori , Coler-Reilly Ariella , Tasaka Tomohiko , Yamauchi Shunsuke , Okagawa Tomohiro , Momose Haruka , Tanio Michikazu , Kuramitsu Madoka , Sasaki Daisuke , Yagishita Naoko , Yamauchi Junji , Araya Natsumi , Tanabe Kenichiro , Yamagishi Makoto , Nakashima Makoto , Nakahata Shingo , Iha Hidekatsu , Ogata Masao , Imaizumi Yoshitaka , Uchimaru Kaoru , Miyazaki Yasushi , Konnai Satoru , Yanagihara Katsunori , Morishita Kazuhiro , Watanabe Toshiki , Yamano Yoshihisa , Saito Masumichi 
Published: May 2021

Abstract
Both natural viral infections and therapeutic interventions using viral vectors pose significant risks of malignant transformation. Monitoring for clonal expansion of infected cells is important for detecting cancer. Here we developed a novel method of tracking transgene integration sites. RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) is a sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined with our CLOVA (Clonality Value) software is critical for those without access to expensive next-generation sequencing. To model our method, we analyzed samples from 698 patients infected with the retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL). We defined a clonality value identifying ATL patients with 100% sensitivity and 95.3% specificity, and our preliminary longitudinal analysis suggests this may also be useful for ATL risk assessment. We anticipate future studies will confirm the broad applicability of our technology, especially in the emerging gene therapy sector.
Nonlinear Analysis of L-shaped Pipe Conveying Fluid with the Aid of Absolute Nodal Coordinate Formulation
Authors: Zhou K. , Yi H.R. , Dai Huliang , Yan H , Guo Z.L. , Xiong F.R. , Ni Q. , Hagedorn P. , Wang L. 
Published: May 2021

Abstract
By adopting the absolute nodal coordinate formulation, a novel and general nonlinear theoretical model, which can be applied to solve the dynamics of combined straight-curved fluid-conveying pipes with arbitrary initially configurations and any boundary conditions, is developed in the current study. Based on this established model, the nonlinear behaviors of the cantilevered L-shaped pipe conveying fluid with and without base excitations are systematically investigated. Before starting the research, the developed theoretical model is verified by performing three validation examples. Then, with the aid of this model, the static deformations, linear stability, and nonlinear self-excited vibrations of the L-shaped pipe without the base excitation are determined. It is found that the cantilevered L-shaped pipe suffers from the static deformations when the flow velocity is subcritical, and will undergo the limit-cycle motions as the flow velocity exceeds the critical value. Subsequently, the nonlinear forced vibrations of the pipe with a base excitation are explored. It is indicated that the period-n, quasi-periodic and chaotic responses can be detected for the L-shaped pipe, which has a strong relationship with the flow velocity, excitation amplitude and frequency.
Transcription Factors Linked to the Molecular Signatures in the Development of HCC on a Cirrhotic Background
Authors: Motalebzadeh Jamshid , Eskandari Elaheh 
Published: May 2021

Abstract
Mechanisms underlying the regulation of gene expression in cancer have been surveyed for decades to find novel prognostic factors and new targets for molecular targeted therapies in cancer. Because most cases of liver cancer are associated with liver cirrhosis, we aimed to analyze the gene expression signatures and the gene regulatory mechanism in hepatocellular carcinoma (HCC) on a cirrhotic background using high-throughput data analysis. In the present study, three valid array-based datasets containing HCC and liver cirrhosis samples were obtained to identify common differentially expressed genes (DEGs). Moreover, a comprehensive data analysis was conducted based on RNA-Seq data and using Kaplan-Meier curve analysis to find molecular signatures that reduce patients' overall survival rate. Furthermore, we proposed a gene regulatory network (GRN) to explore the possible regulatory mechanism of these molecular signatures by transcription factors in HCC progression from cirrhosis. Besides, we analyzed protein-protein interactions, gene ontology (GO), and pathway enrichment to elucidate the cellular and molecular function of the GRN elements in HCC. In this way, we found a list of 231 molecular signatures in HCC derived from cirrhosis. We also found the importance of TCF4, RUNX1, HINFP, KDM2B, MAF, JUN, NR5A2, NFYA, and AR as key differentially expressed transcription factors (DETFs) in the progression of HCC from cirrhosis. In conclusion, the identified molecular signatures and their transcription factors propose candidate prognostic markers and possible molecular targets in the progression of HCC.
Long-Term Dynamics of Bird Dispersal Network Structures Associated with the Functions in Bird Migration and Fruit Abundance
Authors: Ohkawara Kyohsuke , Kimura Kazuya , Satoh Fumio 
Published: May 2021

