bluuebunny/crossref_metadata_2025_split huggingface dataset:
FANCM suppresses DNA replication stress at ALT telomeres by disrupting TERRA R-loops
Authors: Pan Xiaolei , Chen Yun , Biju Beena , Ahmed Naveed , Kong Joyce , Goldenberg Marti , Huang Judy , Mohan Nandakumar , Klosek Stephanie , Parsa Kian , Guh Chia-Yu , Lu Robert , Pickett Hilda A. , Chu Hsueh-Ping , Zhang Dong 
Published: December 2019

AbstractCancer cells maintain their telomeres by either re-activating telomerase or adopting the homologous recombination (HR)-based Alternative Lengthening of Telomere (ALT) pathway. Among the many prominent features of ALT cells, C-circles (CC) formation is considered to be the most specific and quantifiable biomarker of ALT. However, the molecular mechanism behind the initiation and maintenance of CC formation in ALT cells is still largely unknown. We reported previously that depletion of the FANCM complex (FANCM-FAAP24-MHF1&2) in ALT cells induced pronounced replication stress, which primarily takes place at their telomeres. Here, we characterized the changes in ALT associated phenotypes in cells deficient of the FANCM complex. We found that depletion of FAAP24 or FANCM, but not MHF1&2, induces a dramatic increase of CC formation. Most importantly, we identified multiple DNA damage response (DDR) and DNA repair pathways that stimulate the dramatic increase of CC formation in FANCM deficient cells, including the dissolvase complex (BLM-TOP3A-RMI1/2, or BTR), DNA damage checkpoint kinases (ATR and Chk1), HR proteins (BRCA2, PALB2, and Rad51), as well as proteins involved in Break-Induced Replication (BIR) (POLD1 and POLD3). In addition, FANCD2, another Fanconi Anemia (FA) protein, is also required for CC formation, likely through promoting the recruitment of BLM to the replication stressed ALT telomeres. Finally, we demonstrated that TERRA R-loops accumulate at telomeres in FANCM deficient ALT cells and downregulation of which attenuates the ALT-associated PML bodies (APBs), replication stress and CC formation. Taken together, our data suggest that FANCM prevents replisomes from stalling/collapsing at ALT telomeres by disrupting TERRA R-loops.
Effect of axial length and age on the visual outcome of patients with idiopathic epiretinal membrane after pars plana vitrectomy
Authors: Minami Sakiko , Shinoda Hajime , Shigeno Yuta , Nagai Norihiro , Kurihara Toshihide , Watanabe Kazuhiro , Sonobe Hideki , Takagi Hitoshi , Tsubota Kazuo , Ozawa Yoko 
Published: December 2019

AbstractWe evaluated predictive factors for visual outcomes in patients with idiopathic epiretinal membrane (iERM) after pars plana vitrectomy (PPV). Clinical records for 114 eyes (114 patients, mean age: 70.6 years) with iERM treated by PPV between March 2012 and March 2018 were retrospectively reviewed. Overall, the mean postoperative best-corrected visual acuity (BCVA) and central retinal thickness measured by optical coherence tomography improved as early as 1 month after surgery, and further improved until 3 months (P < 0.01). Multiple linear regression analyses adjusted for the preoperative BCVA showed that older age (B, 0.010; 95% confidence interval, 0.003 to 0.016; P = 0.003) and a shorter axial length (AL; B, −0.059; 95% confidence interval, −0.099 to −0.019; P = 0.005) predicted worse postoperative BCVA. The Mann-Whitney U test showed that the postoperative BCVA was worse in eyes with AL < 23.6 mm than in eyes with AL ≥ 23.6 mm (P = 0.037), and in patients aged ≥69 years than in patients aged <69 years (P = 0.024). The findings may help in evaluating surgical indications for each patient to obtain satisfactory outcomes, irrespective of the preoperative BCVA.
Mandibular prognathism attenuates brain blood flow induced by chewing
Authors: Kanzaki Hiroyuki , Wada Satoshi , Kumazawa Masao , Yamada Yuko , Sudo Tomomi , Ozawa Erika , Seko Takuya , Akaike Shun , Murakami Masumi , Oikawa Takashi , Okumura Satoshi , Nakamura Yoshiki , Tomonari Hiroshi 
Published: December 2019

