bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer
Authors: Giles Katherine A. , Gould Cathryn M. , Achinger-Kawecka Joanna , Page Scott G. , Kafer Georgia R. , Rogers Samuel , Luu Phuc-Loi , Cesare Anthony J. , Clark Susan J. , Taberlay Phillippa C. 
Published: February 2021

Abstract
Background
BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour.

Results
Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest.

Conclusions
Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis.
DNA methylation profiles of bronchoscopic biopsies for the diagnosis of lung cancer
Authors: Goldmann Torsten , Schmitt Bernhard , Müller Julia , Kröger Maren , Scheufele Swetlana , Marwitz Sebastian , Nitschkowski Dörte , Schneider Marc A. , Meister Michael , Muley Thomas , Thomas Michael , Kugler Christian , Rabe Klaus F. , Siebert Reiner , Reck Martin , Ammerpohl Ole 
Published: February 2021

Abstract
Background
Lung cancer is the leading cause of cancer-related death in most western countries in both, males and females, accounting for roughly 20–25% of all cancer deaths. For choosing the most appropriate therapy regimen a definite diagnosis is a prerequisite. However, histological characterization of bronchoscopic biopsies particularly with low tumor cell content is often challenging. Therefore, this study aims at (a) determining the value of DNA methylation analysis applied to specimens obtained by bronchoscopic biopsy for the diagnosis of lung cancer and (b) at comparing aberrantly CpG loci identified in bronchoscopic biopsy with those identified by analyzing surgical specimens.

Results
We report the HumanMethylation450-based DNA methylation analysis of paired samples of bronchoscopic biopsy specimens either from the tumor side or from the contralateral tumor-free bronchus in 37 patients with definite lung cancer diagnosis and 18 patients with suspicious diagnosis. A differential DNA methylation analysis between both biopsy sites of patients with definite diagnosis identified 1303 loci. Even those samples were separated by the set of 1303 loci in which histopathological analysis could not unambiguously define the dignity. Further differential DNA methylation analyses distinguished between SCLC and NSCLC. We validated our results in an independent cohort of 40 primary lung cancers obtained by open surgical resection and their corresponding controls from the same patient as well as in publically available DNA methylation data from a TCGA cohort which could also be classified with high accuracy.

Conclusions
Considering that the prognosis correlates with tumor stage at time of diagnosis, early detection of lung cancer is vital and DNA methylation analysis might add valuable information to reliably characterize lung cancer even in histologically ambiguous sample material.
Effects of microbial organic fertilizers on Astragalus membranaceus growth and rhizosphere microbial community
Authors: Liang Jian-Ping , Xue Zhi-Quan , Yang Zhen-Yu , Chai Zhi , Niu Jing-Ping , Shi Zhi-Yong 
Published: February 2021

Abstract
Purpose
The application of excessive chemical fertilizers during the cultivation of Astragalus membranaceus leads to a decline in the quality of this medicinal plant as well as the soil’s sustainable productivity. In this study, we developed a special microbial organic fertilizer for A. membranaceus and investigated its effects on plant growth and rhizosphere microbial communities.

Methods
The root biomass and main active components of A. membranaceus in different growth stages were measured to assess the impacts of microbial organic manure on plant growth. Meanwhile, 16S rRNA and ITS1 amplicons were amplified and high-throughput sequencing was performed to detect the dynamic impacts of microbial organic manure on rhizosphere microbial communities.

Result
The results demonstrated that microbial organic manure significantly increased wet and dry weights of A. membranaceus seedlings and the accumulation of two effective components (flavonoids and saponin) in bacterial fertilizer treatment groups are significant higher than the control group. Research on rhizosphere microbial flora shows that the number and polymorphism of bacteria and fungi were decreased after the application of special fertilizer during the rapid growth period of plant and then gradually increased with seedling growth. The community structure of bacteria was regulated after the application of special fertilizer, and the beneficial bacteria for plant growth are enriched. Functional profiles prediction showed that significant shifts in metabolic functions impacting KEGG pathways of the microbial fertilizer treatment groups are related to metabolism and biosynthesis.

