bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide atlas of alternative polyadenylation in the forage legume red clover
Authors: Chakrabarti Manohar , Dinkins Randy D. , Hunt Arthur G. 
Published: July 2018

AbstractStudies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called ‘poly(A)-tag sequencing’ (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between tissue types were determined. Analysis of spatial expression of genes encoding different poly(A) factors showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation in diverse plant species of APA events in mRNAs encoding two key polyadenylation factors, CPSF30 and FIP1(V). Together with our previously reported study of spatial gene expression in red clover, this study will provide a comprehensive account of transcriptome dynamics in this non-model forage legume.
Associations of unconventional natural gas development with depression symptoms and disordered sleep in Pennsylvania
Authors: Casey Joan A. , Wilcox Holly C. , Hirsch Annemarie G. , Pollak Jonathan , Schwartz Brian S. 
Published: July 2018

AbstractEnvironmental and community factors may influence the development or course of depression and sleep problems. We evaluated the association of unconventional natural gas development (UNGD) with depression symptoms and disordered sleep diagnoses using the Patient Health Questionnaire-8 and electronic health record data among Geisinger adult primary care patients in Pennsylvania. Participants received a retrospective metric for UNGD at their residence (very low, low, medium, and high) that incorporated dates and durations of well development, distance from patient homes to wells, and well characteristics. Analyses included 4,762 participants with no (62%), mild (23%), moderate (10%), and moderately severe or severe (5%) depression symptoms in 2014–2015 and 3,868 disordered sleep diagnoses between 2009–2015. We observed associations between living closer to more and bigger wells and depression symptoms, but not disordered sleep diagnoses in models weighted to account for sampling design and participation. High UNGD (vs. very low) was associated with depression symptoms in an adjusted negative binomial model (exponentiated coefficient = 1.18, 95% confidence interval [CI]: 1.04–1.34). High and low UNGD (vs. very low) were associated with depression symptoms (vs. none) in an adjusted multinomial logistic model. Our findings suggest that UNGD may be associated with adverse mental health in Pennsylvania.
Evaluation and validation of HPV real-time PCR assay for the detection of HPV DNA in oral cytobrush and FFPE samples
Authors: Harlé Alexandre , Guillet Julie , Thomas Jacques , Sastre-Garau Xavier , Rouyer Marie , Ramacci Carole , Gilson Pauline , Dubois Cindy , Dolivet Gilles , Leroux Agnès , Salleron Julia , Merlin Jean-Louis 
Published: July 2018

AbstractSpecific HPV genotypes have been recognized as risk factors inducing head and neck cancers (HNC). The aim of this study was to validate a real-time PCR assay to detect accurately High Risk HPV DNA in Formalin Fixed Paraffin Embedded (FFPE) and oral cytobrush samples and compare the results with conventional PCR. Repeatability, reproducibility and limit of detection of Cobas assay were estimated for oral cytobrush and FFPE samples of patients with HNC. 53 samples of patients with a HNC were then used for assay comparison with conventional PCR. Finally, 26 samples of patients with anogenital neoplasia cancer were analyzed as control and assays comparison. Among the 53 samples of patients with HNC, 12 (26.7%) were HPV positive, 33 (73.3%) were HPV negative and 8 (15.1%) were non contributive with the Cobas assay. Among the 26 samples of patients with anogenital neoplasia, 15 (57.7%) were HPV positive and 11 were HPV negative (42.3%). One sample was found with an HPV 16 and HPV 18 co-infection. Only 3 samples were found with discrepant results. Cobas assay was found suitable for routine HPV detection with a very good repeatability and reproducibility for all HPV genotypes (CV < 0.6% and <0.4% respectively). Sensitivity and specificity for Cobas assay were 91.7% [61.5%;99.8%] and 96.9% [83.8%;99.9%] respectively. Ten nanograms of DNA were sufficient for the detection of HPV 16, HPV 18 and HPV in FFPE and oral cytobrush samples. Cobas assay was found comparable to conventional PCR and can detect accurately and rapidly HPV DNA in FFPE and oral cytobrush samples for the management of HNC and other types of HPV-associated neoplasia.
LncRNA MALAT1 up-regulates VEGF-A and ANGPT2 to promote angiogenesis in brain microvascular endothelial cells against oxygen–glucose deprivation via targettingmiR-145
Authors: Ren Lanfen , Wei Chunxia , Li Kui , Lu Zuneng 
Published: July 2018

