bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences
Authors: Nechin Julianna , Tunstall Emma , Raymond Naideline , Hamagami Nicole , Pathmanabhan Chris , Forestier Samantha , Davis Tamara L. 
Published: October 2019

Abstract

Background
In mammals, the regulation of imprinted genes is controlled by differential methylation at imprinting control regions which acquire parent of origin-specific methylation patterns during gametogenesis and retain differences in allelic methylation status throughout fertilization and subsequent somatic cell divisions. In addition, many imprinted genes acquire differential methylation during post-implantation development; these secondary differentially methylated regions appear necessary to maintain the imprinted expression state of individual genes. Despite the requirement for both types of differentially methylated sequence elements to achieve proper expression across imprinting clusters, methylation patterns are more labile at secondary differentially methylated regions. To understand the nature of this variability, we analyzed CpG dyad methylation patterns at both paternally and maternally methylated imprinted loci within multiple imprinting clusters.

Results
We determined that both paternally and maternally methylated secondary differentially methylated regions associated with imprinted genes display high levels of hemimethylation, 29–49%, in comparison to imprinting control regions which exhibited 8–12% hemimethylation. To explore how hemimethylation could arise, we assessed the differentially methylated regions for the presence of 5-hydroxymethylcytosine which could cause methylation to be lost via either passive and/or active demethylation mechanisms. We found enrichment of 5-hydroxymethylcytosine at paternally methylated secondary differentially methylated regions, but not at the maternally methylated sites we analyzed in this study.

Conclusions
We found high levels of hemimethylation to be a generalizable characteristic of secondary differentially methylated regions associated with imprinted genes. We propose that 5-hydroxymethylcytosine enrichment may be responsible for the variability in methylation status at paternally methylated secondary differentially methylated regions associated with imprinted genes. We further suggest that the high incidence of hemimethylation at secondary differentially methylated regions must be counteracted by continuous methylation acquisition at these loci.
Ultrasound-guided peripheral venous cannulation in critically ill patients: a practical guideline
Authors: Blanco Pablo 
Published: October 2019

Abstract

Background
Up to one-third of critically ill patients have difficult intravenous access (DIVA). This occurs often in obese patients, those with generalized edemas or in patients with previous venous cannulations. In DIVA patients, the conventional technique often fails. In contrast, ultrasound-guided cannulation has demonstrated a high success rate, improving patient satisfaction and even a reduction in the need of central venous lines. However, a high rate of premature catheter failure has been shown in cannulations performed by ultrasound guidance and thus a comprehensive knowledge of several aspects related to this procedure is mandatory to improve cannulation success, avoid complications and lengthen the survival of the catheter.

Main text
Several practical issues related to peripheral venous cannulation are described: peripheral venous anatomy, vein size and catheter selection, distance from skin to vein, insertion angle and selection of the catheter length, cannulation technique itself (out-of-plane or in-plane) and checking catheter position.

Conclusion
Key concepts regarding ultrasound-guided peripheral vein cannulation should be well known for practitioners, aiding in improving cannulation success and catheter dwell time, and avoiding complications.
Osteogenic potential of induced pluripotent stem cells from human adipose-derived stem cells
Authors: Mao Shih-Hsuan , Chen Chih-Hao , Chen Chien-Tzung 
Published: October 2019

Abstract

Background
Bone regeneration is a crucial and challenging issue in clinical practice. Bone tissue engineering (BTE) with an optimal cell source may provide an ideal strategy for the reconstruction of bone defects. This study examined whether induced pluripotent stem cells (iPSCs) derived from adipose-derived stem cells (ASCs) could act as an osteogenic substitute and whether these ASC-iPSCs yield more new bone formation than ASCs in hydrogel scaffolds.

Methods
ASC-iPSCs were reprogrammed from ASCs through a retroviral system. ASCs were harvested and isolated from adipose tissue of humans. An aliquot of cell suspension (1 × 106 cells/mL) was seeded directly onto the nHAP-gelatin cryogel scaffolds. Nude mice back implantation of cell-seeded scaffolds was designed for in vivo comparison of osteogenic potentials between ASCs and ASC-iPSCs. Samples were harvested 4 and 8 weeks after implantation for further analysis based on histology and RT-PCR.