Conclusion
The results indicate that the microbial organic manure can improve A. membranaceus growth by providing appropriate nutrients and regulating the rhizosphere microbial community which has good potential in ecological cultivation of A. membranaceus.
Human fetal liver MSCs are more effective than adult bone marrow MSCs for their immunosuppressive, immunomodulatory, and Foxp3+ T reg induction capacity
Authors: Yu Yi , Valderrama Alejandra Vargas , Han Zhongchao , Uzan Georges , Naserian Sina , Oberlin Estelle 
Published: February 2021

Abstract
Background
Mesenchymal stem cells (MSCs) exhibit active abilities to suppress or modulate deleterious immune responses by various molecular mechanisms. These cells are the subject of major translational efforts as cellular therapies for immune-related diseases and transplantations. Plenty of preclinical studies and clinical trials employing MSCs have shown promising safety and efficacy outcomes and also shed light on the modifications in the frequency and function of regulatory T cells (T regs). Nevertheless, the mechanisms underlying these observations are not well known. Direct cell contact, soluble factor production, and turning antigen-presenting cells into tolerogenic phenotypes, have been proposed to be among possible mechanisms by which MSCs produce an immunomodulatory environment for T reg expansion and activity. We and others demonstrated that adult bone marrow (BM)-MSCs suppress adaptive immune responses directly by inhibiting the proliferation of CD4+ helper and CD8+ cytotoxic T cells but also indirectly through the induction of T regs. In parallel, we demonstrated that fetal liver (FL)-MSCs demonstrates much longer-lasting immunomodulatory properties compared to BM-MSCs, by inhibiting directly the proliferation and activation of CD4+ and CD8+ T cells. Therefore, we investigated if FL-MSCs exert their strong immunosuppressive effect also indirectly through induction of T regs.

Methods
MSCs were obtained from FL and adult BM and characterized according to their surface antigen expression, their multilineage differentiation, and their proliferation potential. Using different in vitro combinations, we performed co-cultures of FL- or BM-MSCs and murine CD3+CD25−T cells to investigate immunosuppressive effects of MSCs on T cells and to quantify their capacity to induce functional T regs.

Results
We demonstrated that although both types of MSC display similar cell surface phenotypic profile and differentiation capacity, FL-MSCs have significantly higher proliferative capacity and ability to suppress both CD4+ and CD8+ murine T cell proliferation and to modulate them towards less active phenotypes than adult BM-MSCs. Moreover, their substantial suppressive effect was associated with an outstanding increase of functional CD4+CD25+Foxp3+ T regs compared to BM-MSCs.

Conclusions
These results highlight the immunosuppressive activity of FL-MSCs on T cells and show for the first time that one of the main immunoregulatory mechanisms of FL-MSCs passes through active and functional T reg induction.
The role and mechanism of mitochondrial functions and energy metabolism in the function regulation of the mesenchymal stem cells
Authors: Yan Wanhao , Diao Shu , Fan Zhipeng 
Published: February 2021

AbstractMesenchymal stem cells (MSCs) are multipotent cells that show self-renewal, multi-directional differentiation, and paracrine and immune regulation. As a result of these properties, the MSCs have great clinical application prospects, especially in the regeneration of injured tissues, functional reconstruction, and cell therapy. However, the transplanted MSCs are prone to ageing and apoptosis and have a difficult to control direction differentiation. Therefore, it is necessary to effectively regulate the functions of the MSCs to promote their desired effects. In recent years, it has been found that mitochondria, the main organelles responsible for energy metabolism and adenosine triphosphate production in cells, play a key role in regulating different functions of the MSCs through various mechanisms. Thus, mitochondria could act as effective targets for regulating and promoting the functions of the MSCs. In this review, we discuss the research status and current understanding of the role and mechanism of mitochondrial energy metabolism, morphology, transfer modes, and dynamics on MSC functions.
Dynamics of myogenic differentiation using a novel Myogenin knock-in reporter mouse
Authors: Benavente-Diaz Maria , Comai Glenda , Di Girolamo Daniela , Langa Francina , Tajbakhsh Shahragim 
Published: February 2021

Abstract
Background
Myogenin is a transcription factor that is expressed during terminal myoblast differentiation in embryonic development and adult muscle regeneration. Investigation of this cell state transition has been hampered by the lack of a sensitive reporter to dynamically track cells during differentiation.