AbstractMastication is closely related to brain function. Animal experiments have revealed that tooth loss has a negative influence on brain function. Clinical studies also suggest that normal occlusion is an essential factor for favorable brain function. Mandibular prognathism (MP) usually results in occlusal dysfunction. However, the relationship between MP and brain function remains unclear. In the present study, we examined the relationship between MP and brain function by measuring brain blood flow (BBF). Seventeen subjects with normal occlusion (NORM) and 25 patients with MP participated in this study. The number of occlusal contacts were counted. Electromyography of the masseter muscles during clenching was also recorded. BBF was measured with non-invasive functional near-infrared spectroscopy during calculation task and chewing task. The number of the occlusal contacts and masseter muscle activity were lower in MP compared with NORM. The calculation task increased BBF in both groups. The chewing task also increased BBF in the inferior frontal gyrus in both groups, although the increase in MP was smaller than in NORM. We discovered that patients with MP exhibited a smaller increase in BBF at the inferior frontal gyrus during chewing as compared with NORM. As such, MP would negatively affect brain function.
Macrophage-derived HIV-1 carries bioactive TGF-beta
Authors: Arakelyan Anush , Petersen Jennifer D. , Blazkova Jana , Margolis Leonid 
Published: December 2019

AbstractInfected T cells and macrophages are the main producers of HIV-1 in infected individuals. Upon release from infected cells, HIV-1 incorporates various cellular membrane proteins, some of which are specific for these cells. However, the functions of cell-encoded proteins in virions remain largely unknown. We performed flow virometry to identify, in plasma of HIV-infected individuals, macrophage- and T-cell-derived HIV-1 virions, using cell-specific markers CD36 and CD27, respectively. Using four different methods, we demonstrated that CD36 on virions binds the immunosuppressive cytokine transforming growth factor beta (TGF-β) through a ligand, thrombospondin one (TSP-1). Flow virometry of individual virions showed that TGF-β was present on CD36+ virions (average, 28.2% ± 6.6% (n = 3)) but not on CD27+ virions (average, 1% ± 0.1% (n = 3)). TGF-β molecules present on captured CD36+ virions were biologically active, as evaluated with a reporter cell line. Delivery of TGF-β on HIV virions to HIV target cells may affect them, playing a significant role in viral pathogenesis.
A Hybrid Process for Printing Pure and High Conductivity Nanocrystalline Copper and Nickel on Flexible Polymeric Substrates
Authors: Bhuiyan Md Emran Hossain , Behroozfar Ali , Daryadel Soheil , Moreno Salvador , Morsali Seyedreza , Minary-Jolandan Majid 
Published: December 2019

AbstractPrinting functional devices on flexible substrates requires printing of high conductivity metallic patterns. To prevent deformation and damage of the polymeric substrate, the processing (printing) and post-processing (annealing) temperature of the metal patterns must be lower than the glass transition temperature of the substrate. Here, a hybrid process including deposition of a sacrificial blanket thin film, followed by room environment nozzle-based electrodeposition, and subsequent etching of the blanket film is demonstrated to print pure and nanocrystalline metallic (Ni and Cu) patterns on flexible substrates (PI and PET). Microscopy and spectroscopy showed that the printed metal is nanocrystalline, solid with no porosity and with low impurities. Electrical resistivity close to the bulk (~2-time) was obtained without any thermal annealing. Mechanical characterization confirmed excellent cyclic strength of the deposited metal, with limited degradation under high cyclic flexure. Several devices including radio frequency identification (RFID) tag, heater, strain gauge, and temperature sensor are demonstrated.
The Catenulida flatworm can express genes from its microbiome or from the DNA it ingests
Authors: Rosa Marcos Trindade , Loreto Elgion L. S. 
Published: December 2019

AbstractStenostomum are tiny planarians of the phylum Platyhelminthes that reproduce asexually. We transfected these worms using plasmids containing a gfp reporter gene. Here we show that they can express genes present in plasmids carried by bacteria and those that are encoded by naked DNA, such as plasmids or PCR fragments, transfected by electroporation; they can also express genes taken up during feeding. The microbiome associated with worm maintenance was evaluated, and the results indicated that when a plasmid is maintained in the microbiome, gfp gene expression is stable. When genes originate from naked DNA or bacteria not maintained in the microbiome, GFP expression is transient. Therefore, changes in the microbiome can modify the ability of worms to express foreign genes. In stable GFP-expressing worms, NSG showed that the gfp gene was maintained in the plasmid and was not integrated into the chromosome. These results suggest that, at least for some organisms such as flatworms, the expression of genes provided by the microbiome or the environment can be considered among the potential sources of phenotypic plasticity, which can have implications for evolvability.
Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma
Authors: Wang Qian , Rao Yuting , Guo Xiaobing , Liu Na , Liu Shuxiu , Wen Peipei , Li Shuang , Li Yuan 
Published: December 2019