AbstractStroke is one of the leading causes of death and long-term disability around the world. Angiogenesis is supposed to protect brain microvascular endothelial cells (BMECs) from oxidative and ischemic stress. Previous studies indicated that interaction between metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and miR-145 was involved in myocardial ischemia reperfusion, suggesting MALAT1 and miR-145 were also mediated with the progress of angiogenesis and cell migration in oxygen–glucose deprivation (OGD)-induced BMECs. The present study aimed to investigate the functional roles of MALAT1 in regulating miR-145 and its downstream pro-angiogenesis factors, vascular endothelial growth factor (VEGF)-A and Angiopoietin-2 (ANGPT2) during the progress of angiogenesis in OGD-induced BMECs. An in vitro OGD model was employed in mouse BMECs to mimic brain hypoxic and ischemic conditions; MTT was used to determine cell viability. qRT-PCR was used to determine the expression of long non-coding RNA (lncRNA)-MALAT1 and miR-145 under OGD conditions; in vitro tube formation assay was used to investigate angiogenic effect of MALAT1 and miR-145. The relationship between lncRNA-MALAT1/miR-145 and miR-145/VEGF-A/ANGPT2 was evaluated by qRT-PCR and Western blot, and direct binding was assessed using dual luciferase assay. Results showed that the levels of lncRNA-MALAT1 and miR-145 were up-regulated in OGD-induced BMECs. miR-145 functioned as an anti-angiogenic and pro-apoptotic factor in OGD treated BMECs via down-regulating VEGF-A and ANGPT2 directly. While lncRNA-MALAT1 enhanced the expressions of VEGF-A and ANGPT2 by targetting miR-145 to promote angiogenesis and proliferation of BMECs under OGD conditions. Our present study revealed the inhibitory functions of miR-145 on angiogenesis through direct targetting on VEGF-A and ANGPT2 for the first time and proved the protective role of lncRNA-MALAT1 for BMECs under OGD conditions through the direct regulation of miR-145.
Modulation of the renin–angiotensin system in white adipose tissue and skeletal muscle: focus on exercise training
Authors: Frantz Eliete Dalla Corte , Prodel Eliza , Braz Igor Dutra , Giori Isabele Gomes , Bargut Thereza Cristina Lonzetti , Magliano D’Angelo Carlo , Nobrega Antonio Claudio Lucas 
Published: July 2018

Overactivation of the renin–angiotensin (Ang) system (RAS) increases the classical arm (Ang-converting enzyme (ACE)/Ang II/Ang type 1 receptor (AT1R)) to the detriment of the protective arm (ACE2/Ang 1-7/Mas receptor (MasR)). The components of the RAS are present locally in white adipose tissue (WAT) and skeletal muscle, which act co-operatively, through specific mediators, in response to pathophysiological changes. In WAT, up-regulation of the classical arm promotes lipogenesis and reduces lipolysis and adipogenesis, leading to adipocyte hypertrophy and lipid storage, which are related to insulin resistance and increased inflammation. In skeletal muscle, the classical arm promotes protein degradation and increases the inflammatory status and oxidative stress, leading to muscle wasting. Conversely, the protective arm plays a counter-regulatory role by opposing the effect of Ang II. The accumulation of adipose tissue and muscle mass loss is associated with a higher risk of morbidity and mortality, which could be related, in part, to overactivation of the RAS. On the other hand, exercise training (ExT) shifts the balance of the RAS towards the protective arm, promoting the inhibition of the classical arm in parallel with the stimulation of the protective arm. Thus, fat mobilization and maintenance of muscle mass and function are facilitated. However, the mechanisms underlying exercise-induced changes in the RAS remain unclear. In this review, we present the RAS as a key mechanism of WAT and skeletal muscle metabolic dysfunction. Furthermore, we discuss the interaction between the RAS and exercise and the possible underlying mechanisms of the health-related aspects of ExT.
A phylogenetic approach to chemical tagging
Authors: Blanco-Cuaresma Sergi , Fraix-Burnet Didier 
Published: July 2018