Results
Here, we report a knock-in mouse line expressing the tdTOMATO fluorescent protein from the endogenous Myogenin locus. Expression of tdTOMATO in MyogntdTom mice recapitulated endogenous Myogenin expression during embryonic muscle formation and adult regeneration and enabled the isolation of the MYOGENIN+ cell population. We also show that tdTOMATO fluorescence allows tracking of differentiating myoblasts in vitro and by intravital imaging in vivo. Lastly, we monitored by live imaging the cell division dynamics of differentiating myoblasts in vitro and showed that a fraction of the MYOGENIN+ population can undergo one round of cell division, albeit at a much lower frequency than MYOGENIN− myoblasts.

Conclusions
We expect that this reporter mouse will be a valuable resource for researchers investigating skeletal muscle biology in developmental and adult contexts.
Two CD9 tetraspanin family members of Japanese flounder (Paralichthys olivaceus): characterization and comparative analysis of the anti-infectious immune function
Authors: He Jiaojiao , Gu Hanjie , Wang Wenqi , Hu Yonghua 
Published: February 2021

AbstractCD9 is a glycoprotein of the transmembrane 4 superfamily that is involved in various cellular processes. Studies related to the immune functions and activities of CD9 in teleost fish are limited. In this study, we characterized two CD9 homologs, PoCD9.1 and PoCD9.3, from Japanese flounder (Paralichthys olivaceus). Sequence analysis showed that PoCD9.1 and PoCD9.3 possess characteristic transmembrane 4 superfamily (TM4SF) structures. PoCD9.1 shares 70.61% sequence identity with PoCD9.3. The expression of PoCD9.1 and PoCD9.3 in the three main immune tissues was significantly induced in a time-dependent manner by extracellular and intracellular pathogen infection, which indicates that the two CD9 homologs play an important role in the response to pathogenic infection. Following infection with the extracellular pathogen Vibrio anguillarum, the expression profiles of both PoCD9.1 and PoCD9.3 were similar. After infection with the intracellular pathogen Edwardsiella piscicida, the expression levels of PoCD9.1 and PoCD9.3 were different at different stages of infection, especially in the spleen. The spleen was the most important tissue for the PoCD9.1 and PoCD9.3 responses to pathogen infection among the three examined immune tissues. Knockdown of PoCD9.1 and PoCD9.3 attenuated the ability of host cells to eliminate pathogenic bacteria, and PoCD9.1 knockdown was more lethal than PoCD9.3 knockdown for host cells with E. piscicida infection. Overexpression of PoCD9.1 and PoCD9.3 promoted host or host cell defence against E. piscicida infection. These findings suggest that PoCD9.1 and PoCD9.3 serve as immune-related factors, play an important role in the immune defence system of Japanese flounder, and display different functions in response to different pathogens at different stages of infection.
Adaptive offloading in mobile-edge computing for ultra-dense cellular networks based on genetic algorithm
Authors: Liao Zhuofan , Peng Jingsheng , Xiong Bing , Huang Jiawei 
Published: February 2021