Abstract
In temperate zones, the complex network of seed dispersal by migrant birds is formed and the structure is dynamic on long time scale. Over 12 years, we examined interannual variability of structures of bird dispersal networks and factors affecting them by observing the characteristics of fruit abundance, bird migration and bird dispersal interactions in central Japan. The fruit abundance exhibited a remarkable fluctuation across years, with the number of fruiting trees and matured fruits fluctuating repeatedly every other year, leading to the periodic fluctuations. The abundance of migrants was also fluctuated. According to the abundance of fruits and migrants, the 12 years as study period was classified into three types. The seed transporting frequency and the dispersal networks were investigated by collecting faeces of migrants. Of the 6652 samples collected from 15 bird species, 1671 (25.1%) included seeds from 60 plant species. Main dispersers were composed of Turdus pallidus, T. obscurus and Zosterops japonicus. The structures of bird dispersal networks were highly nested over 12 years, suggesting the networks are stable. Specifically, the nested structure developed in years when fruit abundance was low. GLM analyses showed the abundance of migrants, particularly T. pallidus and T. obscurus, had strong positive effects on construction of nested structure. The development of nested structure may be caused by the fact the two Turdus species were more frequently functioning as generalist dispersers when fruit abundance was lower. Our study revealed one of the mechanisms determining the structure of bird dispersal network on long time scale.
Mutational signatures of complex genomic rearrangements in human cancer
Authors: Yang Lixing , Bao Lisui , Zhong Xiaoming , Yang Yang 
Published: May 2021

Abstract
Complex genomic rearrangements (CGRs) are common in cancer and are known to form via two aberrant cellular structures—micronuclei and chromatin bridge. However, which mechanism is more relevant to CGR formation in cancer cells and whether there are other undiscovered mechanisms remain open questions. Here, we analyze 2,014 CGRs from 2,428 whole-genome sequenced tumors and deconvolute six CGR signatures based on the topology of CGRs. Through rigorous benchmarking, we show that our CGR signatures are highly accurate and biologically meaningful. Three signatures can be attributed to known biological processes—micronuclei- and chromatin-bridge-induced chromothripsis and extrachromosomal DNA. More than half of the CGRs belong to the remaining three newly discovered signatures. A unique signature (we named “hourglass chromothripsis”) with highly localized breakpoints and small amount of DNA loss is abundant in prostate cancer. Through genetic association analysis, we find SPOP as a candidate gene causing hourglass chromothripsis and playing important role in maintaining genome integrity. Our study offers valuable insights into the formation of CGRs.
A Candidate Multi-epitope Vaccine Against Porcine Reproductive and Respiratory Syndrome Virus and Mycoplasma Hyopneumoniae
Authors: Gao Zhisong , Chen Lingxiao , Pan Xuan , Li Xiaojing , Lu Guangzong , Tang Yajie , Wu Xiang , Zhao Baohua , Zhang Ran 
Published: May 2021

Abstract
Background: Porcine reproductive and respiratory syndrome virus (PRRSV) and Mycoplasma hyopneumoniae (M. hyopneumoniae, Mhp) are two of the most common pathogens involved in the porcine respiratory disease complex (PRDC) which results in significant worldwide economic losses. Vaccination is reported to be the most effective approach to prevent the disease. Since PRRSV and Mhp co-infections are very common, an efficient dual vaccine against PRRSV and Mhp co-infections is required for the global swine industry. Compare with the traditional vaccine, the multi-epitope vaccines have several advantages, such as comparatively easy production and construction, chemical stability, and lack of infectious potential.Results: In this study, to develop a safe and effective vaccine, B cell epitopes and T cell epitopes of PRRSV-GP5, PRRSV-M, Mhp-P46 and Mhp-P65 protein had been screened to construct a recombinant epitope protein rEP-PM which has good hydrophilicity, strong antigenicity and high surface accessibility, and each epitope is independent and complete. After immunization in mice, rEP-PM could induce the production of high levels of antibodies and effective cellular immune response.Conclusions: Our results showed that the rEP-PM protein could be potential candidate to develop into a safe and effective multi-epitope peptide combined vaccine used in the control of PRRSV and Mhp infection.
New Insight into Regulation of αIIbβ3 Integrin Signaling by Filamin A
Authors: Lamrani Lamia , Adam Frédéric , Soukaseum Christelle , Denis Cécile V. , Raslova Hana , Rosa Jean-Philippe , Bryckaert Marijke 
Published: May 2021