Results
ASC-iPSCs were successfully obtained from human adipose-derived stem cells. PCR results also showed that specific genes of iPSCs with the ability to cause the differentiation of cells into the three germ layers were expressed. In our in vivo experiments, iPSCs were subcutaneously injected into nude mice to induce teratoma formation. The morphology of the three germ layers was confirmed by histological staining. ASC is an essential cell source for BTE with benefits of high volume and less-invasive acquisition. With additional transforming Yamanaka factors, ASC-iPSCs showed higher osteogenic differentiation and elevated expression of collagen type I (Col I), osteocalcin (OCN), alkaline phosphate (ALP), and runt-related transcription factor 2 (RunX-2).

Conclusions
This report suggests that ASC-iPSCs could be a superior cell source in BTE with better osteogenic differentiation efficacy for future clinical applications.
Antioxidants inhibit cell senescence and preserve stemness of adipose tissue-derived stem cells by reducing ROS generation during long-term in vitro expansion
Authors: Liao Naishun , Shi Yingjun , Zhang Cuilin , Zheng Youshi , Wang Yingchao , Zhao Bixing , Zeng Yongyi , Liu Xiaolong , Liu Jingfeng 
Published: October 2019

Abstract

Background
Adipose tissue-derived mesenchymal stem cells (ADSCs) are promising candidates for regenerative medicine. However, long-term in vitro passaging leads to stemness loss and cell senescence of ADSCs, resulting in failure of ADSC-based therapy.

Methods
In this study, ADSCs were treated with low dose of antioxidants (reduced glutathione and melatonin) with anti-aging and stem cell protection properties in the in vitro passaging, and the cell functions including stem cell senescence, cell migration, cell multidirectional differentiation potential, and ROS content were carefully analyzed.

Results
We found that GSH and melatonin could maintain ADSC cell functions through reducing cell senescence and promoting cell migration, as well as by preserving stemness and multidirectional differentiation potential, through inhibiting ROS generation during long-term expansion of ADSCs.

Conclusions
Our results suggested that antioxidant treatment could efficiently prevent the dysfunction and preserve cell functions of ADSCs after long-term passaging, providing a practical strategy to facilitate ADSC-based therapy.
Anti-inflammatory and vasculogenic conditioning of peripheral blood mononuclear cells reinforces their therapeutic potential for radiation-injured salivary glands
Authors: I Takashi , Sumita Yoshinori , Yoshida Takako , Honma Ryo , Iwatake Mayumi , Raudales Jorge Luis Montenegro , Shizuno Tomoko , Kuroshima Shinichiro , Masuda Haruchika , Seki Makoto , Tran Simon D. , Asahara Takayuki , Asahina Izumi 
Published: October 2019

Abstract

Background
There are currently no effective treatments available for patients with irreversible loss of salivary gland (SG) function caused by radiation therapy for head and neck cancer. In this study, we have developed an effective culture method to enhance the anti-inflammatory and vasculogenic phenotypes of peripheral blood mononuclear cells (PBMNCs) and investigated whether such effectively conditioned PBMNCs (E-MNCs) could regenerate radiation-injured SGs and ameliorate salivary secretory function in mice.

Methods
Mouse PBMNCs were expanded in primary serum-free culture with five vasculogenic proteins for 5 days, and then the resulting cells (E-MNCs) were analyzed for their characteristics. Subsequently, 5 × 104 E-MNCs (labeled with EGFP in some experiments) were injected intra-glandularly into a mouse model of radiation-injured atrophic submandibular glands. After 2–3 weeks, the submandibular glands were harvested, and then the injected E-MNCs were tracked. Four, 8, and 12 weeks after irradiation (IR), salivary outputs were measured to evaluate the recovery of secretory function, and the gland tissues were harvested for histological and gene expression analyses to clarify the effects of cell transplantation.