Context. The chemical tagging technique is a promising approach to reconstructing the history of the Galaxy by only using stellar chemical abundances. Multiple studies have undertaken this analysis and they have raised several challenges.
Aims. Using a sample of open cluster stars, we wish to address two issues: minimize chemical abundance differences whose origin is linked to the evolutionary stage of the stars and not their original composition and evaluate a phylogenetic approach to group stars based on their chemical composition.
Methods. We derived differential chemical abundances for 207 stars, belonging to 34 open clusters, using the Sun as reference star (classical approach) and a dwarf plus a giant star from the open cluster M 67 as reference (new approach). These abundances were then used to perform two phylogenetic analyses: cladistics (maximum parsimony) and neighbor joining, together with a partitioning unsupervised classification analysis with k-means. The resulting groupings were finally confronted to the true open cluster memberships of the stars.
Results. We successfully reconstruct most of the original open clusters when carefully selecting a subset of the abundances derived differentially with respect to M 67. We find a set of eight chemical elements that yield the best result and discuss the possible reasons for these elements to be good tracers of the history of the Galaxy.
Conclusions. Our study shows that unraveling the history of the Galaxy by only using stellar chemical abundances is greatly improved provided that i) we perform a differential spectroscopic analysis with respect to an open cluster instead of the Sun, ii) select the chemical elements that are good tracers of the history of the Galaxy, and iii) use tools that are adapted to detect evolutionary tracks such as phylogenetic approaches.
Duty cycle of the radio galaxy B2 0258+35
Authors: Brienza M. , Morganti R. , Murgia M. , Vilchez N. , Adebahr B. , Carretti E. , Concu R. , Govoni F. , Harwood J. , Intema H. , Loi F. , Melis A. , Paladino R. , Poppi S. , Shulevski A. , Vacca V. , Valente G. 
Published: July 2018

Context. Radio loud active galactic nuclei (AGN) are episodic in nature, cycling through periods of activity and quiescence. The study of this duty cycle has recently gained new relevance because of the importance of AGN feedback for galaxy evolution.Aims. In this work we investigate the duty cycle of the radio galaxy B2 0258+35, which was previously suggested to be a restarted radio galaxy based on its morphology. The radio source consists of a pair of kpc-scale jets embedded in two large-scale lobes (∼240 kpc) with relaxed shape and very low surface brightness, which resemble remnants of a past AGN activity.Methods. We have combined new LOFAR data at 145 MHz and new Sardinia Radio Telescope data at 6600 MHz with available WSRT data at 1400 MHz to investigate the spectral properties of the outer lobes and derive their age.Results. Interestingly, the spectrum of both the outer northern and southern lobes is not ultra-steep as expected for an old ageing plasma with spectral index values equal to α1451400= 0.48 ± 0.11 and α14006600= 0.69 ± 0.20 in the outer northern lobe, and α1451400= 0.73 ± 0.07 in the outer southern lobe. Moreover, despite the wide frequency coverage available for the outer northern lobe (145–6600 MHz), we do not identify a significant spectral curvature (SPC ≃ 0.2 ± 0.2).Conclusions. While mechanisms such as in-situ particle reacceleration, mixing or compression can temporarily play a role in preventing the spectrum from steepening, in no case seem the outer lobes to be compatible with being very old remnants of past activity as previously suggested (with age ≳ 80 Myr). We conclude that either the large-scale lobes are still fuelled by the nuclear engine or the jets have switched off no more than a few tens of Myr ago, allowing us to observe both the inner and outer structure simultaneously. Our study shows the importance of combining morphological and spectral properties to reliably classify the evolutionary stage of low surface brightness, diffuse emission that low frequency observations are revealing around a growing number of radio sources.
Cryptotanshinone from Salvia miltiorrhiza Roots Reduces Cytokeratin CK1/10 Expression in Keratinocytes by Activation of Peptidyl-prolyl-cis-trans-isomerase FKBP1A
Authors: Esch Stefan , König Simone , Bopp Bertan , Jose Joachim , Brandt Simone , Hensel Andreas 
Published: July 2018