AbstractTo investigate the oral microflora of patients with oesophageal squamous cell carcinoma (ESCC), saliva samples were collected from 20 patients with ESCC and 21 healthy controls. The V3-V4 region of 16S rDNA was amplified and sequenced by the Illumina MiSeq high-throughput sequencing platform. The final sequences were used for OTU analysis. Alpha and beta diversity analysis showed that the bacterial diversity and richness of the ESCC group were lower than those of the control group, while the variability of the ESCC group was higher than that of the control group. According to the Metastats difference analysis and LEfSe analysis, the high risk of ESCC may be related to Actinomyces and Atopobium, while the healthy control group is closely related to Fusobacterium and Porphyromonas (the analysis was performed at the genus level). The establishment of the relationship between oral microbiota and risk of ESCC may lead to significant advances in understanding the aetiology of cancer and may open a new research paradigm for cancer prevention.
Prognostic role of ABO blood group and Rhesus factor in cirrhotic patients with hepatocellular carcinoma
Authors: Oral Alihan , Sahin Tolga 
Published: December 2019

AbstractHepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide. There are many factors in the etiology of HCC such as hepatitis B virus (HBV), hepatitis C virus (HCV), alcohol, obesity, smoking and aflatoxin. Many types of cancer are assumed to be associated with ABO blood group and Rhesus factor (RH). In this study we aimed to evaluate the relationship between tumor characteristics and overall survival (OS), ABO blood group and RH factor in patients with HCC. A total of 507 patients with chronic liver disease (252 patients with HCC and 255 patients without HCC) were included in the study. All demographic, clinic and laboratory (biochemical parameters and blood type) features were collected retrospectively. The mean age of the patients was 54.50 ± 9.30. There was no significant difference in both ABO groups and RH factors between the two groups. We found that vascular invasion rate of the tumor was higher in the B blood group and multicentric localization of tumor was significantly higer in patients with positive RH but there was no difference between OS in ABO and RH blood groups. In addition, the tumor was less multicentric in the AB blood group. Blood groups and RH factor can be used to predict the prognosis in cirrhotic patients with HCC.
Molecular stratification within triple-negative breast cancer subtypes
Authors: Wang Dong-Yu , Jiang Zhe , Ben-David Yaacov , Woodgett James R. , Zacksenhaus Eldad 
Published: December 2019

AbstractTriple-negative breast cancer (TNBC) has been subdivided into six distinct subgroups: basal-like 1 (BL1), basal-like 2 (BL2), mesenchymal (M), mesenchymal stem–like (MSL), immunomodulatory (IM), and luminal androgen receptor (LAR). We recently identified a subgroup of TNBC with loss of the tumor suppressor PTEN and five specific microRNAs that exhibits exceedingly poor clinical outcome and contains TP53 mutation, RB1 loss and high MYC and WNT signalling. Here, show that these PTEN-low/miRNA-low lesions cluster with BL1 TNBC. These tumors exhibited high RhoA signalling and were significantly stratified on the basis of PTEN-low/RhoA-signalling-high with hazard ratios (HRs) of 8.2 (P = 0.0009) and 4.87 (P = 0.033) in training and test cohorts, respectively. For BL2 TNBC, we identified AKT1 copy gain/high mRNA expression as surrogate for poor prognosis (HR = 3.9; P = 0.02 and HR = 6.1; P = 0.0032). In IM, programmed cell death 1 (PD1) was elevated and predictive of poor prognosis (HR = 5.3; P = 0.01 and HR = 3.5; P < 0.004). Additional alterations, albeit without prognostic power, characterized each subtype including high E2F2 and TGFβ signalling and CXCL8 expression in BL2, high IFNα and IFNγ signalling and CTLA4 expression in IM, and high EGFR signalling in MSL, and may be targeted for therapy. This study identified PTEN-low/RhoA-signalling-high, and high AKT1 and PD1 expression as potent prognostications for BL1, BL2 and IM subtypes with survival differences of over 14, 2.75 and 10.5 years, respectively. This intrinsic heterogeneity could be exploited to prioritize patients for precision medicine.
Low skeletal muscle area as a prognostic marker for chronic obstructive pulmonary disease in elderly patients admitted to ICU
Authors: Zhi Jiehua , Shan Qing , Liang Lanyu , Liu Han , Huang Hua 
Published: December 2019