Results
The resulting E-MNCs contained an enriched population of definitive CD11b/CD206-positive (M2 macrophage-like) cells and showed anti-inflammatory and vasculogenic characteristics. Salivary secretory function in E-MNC-transplanted mice gradually recovered after 4 weeks post-irradiation (post-IR) and reached 3.8-fold higher than that of non-transplanted mice at 12 weeks. EGFP-expressing E-MNCs were detected in a portion of the vascular endothelium and perivascular gland tissues at 2 weeks post-IR, but mainly in some microvessels at 3 weeks. Between 4 and 12 weeks post-IR, mRNA expression and histological analyses revealed that E-MNC transplantation reduced the expression of inflammatory genes and increased the level of tissue-regenerative activities such as stem cell markers, cell proliferation, and blood vessel formation. At 12 weeks post-IR, the areas of acinar and ductal cells regenerated, and the glands had less fibrosis.

Conclusions
This effective conditioning of PBMNCs is a simple, rapid, and efficient method that provides a non-invasive source of therapeutic cells for regenerating radiation-injured atrophic SGs.
Towards the understanding of the enzymatic cleavage of polyisoprene by the dihaem-dioxygenase RoxA
Authors: Schmitt Georg , Birke Jakob , Jendrossek Dieter 
Published: October 2019

AbstractUtilization of polyisoprene (natural rubber) as a carbon source bySteroidobacter cummioxidans35Y (previouslyXanthomonassp. strain 35Y) depends on the formation and secretion of rubber oxygenase A (RoxA). RoxA is a dioxygenase that cleaves polyisoprene to 12-oxo-4,8-dimethyl-trideca-4,8-diene-1-al (ODTD), a suitable growth substrate forS. cummioxidans. RoxA harbours two non-equivalent, spectroscopically distinguishable haem centres. A dioxygen molecule is bound to the N-terminal haem of RoxA and identifies this haem as the active site. In this study, we provide insights into the nature of this unusually stable dioxygen-haem coordination of RoxA by a re-evaluation of previously published together with newly obtained biophysical data on the cleavage of polyisoprene by RoxA. In combination with the meanwhile available structure of RoxA we are now able to explain several uncommon and previously not fully understood features of RoxA, the prototype of rubber oxygenases in Gram-negative rubber-degrading bacteria.
Sources and reservoirs of Staphylococcus capitis NRCS-A inside a NICU
Authors: Butin Marine , Dumont Yann , Monteix Alice , Raphard Aurane , Roques Christine , Martins Simoes Patricia , Picaud Jean-Charles , Laurent Frédéric 
Published: October 2019

Abstract

Background
The methicillin-resistant clone Staphylococcus capitis NRCS-A, involved in sepsis in neonatal intensive care units (NICUs) worldwide, is able to persist and spread in NICUs, suggesting the presence of reservoirs inside each setting. The purpose of the present study was to identify these reservoirs and to investigate the cycle of transmission of NRCS-A in one NICU.

Methods
In a single institution study, NRCS-A was sought in 106 consecutive vaginal samples of pregnant women to identify a potential source of NRCS-A importation into the NICU. Additionally NICU caregivers and environmental including incubators were tested to identify putative secondary reservoirs. Finally, the efficacy of disinfection procedure in the elimination of NRCS-A from incubators was evaluated.

Results
No S. capitis was isolated from vaginal samples of pregnant women. Three of the 21 tested caregivers (14%) carried S. capitis on their hands, but none remain positive after a five-day wash-out period outside NICU. Moreover, the clone NRCS-A persisted during six consecutive weeks in the NICU environment, but none of the sampled sites was constantly contaminated. Finally in our before/after disinfection study, all of 16 incubators were colonized before disinfection and 10 (62%) incubators remained colonized with NRCS-A after the disinfection procedure.