AbstractCryptotanshinone (CTS) (1 µM) from the roots of Salvia miltiorrhiza exerts a strong influence on the terminal differentiation of human keratinocytes (HaCaT cell line, primary natural human keratinocytes) and downregulates the expression of differentiation-specific cytokeratins CK1 and CK10 on protein and gene level. Other differentiation specific proteins as involucrin, filaggrin, loricrin, and transglutaminase were not affected to a higher extent. CTS (1 µM) did not influence the cell viability and the proliferation of keratinocytes. Using a combination of drug affinity response target stability assay in combination with a proteomic approach and multivariate statistics for target elucidation, peptidyl-prolyl-cis-trans-isomerase FKBP1A (known target of inhibitors such as tacrolimus or rapamycin) was addressed as potential molecular target of CTS. The interaction of CTS with FKBP1A was additionally shown by thermal shift and enzymatic activity assays. Interestingly, CTS served as an activator of FKBP1A, which led to a reduced activity of the TGFβ receptor pathway and therefore to a diminished CK1 and CK10 expression. The combination of the FKBP1A activator CTS with the inhibitor tacrolimus neutralized the effects of both compounds. From these data, a potential dermatological use of CTS and CTS-containing plant extracts (e.g., hydroalcoholic extract from the roots of S. miltiorrhiza) for keratinopathic ichthyosis, a disease characterized by overexpression of CK1 and CK10, is discussed. This study displays an experimental strategy for combining phytochemical aspects on active natural products with systematic identification of molecular targets on gene, protein, and cell level.
Syntheses and Redox Chemistry of Antiaromatic Core-Modified Isophlorinoids
Authors: Anand Venkataramanarao , Panchal Santosh , Reddy Baddigam 
Published: July 2018

During the attempted total synthesis of chlorophyll, Woodward hypothesized the formation of tetrapyrrolic 20π isophlorin as a transient antiaromatic intermediate which provides a plausible template to synthesize stable antiaromatic molecules. Despite its structural similarity with the 18π aromatic porphyrin, it significantly differs in its electronic and chemical properties. However, due to its unstable nature under ambient conditions it immediately gets oxidized to stable 18π aromatic porphyrin. Similar macrocyclic structures with β-substituted heterocycles, such as furan/thiophene/selenophene, have been synthesized, which undergo facile oxidation to yield the 18π porphyrin dication. Attempts to synthesize stable tetrapyrrolic isophlorin and its metal complex have remained unaccomplished till date. Strategies to synthesize stable core-modified 20π isophlorin and its confused isophlorin derivative have met with considerable success. Predominantly, they are synthesized by replacing three or four pyrroles with furan/thiophene. The 20π systems either with four furan units or with a ‘pair’ of furan and thiophene units were sufficiently stable enough to resist oxidation towards the corresponding porphyrin dication. The 20π isophlorins displayed noncovalent interactions with the curved π surface of fullerene which predominantly rises due to van der Waals attraction between the dissimilar π systems. This antiaromatic isophlorin-fullerene complexes were obtained and successfully characterized by single-crystal X-ray diffraction studies. Replacing only three pyrroles by furan rings yielded the first stable pyrrole derivative of antiaromatic 20π isophlorin, which can be reversibly oxidized to 18π aromatic porphyrin without deprotonating the inner pyrrole NH. In addition, replacing all the pyrrole units of N-confused porphyrin with thiophene yielded the first derivative of confused isophlorin. Further, its two-electron oxidation led to the formation of 18π aromatic cation with enhanced aromaticity. The structure and electronic properties of the oxidized and neutral species were unambiguously determined from a combination of spectroscopic techniques, X-ray crystallography, and computational methods. These studies reveal that antiaromatic systems like isophlorin and its confused isophlorin derivative can be stabilized under ambient conditions and they offer potential to explore the chemistry of 4nπ systems. This Account focuses of recent advances in 20π antiaromatic isophlorins, confused isophlorins, and nocorroles along with their redox chemistry.
1	Introduction2	Stable 20π Isophlorins2.1	Furan-/Thiophene-Based Isophlorins2.2	Pyrrole Isophlorins3	Confused Isophlorins3.1	Isophlorin-Fullerene3.2	meso-meso-Bridged Tetraoxaisophlorin Dimer4.	Norcorroles5.	Conclusion and Outlook
Perioperative Use of Anticoagulant and Platelet-inhibiting Medications for Elective Spine Surgery: Results of a Nationwide Survey
Authors: Oberle Joachim , Grubhofer Florian , Schmid Samuel , Baschera Dominik 
Published: July 2018