AbstractLow L3 skeletal muscle area (SMA), which is assessed on computed tomography (CT) images, has been reported to indicate poor clinical outcomes of patients with acute exacerbation of chronic obstructive pulmonary disease (COPD). The dorsal muscle group area at the T12 vertebral level (T12DMA) was used as an alternative to L3 SMA. This study aimed to investigate whether T12DMA could be used as a predictor of in-hospital mortality and long-term survival in elderly patients with COPD admitted to the intensive care unit (ICU). This single-center retrospective case–control study was performed by analyzing the clinical information and measuring T12DMA on chest CT images of elderly patients with COPD admitted to the ICU between May 2013 and May 2018. This study included 136 patients. The multivariate logistic regression analysis showed that T12DMA, neutrophil–lymphocyte ratio, invasive mechanical ventilation, and systemic steroid therapy were independent risk factors for predicting the hospital mortality. The median survival was significantly higher in the high-T12DMA group (214 days) than in the low-T12DMA group (32 days).
The FTO gene polymorphism rs9939609 is associated with obesity and disability in multiple sclerosis patients
Authors: Al-Serri Ahmad , Alroughani Raed , Al-Temaimi Rabeah A. 
Published: December 2019

AbstractObesity is a well-known risk factor for multiple diseases including multiple sclerosis (MS). Polymorphisms in the fat-mass obesity (FTO) gene have been consistently found to be associated with obesity, and recently found to increase the risk of developing MS. We therefore assessed the common FTO gene polymorphism (rs9939609) in relation to obesity, risk of developing MS and its disability in a cohort of MS patients. A cohort of 200 MS patients (135 females and 65 males) were genotyped for the FTO rs9939609 polymorphism. Using both logistic and linear regression we assessed the relationship between the variant and the selected phenotypes under both an additive and recessive genetic models. The A-allele was found to be associated with being overweight/obese in MS patients (OR = 2.48 (95% CI 1.17–5.29); p = 0.01). In addition, The A-allele was also found to be associated with increased MS disability (β = 0.48 (95% CI 0.03–0.92); p = 0.03). However, no association was found with risk of developing MS (p > 0.05). Moreover, our association with obesity is consistent with previous reports, whereas the association with disability is novel and warrants further investigation on the role of FTO in disease progression.
A synergic approach for nutrient recovery and biodiesel production by the cultivation of microalga species in the fertilizer plant wastewater
Authors: Ambat Indu , Bec Sabina , Peltomaa Elina , Srivastava Varsha , Ojala Anne , Sillanpää Mika 
Published: December 2019

AbstractThe combination of wastewater treatment and biodiesel production using algal cultivation was studied in the present work. The two main goals of the work were achieved by the cultivation of freshwater microalgae such as Chlamydomonas sp., Scenedesmus ecornis, and Scenedesmus communis in two different dilutions of fertilizer plant wastewater (FWWD1 and FWWD2) collected from Yara Suomi Oy, Finland. The growth pattern of different algal species in FWWD1 and FWWD2 was observed. The effect of pH on biomass concentration, lipid content, biomass productivity, and lipid productivity by all three algal species in FWWD1 and FWWD2 were monitored. The maximum biomass concentration and productivity were observed in FWWD1 at pH7.5 for Chlamydomonas sp. and at pH 8.5 for S. ecornis and S. communis. The maximum lipid content was detected in Chlamydomonas sp at pH5.5, followed by S. ecornis and then S. communis at pH 7.5 in FWWD2 obtained after co-solvent extraction method. The most significant removal percentage of COD by all algal species were observed in FWWD1, whereas the highest removal percentage of TN and TP were detected in FWWD2, respectively. The fatty acid methyl ester (FAME) characterization of each algal species in FWWD1 and FWWD2 at their optimum pH was investigated to determine the quality of obtained biodiesel.
Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces
Authors: Hu Xingming , Cui Yongtao , Dong Guojun , Feng Anhui , Wang Danying , Zhao Chunyan , Zhang Yu , Hu Jiang , Zeng Dali , Guo Longbiao , Qian Qian 
Published: December 2019