Conclusions
The partial ineffectiveness of incubators’ disinfection procedures is responsible for persistence of NRCS-A inside a NICU, and the passive hand contamination of caregivers could be involved in the inter-patient transmission of S. capitis.
HIF-1α contributes to Ang II-induced inflammatory cytokine production in podocytes
Authors: Huang Hao , Fan Yanqin , Gao Zhao , Wang Wei , Shao Ning , Zhang Lu , Yang Yingjie , Zhu Weifang , Chen Zhaowei , Hu Jijia , Ding Guohua 
Published: October 2019

Abstract

Background
Studies have indicated that changed expression of hypoxia-inducible factor-1α (HIF-1α) in epithelial cells from the kidney could affect the renal function in chronic kidney disease (CKD). As Angiotensin II (Ang II) is a critical active effector in the renin-angiotensin system (RAS) and was proved to be closely related to the inflammatory injury. Meanwhile, researchers found that Ang II could alter the expression of HIF-1α in the kidney. However, whether HIF-1α is involved in mediating Ang II-induced inflammatory injury in podocytes is not clear.

Methods
Ang II perfusion animal model were established to assess the potential role of HIF-1α in renal injury in vivo. Ang II stimulated podocytes to observe the corresponding between HIF-1α and inflammatory factors in vitro.

Results
The expression of inflammatory cytokines such as MCP-1 and TNF-α was increased in the glomeruli from rats treated with Ang II infusion compared with control rats. Increased HIF-1α expression in the glomeruli was also observed in Ang II-infused rats. In vitro, Ang II upregulated the expression of HIF-1α in podocytes. Furthermore, knockdown of HIF-1α by siRNA decreased the expression of MCP-1 and TNF-α. Moreover, HIF-1α siRNA significantly diminished the Ang II-induced overexpression of HIF-1α.

Conclusion
Collectively, our results suggest that HIF-1α participates in the inflammatory response process caused by Ang II and that downregulation of HIF-1α may be able to partially protect or reverse inflammatory injury in podocytes.
An analytical study of information extraction from unstructured and multidimensional big data
Authors: Adnan Kiran , Akbar Rehan 
Published: October 2019

AbstractProcess of information extraction (IE) is used to extract useful information from unstructured or semi-structured data. Big data arise new challenges for IE techniques with the rapid growth of multifaceted also called as multidimensional unstructured data. Traditional IE systems are inefficient to deal with this huge deluge of unstructured big data. The volume and variety of big data demand to improve the computational capabilities of these IE systems. It is necessary to understand the competency and limitations of the existing IE techniques related to data pre-processing, data extraction and transformation, and representations for huge volumes of multidimensional unstructured data. Numerous studies have been conducted on IE, addressing the challenges and issues for different data types such as text, image, audio and video. Very limited consolidated research work have been conducted to investigate the task-dependent and task-independent limitations of IE covering all data types in a single study. This research work address this limitation and present a systematic literature review of state-of-the-art techniques for a variety of big data, consolidating all data types. Recent challenges of IE are also identified and summarized. Potential solutions are proposed giving future research directions in big data IE. The research is significant in terms of recent trends and challenges related to big data analytics. The outcome of the research and recommendations will help to improve the big data analytics by making it more productive.
Impacts of fire severity and cattle grazing on early plant dynamics in old-growth Araucaria-Nothofagus forests
Authors: Arroyo-Vargas Paola , Fuentes-Ramírez Andres , Muys Bart , Pauchard Aníbal 
Published: October 2019

Abstract

Background
Fire has historically shaped the dynamics of Araucaria araucana-Nothofagus pumilio forests in the Andean region of South America. Nevertheless, human disturbances and stronger drought events have resulted in increased occurrence and severity of wildfires. Regardless of their conservation relevance, the initial response to fire of Araucaria-Nothofagus forests has not been well documented. Through this research we tested the hypothesis that plant composition of Araucaria-Nothofagus forest after fire will initially differ in its recovery depending on fire severity, but over time, plant similarity will increase among areas with different levels of fire severity. The study was carried out in old-growth Araucaria-Nothofagus forests in south-central Chile (38°S) that were burned in 2015. We studied vegetation response to three levels of fire severity (low (LS), moderate (MS) and high (HS) severity), also including an adjacent unburned forest (UN), which were assessed one, two and three years after fire. We also evaluated the impact of cattle on plant recovery after fire. We measured species richness, abundance, plant diversity and origin of all vascular plant species.