Background and Study Aims Perioperative use of anticoagulant and platelet-inhibiting agents by patients undergoing spine surgery poses the dilemma of increased risk of hemorrhage. We examined the standards of use for these medications and expert opinions through a nationwide survey.
Materials and Methods An online-based survey was conducted by invitation. A personal token to access the survey was sent to one representative of each neurosurgical and orthopaedic unit performing spine surgery and to all other active members of the Swiss Society of Neurosurgery and the Swiss Society of Spinal Surgery. A total of 97 e-mail invitations were sent to 19 representatives of neurosurgical or orthopaedic units and 78 registered neurosurgeons and orthopaedic surgeons who potentially perform spine surgery.
Results From February to April 2016, 40 surgeons (26 neurosurgeons, 14 orthopaedic surgeons) completed the survey (41%). Among the respondents, 55% prescribed prophylactic heparin preoperatively; depending on the procedure, 83 to 95% prescribed heparin postoperatively. Depending on the type of surgery, 23 to 48% discontinued acetylic acid preoperatively, and 80 to 87% always discontinued clopidogrel preoperatively. On average, platelet inhibition was resumed 4 ± 2.5 days postoperatively. Orthopaedic surgeons recommenced platelet inhibition earlier than neurosurgeons (p = 0.013). Anticoagulation with rivaroxaban was discontinued 3 ± 2 days before surgery. Depending on the indication, 72 to 98% of respondents temporarily replaced traditional anticoagulation therapy (vitamin K antagonists) with heparin perioperatively.
Conclusion Administration and discontinuation of anticoagulant and platelet-inhibiting medications in the perioperative setting of spinal surgery differ vastly between different units and surgeons. Recommendations from the spine surgeon societies may be helpful to develop nationwide guidelines.
Percutaneous Endoscopic Interlaminar Unilateral Ventral Dural Approach for Symptomatic Bilateral L5–S1 Herniated Nucleus Pulposus: Technical Note
Authors: Choi Sung , Adsul Nitin , Kim Ki , Kim Jeong , Chung Sung , Choi Jeong , Jang Jee , Jang Il , Oh Seong , Kim Hyeun 
Published: July 2018

Background Percutaneous endoscopic lumbar diskectomy is a good treatment modality for lumbar disk herniation. However, when a patient complains of bilateral lower limb radicular pain with severe disk protrusion at the L5–S1 level, the transforaminal approach is often unable to resolve both lesions owing to anatomical limitations. It is also very difficult to resolve both lesions in an ipsilateral direction using the percutaneous interlaminar approach. We report our surgical technique and clinical results using a ventral dural approach of percutaneous endoscopic interlaminar lumbar diskectomy for L5–S1 herniated nucleus pulposus (HNP) in patients with bilateral radiculopathy due to a severe disk protrusion.
Methods Twenty-seven patients with severe L5–S1 HNP complaining of back pain and bilateral lower limb pain were included in the study. The unilateral ventral dural approach of percutaneous full endoscopic interlaminar lumbar diskectomy technique was used. The visual analog scale (VAS) and Macnab criteria were used for clinical evaluation. All assessments were completed 1 day before surgery, 1 week after surgery, 6 months after surgery, and at final follow-up after surgery.
Results The mean preoperative back and leg pain VAS scores decreased from 5.67 ± 0.78 and 7.81 ± 0.83 to 2.44 ± 0.58 and 2.26 ± 0.53 at 1 week, 1.78 ± 0.51 and 1.52 ± 0.58 at 6 months, and 1.56 ± 0.70 and 1.67 ± 0.96, respectively, at the final follow-up after surgery. With respect to the Macnab criteria, 51.85% of the results were excellent, 44.44% were good, and 3.70% were fair. Four cases recurred: three patients underwent conservative treatment and one patient operated with percutaneous endoscopic interlaminar lumbar diskectomy.
Conclusion According to the results of this study, the ventral dural approach of percutaneous full endoscopic interlaminar lumbar diskectomy in patients with L5–S1 HNP associated with bilateral lower limb pain due to a severely protruded HNP is a good option for a minimally invasive surgical approach.
Laminar Flow Induces Cell Polarity and Leads to Rearrangement of Proteoglycan Metabolism in Endothelial Cells
Authors: Grimm Johannes , Keller Ruprecht , Groot Philip G de 
Published: July 2018

SummaryBovine aortic endothelial cells in tissue culture were incubated with [35S]-sulfate to examine the pattern of proteoglycan production at various shear rates. It was observed that culturing bovine aortic endothelial cells under laminar flow changes the secretion pattern of proteoglycans to that observed in perfused organ cultures, induces polarity of secretion, down-regulates proteoglycan biosynthesis and decreases uptake of sulfate. These results indicate that surface shear is a major force influencing the endothelial cellular phenotype. The changed pattern of proteogly can release under static conditions may contribute to the anticoagulant effect of endothelial cells which is much needed when activated coagulation factors are not dispersed by flow.