AbstractWith the combination of Mobile Edge Computing (MEC) and the next generation cellular networks, computation requests from end devices can be offloaded promptly and accurately by edge servers equipped on Base Stations (BSs). However, due to the densified heterogeneous deployment of BSs, the end device may be covered by more than one BS, which brings new challenges for offloading decision, that is whether and where to offload computing tasks for low latency and energy cost. This paper formulates a multi-user-to-multi-servers (MUMS) edge computing problem in ultra-dense cellular networks. The MUMS problem is divided and conquered by two phases, which are server selection and offloading decision. For the server selection phases, mobile users are grouped to one BS considering both physical distance and workload. After the grouping, the original problem is divided into parallel multi-user-to-one-server offloading decision subproblems. To get fast and near-optimal solutions for these subproblems, a distributed offloading strategy based on a binary-coded genetic algorithm is designed to get an adaptive offloading decision. Convergence analysis of the genetic algorithm is given and extensive simulations show that the proposed strategy significantly reduces the average latency and energy consumption of mobile devices. Compared with the state-of-the-art offloading researches, our strategy reduces the average delay by 56% and total energy consumption by 14% in the ultra-dense cellular networks.
Laparoscopic removal of an aberrant acupuncture needle in the gluteus that reached the pelvic cavity: a case report
Authors: Yamamoto Akira , Hiro Junichiro , Omura Yusuke , Ichikawa Takashi , Ide Shozo , Imaoka Hiroki , Yasuda Hiromi , Fujikawa Hiroyuki , Okita Yoshiki , Yokoe Takeshi , Ohi Masaki , Toiyama Yuji 
Published: February 2021

Abstract
Background
Intrapelvic aberrant needles are rare in clinical practice. Long-term foreign bodies in the abdominal cavity may form granulation tissue or an abscess, and may cause organ injury. Therefore, such foreign bodies need prompt removal.

Case presentation
A 26-year-old male athlete was referred to our hospital for investigation of an aberrant acupuncture needle in the gluteus. The needle was unable to be removed during acupuncture treatment, and the end broke off and remained in the gluteus. Abdominal X-ray examination showed a thin, 40-mm-long, metallic foreign body resembling an acupuncture needle. Abdominal computed tomography showed an abnormal shadow in the gluteus. However, it was unclear whether the tip of the needle reached the pelvic cavity. Thus, it was decided to surgically extract the needle via laparoscopic surgery under X-ray guidance as a safe and minimally invasive method. Although X-ray fluoroscopy confirmed that the aberrant needle was located in the gluteus, the needle could not be felt with the forceps, as the peritoneum surrounding the needle had granulomatous changes due to inflammation. Therefore, the retroperitoneum was further dissected to search for the needle. Once the needle was identified, its flexibility enabled it to be easily removed by grasping it directly with a needle holder. The length of the aberrant needle was 40 mm. The postoperative course was uneventful, and the patient was discharged from hospital on postoperative day 2.

Conclusions
When a foreign body remains in the gluteus and its tip touches intrapelvic organs, such as the rectum, it is critical to determine the best approach for its safe removal. Given the anatomical location of the foreign body and the patient background, laparoscopic removal was considered the best approach in the present case.
Performance comparison of four types of target enrichment baits for exome DNA sequencing
Authors: Zhou Juan , Zhang Mancang , Li Xiaoqi , Wang Zhuo , Pan Dun , Shi Yongyong 
Published: February 2021

Abstract
Background
Next-generation sequencing technology is developing rapidly and target capture sequencing has become an important technique. Several different platforms for library preparation and target capture with different bait types respectively are commercially available. Here we compare the performance of the four platforms with different bait types to find out their advantages and limitations. The purpose of this study is to help investigators and clinicians select the appropriate platform for their particular application and lay the foundation for the development of a better target capture platform for next-generation sequencing.

Results
We formulate capture efficiency as a novel parameter that can be used to better evaluations of specificity and coverage depth among the different capture platforms. Target coverage, capture efficiency, GC bias, AT Dropout, sensitivity in single nucleotide polymorphisms, small insertions and deletions detection, and the feature of each platform were compared for low input samples. In general, all platforms perform well and small differences among them are revealed. In our results, RNA baits have stronger binding power than DNA baits, and with ultra deep sequencing, double stranded RNA baits perform better than single stranded RNA baits in all aspects. DNA baits got better performance in the region with high GC content and RNA baits got lower AT dropout suggesting that the binding power is different between DNA and RNA baits to genome regions with different characteristics.