AbstractGenetic erosion refers to the loss of genetic variation in a crop. In China, only a few original landraces of rice (Oryza sativa) were used in breeding and these became the primary genetic background of modern varieties. Expanding the genetic diversity among Chinese rice varieties and cultivating high-yielding and high-quality varieties with resistance to different biotic and abiotic stresses is critical. Here, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9(Cas9) genome editing system to edit Semi-Dwarf1 (SD1) in the elite landraces Kasalath and TeTePu (TTP), which contain many desired agronomic traits such as tolerance to low phosphorous and broad-spectrum resistance to several diseases and insects. Mutations of SD1 confer shorter plant height for better resistance to lodging. Field trials demonstrated that the yield of the new Kasalath and TTP mutant lines was better than that of the wild type under modern cultivation and that the lines maintained the same desirable agronomic characteristics as their wild-type progenitors. Our results showed that breeding using available landraces in combination with genomic data of different landraces and gene-editing techniques is an effective way to relieve genetic erosion in modern rice varieties.
Influence of dietary protein content on the chemico-physical profile of dry-cured hams produced by pigs of two breeds
Authors: Carcò Giuseppe , Schiavon Stefano , Casiraghi Ernestina , Grassi Silvia , Sturaro Enrico , Dalla Bona Mirco , Novelli Enrico , Gallo Luigi 
Published: December 2019

AbstractThe use of low-protein (LP) feeds is a good strategy to reduce the environmental release of N compounds, but their influence on the quality of the products must be considered. This study explored the influence of LP diet and two pig breeds (BR) with different lean growth ability on the quality traits of dry-cured hams. We analysed 40 left dry-cured hams from pigs of two BR [Duroc-Danbred crosses (Danbred) and Duroc × Large White crosses (Anas)] fed either conventional (147 to 132 g/kg, crude protein) or LP diet. The LP had a crude protein content reduced by 20% with respect to the conventional. The differences in ham quality resulting from protein reduction were small, with a decrease of the protein and an increase of the lipid content of the ham slice in Anas, but not in Danbred (BR × Diet interaction; P = 0.043). Therefore, the use of LP would be feasible and sustainable, without detrimental effects on products. It was found the pig genotypes with different potentials for lean growth may affect the initial ham weight, fat cover and seasoning losses of hams, but they appear to affect little other chemical, physical and textural quality traits of the dry-cured hams.
Unaltered intravenous prion disease pathogenesis in the temporary absence of marginal zone B cells
Authors: Bradford Barry M. , Mabbott Neil A. 
Published: December 2019

AbstractPrion diseases are a unique, infectious, neurodegenerative disorders that can affect animals and humans. Data from mouse transmissions show that efficient infection of the host after intravenous (IV) prion exposure is dependent upon the early accumulation and amplification of the prions on stromal follicular dendritic cells (FDC) in the B cell follicles. How infectious prions are initially conveyed from the blood-stream to the FDC in the spleen is uncertain. Addressing this issue is important as susceptibility to peripheral prion infections can be reduced by treatments that prevent the early accumulation of prions upon FDC. The marginal zone (MZ) in the spleen contains specialized subsets of B cells and macrophages that are positioned to continuously monitor the blood-stream and remove pathogens, toxins and apoptotic cells. The continual shuttling of MZ B cells between the MZ and the B-cell follicle enables them to efficiently capture and deliver blood-borne antigens and antigen-containing immune complexes to splenic FDC. We tested the hypothesis that MZ B cells also play a role in the initial shuttling of prions from the blood-stream to FDC. MZ B cells were temporarily depleted from the MZ by antibody-mediated blocking of integrin function. We show that depletion of MZ B cells around the time of IV prion exposure did not affect the early accumulation of blood-borne prions upon splenic FDC or reduce susceptibility to IV prion infection. In conclusion, our data suggest that the initial delivery of blood-borne prions to FDC in the spleen occurs independently of MZ B cells.