Abstract
Filamin (FLN) regulates many cell functions through its scaffolding activity cross-linking cytoskeleton and integrins. FLN was shown to inhibit integrin activity, but the exact mechanism remains unclear. Here, we report on the regulation of platelet integrin αIIbβ3 signaling by the FLNa subtype. Three FLNa deletion mutants were overexpressed in the erythro-megakaryocytic leukemic cell line HEL: Del1 which lacks the N-terminal CH1-CH2 domains mediating the FLNa-actin interaction; Del2 lacking the immunoglobulin-like (Ig) repeat 21 which mediates the FLNa-β3 interaction; and Del3 lacking the C-terminal Ig repeat 24, responsible for FLNa dimerization and interaction with the small Rho GTPase involved in actin cytoskeleton reorganisation. Fibrinogen binding to HEL cells in suspension and talin-β3 interaction in cells adherent to immobilized fibrinogen were assessed using the PKC agonist (phorbol 12-myristate 13-acetate) also to activate αIIbβ3. Our results show that FLNa-actin and FLNa-β3 interactions negatively regulate αIIbβ3 activation. Moreover FLNa-actin interaction represses Rac activation, contributing to the negative regulation of αIIbβ3 activation. In contrast, the FLNa dimerization domain which maintains Rho inactive, was found to negatively regulate αIIbβ3 outside-in signaling. We conclude that FLNa negatively controls αIIbβ3 activation by regulating actin polymerization and restraining activation of Rac, as well as outside-in signaling by repressing Rho.
A Non-negative Matrix Factorization Based Method for Identifying Essential Proteins
Authors: Zhang Zhihong , Hu Sai , Yan Wei , Zhao Bihai , Wang Lei 
Published: May 2021

Abstract
BackgroundIdentification of essential proteins is very important for understanding the basic requirements to sustain a living organism. In recent years, various different computational methods have been proposed to identify essential proteins based on protein-protein interaction (PPI) networks. However, there has been reliable evidence that a huge amount of false negatives and false positives exist in PPI data. Therefore, it is necessary to reduce the influence of false data on accuracy of essential proteins prediction by integrating multi-source biological information with PPI networks.ResultsIn this paper, we proposed a non-negative matrix factorization and multiple biological information based model (NDM) for identifying essential proteins. The first stage in this progress was to construct a weighted PPI network by combing the information of protein domain, protein complex and the topology characteristic of the original PPI network. Then, the non-negative matrix factorization technique was used to reconstruct an optimized PPI network with whole enough weight of edges. In the final stage, the ranking score of each protein was computed by the PageRank algorithm in which the initial scores were calculated with homologous and subcellular localization information. In order to verify the effectiveness of the NDM method, we compared the NDM with other state-of-the-art essential proteins prediction methods. The comparison of the results obtained from different methods indicated that our NDM model has better performance in predicting essential proteins.ConclusionEmploying the non-negative matrix factorization and integrating multi-source biological data can effectively improve quality of the PPI network, which resulted in the led to optimization of the performance essential proteins identification. This will also provide a new perspective for other prediction based on protein-protein interaction networks.
Correlation Between Late-stage Schistosoma Infection and Colorectal Cancer: a Colorectal Cancer Screening Among Elderer in the Qingpu District of Shanghai
Authors: Yu Xi , Wang Sen , Li Gui-fu , Xu Rui-fang , Xue Kun , Zhu Ji 
Published: May 2021