Conclusions
The platforms with double stranded RNA baits have the most balanced capture performance. Our results show the key differences in performance among the four updated platforms with four different bait types. The better performance of double stranded RNA bait with ultra deep sequencing suggests that it may improve the sensitivity of ultra low frequent mutation detection. In addition, we further propose that the mixed baits of double stranded RNA and single stranded DNA may improve target capture performance.
Suitability of α1-microglobulin reduction rate as a biomarker of removal efficiency of online hemodiafiltration: a retrospective cohort study
Authors: Sakurai Kenji , Hosoya Hiromi , Kurihara Yoshitaka , Saito Takeshi 
Published: February 2021

Abstract
Background
Online hemodiafiltration (OL-HDF), whether in pre-dilution OL-HDF (pre-HDF) or post-dilution OL-HDF (post-HDF), is conducted to efficiently remove low molecular weight proteins from the blood of patients requiring dialysis. β2-microglobulin (β2-MG) and α1-microglobulin (α1-MG) are used as biomarkers to evaluate removal efficiency of OL-HDF.
We aimed to evaluate the relationship between β2-MG and α1-MG reduction rates and the amount of albumin leakage. Furthermore, we statistically analyzed the relationship between the α1-MG reduction rate and α1-MG removal amount, and its suitability as a biomarker for evaluating the removal efficiency of OL-HDF.

Methods
We collected the results of regularly conducted routine evaluations to assess the efficiency of OL-HDF from cases of patients undergoing maintenance dialysis at our clinic from 2018 to 2019. Data on was collected on both pre-HDF and post-HDF sessions. β2-MG and α1-MG reduction rates were analyzed. Regression analysis on reduction rates showed a significant correlation between the α1-MG reduction rate and the α1-MG removal amount.

Results
We conducted 435 tests on OL-HDF efficiency in 87 cases undergoing maintenance dialysis at our clinic in 2018 and 2019. There were 80.7 ± 4.5% for the β2-MG reduction rate, 33.8 ± 9.4% for the α1-MG reduction rate, and 3.9 ± 1.8 g/s for the amount of albumin leakage. There was no correlation between the β2-MG reduction rate and the α1-MG reduction rate, or between the amount of albumin leakage and β2-MG reduction rate.

Conclusion
α1-MG reduction rate was found to correlate with its removal amount, demonstrating its suitability as a biomarker for evaluating the removal efficiency of OL-HDF.

Trial registration
Retrospectively registered.
Migrant’s remittance and investment financing nexus in Africa: Does investment climate matter?
Authors: Nwokolo Chinenye Ifeoma , Ogbuagu Matthew Ikechukwu , Isola Wakeel Atanda 
Published: February 2021

AbstractDevelopment economists have enjoined Africans to leverage on remittance as their main source of investment financing due to its constant and undisrupted inflows despite structural distortions and economic weaknesses compared to other sources of financial flows in recent time. This ignited the motivation for this study, to unveil the nexus between migrant’s remittance and investment financing and the modulating effect of the investment climate in this relation on a panel of 28 sub-Saharan African countries over the period 1995 to 2017. Using the panel autoregression distributive lagged estimation technique, the following empirical findings were established. First, the theoretical supposition underpinning the assumption in investment climate as a factor that motivates migrant’s remittance inflow to be channelled to investment received a clear empirical support. Second, it was established that the interaction between remittance and components of investment climate (government size and open market) enhanced the growth of private investment. Last, remittance is found to exert a positive effect on private investment in as much as the former does not exceed the threshold of 78%, above which private investment would decline off the quadratic curve. The study suggests the policy-makers channel deliberate efforts at improving not only the efficiency of the market, but government participation especially in the area of tax policy and fiscal financing.