Results
Species richness and plant abundance responded differently to fire severity. Time-since-fire had a significant effect on plant richness and abundance. Plant composition within LS areas was similar to UN areas, but MS and HS areas were significantly less diverse compared to UN and LS. In absence of other major disturbances, similarity in plant composition tended to increase over time across the different levels of fire severity, becoming more similar to UN. We also found a synergetic effect of cattle and fire on species richness. This interaction promotes the establishment of non-native species and limits the recovery of native species following fire.

Conclusions
Fire severity had a significant impact on the plant community of old-growth Araucaria-Nothofagus forests, especially in areas of high fire severity, where the native tree N. pumilio was completely absent. Nevertheless, plant communities can recover gradually, depending on fire severity, time-since-fire, and the absence of cattle grazing. Management actions should include the exclusion of cattle within fire-affected areas and afforestation with N. pumilio in areas high fire severity due to its unsuccessful recruitment after fire.
Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi
Authors: Kwon Min Jin , Schütze Tabea , Spohner Sebastian , Haefner Stefan , Meyer Vera 
Published: October 2019

AbstractBackgroundWithin the last years, numerous reports described successful application of the CRISPR nucleases Cas9 and Cpf1 for genome editing in filamentous fungi. However, still a lot of efforts are invested to develop and improve protocols for the fungus and genes of interest with respect to applicability, scalability and targeting efficiencies. These efforts are often hampered by the fact that—although many different protocols are available—none have systematically analysed and compared different CRISPR nucleases and different application procedures thereof for the efficiency of single- and multiplex-targeting approaches in the same fungus.ResultsWe present here data for successful genome editing in the cell factoryThermothelomyces thermophilus, formerly known asMyceliophthora thermophila, using the three different nucleases SpCas9, FnCpf1, AsCpf1 guided to four different gene targets of our interest. These included a polyketide synthase (pks4.2), an alkaline protease (alp1), a SNARE protein (snc1) and a potential transcription factor (ptf1). For all four genes, guide RNAs were developed which enabled successful single-targeting and multiplex-targeting. CRISPR nucleases were either delivered toT. thermophiluson plasmids or preassembled with in vitro transcribed gRNA to form ribonucleoproteins (RNPs). We also evaluated the efficiency of single oligonucleotides for site-directed mutagenesis. Finally, we were able to scale down the transformation protocol to microtiter plate format which generated high numbers of positive transformants and will thus pave the way for future high-throughput investigations.ConclusionWe provide here the first comprehensive analysis and evaluation of different CRISPR approaches for a filamentous fungus. All approaches followed enabled successful genome editing inT. thermophilus; however, with different success rates. In addition, we show that the success rate depends on the respective nuclease and on the targeted gene locus. We finally present a practical guidance for experimental considerations aiming to guide the reader for successful implementation of CRISPR technology for other fungi.
A thematic corpus-based study of idioms in the Corpus of Contemporary American English
Authors: Rafatbakhsh Elaheh , Ahmadi Alireza 
Published: October 2019

AbstractThe traditional approach to presenting idioms relies mainly on teachers’ or materials writers’ judgement, one-by-one and quite incidentally; and the existing teaching materials and references for idioms are mostly intuition-based. However, a more recent approach to better teaching and learning idioms is to present them under categories of their common themes and topics. Corpus linguistics can be of much contribution through helping the design and development of more authentic and systematic materials using comprehensive corpora which are typically the best representatives of the target language. In this connection, the present study aimed at searching for the thematic index of 1506 idioms under 81 categories at the end of the Oxford Dictionary of Idioms in the largest freely available corpus, i.e. the Corpus of Contemporary American English (COCA), composed of more than 520 million words. To this end, we used a manuscript in PHP written by a professional computer programmer especially for this purpose. The findings yielded a list of idioms sorted based on their frequencies under their theme-based categories. To focus on the more frequently-used idioms of various themes in real contexts, materials designers, teachers, and learners of English can benefit from this idiom list in textbooks and classroom activities.