Abstract
Cancer monitoring of Shanghai showed a rapid increase in the incidence of colorectal cancer. Colorectal cancer risk assessment allows for rapid screening of high-risk populations. The colorectal cancer screening of elderly residents is ongoing since 2013 in Shanghai. This initiative screened 85,525 people from 11 communities of the Qingpu District. Screening included a questionnaire-based risk assessment and two Fecal Occult Blood Tests (FOBTs). We conducted a retrospective case study of patients with positive screening results that underwent fibro-colonoscopy examinations to investigate their histories of schistosoma infection, smoking, alcohol consumption, and dietary habits. A total of 85,525 people were screened in this study. Colorectal cancer was resulted in a prevalence of 59.84/100,000. And the prevalence of schistosoma infection was 400/100,000. Among patients with schistosoma infection, the positive rate of FOBT was 67.01%, in contrast to an overall positive rate of FOBT among all subjects of 17.00% [(Pearson ⎥2=672.42, P < 0.0001, OR = 3.94 (3.67,4.23)]. The prevalence of colorectal cancer among patients with schistosoma japonicum infections was 4,155.84/100,000, while the prevalence of colorectal cancer among all subjects was 44.15/100,000 [Pearson2 = 980.62, P < 0.001, OR = 94.12 (53.05, 166.97)]. Our study found a high degree of correlation between late stage schistosoma infection of the intestinal tract and the occurrence of colorectal cancer and colonic adenoma. For patients with lesions caused by schistosoma infections of intestinal tract, the risk of colorectal cancer was higher than that of patients without intestinal schistosoma infections. Early screening and risk assessment can facilitate early diagnosis and treatment of colorectal cancer and colonic adenoma.
Caspase-1 Inhibitor Reduces Pyroptosis in Kidney Injury Induced by Brain Death
Authors: Liu Weifeng , Yang Dongjing , Shi Jihua , Wen Peihao , Zhang Jiakai , Wang Zhihui , Hu Bowen , Shi Xiaoyi , Cao Shengli , Guo Wenzhi , Zhang Shuijun 
Published: May 2021

Abstract
Brain death (BD) induces an organ-level inflammatory response, and BD donor kidneys show inferior survival and recovery rates. However, the underlying mechanisms have not been fully elucidated. Here, we investigated the role of caspase-1-mediated pyroptosis in BD-induced kidney injury in rats. A BD model was established in Sprague-Dawley rats. The rats were intravenously injected with a caspase-1 inhibitor (Z-YVAD-FMK) 1 h before BD, and sham-operated rats served as controls. After 0, 1, 2, 4, and 6 h of BD, renal function, renal injury, and renal expression of NLRP3, caspase-1, caspase-11, gasdermin D (GSDMD), IL-1β, and IL-18 were assessed using quantitative reverse transcriptase-polymerase chain reaction, western blotting, and immunohistochemistry. Blood urea nitrogen and serum creatinine levels were measured. Additionally, renal tubular epithelial cells (NRK-52E) were subjected to 3 h of hypoxia followed by 6 h of reoxygenation and incubated with Z-YVAD-FMK before hypoxia and reoxygenation. Caspase-11 was knocked-down using small interfering RNA technology. Cell viability and levels of pyroptosis-associated proteins were assessed thereafter. NLRP3, caspase-1, GSDMD, IL-1β, and IL-18 expression levels were upregulated in BD rats. Treatment with Z-YVAD-FMK reduced mRNA and protein levels, improved renal function, and alleviated renal injury. Z-YVAD-FMK effectively reduced pyroptosis in BD rats; however, it did not affect caspase-11 expression in vivo or in vitro. Thus, it could be considered as a therapeutic target for BD-induced kidney injury.
Transcriptome Profiling for Pericarp Browning During Long-term Storage of Intact Lotus Root (Nelumbo Nucifera)
Authors: Worarad Kanjana , Suzuki Tomohiro , Norii Haruka , Muchizuki Yuya , Ishii Takashi , Shinohara Keiko , Miyamoto Takao , Kuboyama Tsutomu , Inoue Eiichi 
Published: May 2021

Abstract
Lotus root ( Nelumbo nucifera ) is an edible rhizome that the consumption/production has continuously increased as more consumers demand convenient and ready-to-eat foods. However, the processing, storage, and transportation of fresh-cut fruits and vegetables promotes physiological deterioration, such as browning, which leads to a reduction in the value of the product. This study aimed to reduce the browning of lotus root pericarps during long-term storage and long-distance transport , and to clarify the functions of unigenes and browning-associated metabolic pathways using RNA-sequencing techniques. Intact lotus root cv. ‘Kanasumi No.34’ browning decreased after the roots were packed along with an anti-browning solution . Over 200 million short single-end reads were mapped onto the N. nucifera consensus coding sequence set. The significantly differentially expressed genes (DEGs) were identified. Based on the Uniprot, GO, and KEGG databases, secondary metabolism, lipid metabolism, and redox state genes were significantly upregulated in the un-packed (UP) and packed with water (PW) treatments compared to after harvest (AH) sample. Additionally, 16 expected differentially expressed genes (e.g., PPO, PAL, POD, CHS , PDCR , and SOD ), which are affected by browning development, were differentially regulated in lotus root pericarp. The gene expression data presented in this study will help elucidate the molecular mechanism underlying browning development in intact lotus root during long-term storage. The results may also inform future research on improving the post-harvest life of lotus roots.