bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae
Authors: Kundu Shantanu , Kumar Vikas , Tyagi Kaomud , Chakraborty Rajasree , Singha Devkant , Rahaman Iftikar , Pakrashi Avas , Chandra Kailash 
Published: November 2018

AbstractThe characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle,Nilssonia nigricanswas sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency inN. nigricans,N. formosa, andR. swinhoei. InN. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except fortrnS1(GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except fortrnE(TTC),trnQ(TTG), andtrnM(CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome ofN. nigricansalso revealed two unique tandem repeats (ATTAT)8,and (TATTA)20in the CR. Further, the conserved motif 5′-GACATA-3′ and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering ofN. nigricanswithN. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.
A comparison of the Macintosh laryngoscope, McGrath video laryngoscope, and Pentax Airway Scope in paediatric nasotracheal intubation
Authors: Yoo Ji Young , Chae Yun Jeong , Lee Young Bok , Kim Sujin , Lee Jaemoon , Kim Dae Hee 
Published: November 2018

AbstractWe evaluated the performance of the McGrath video laryngoscope and Pentax Airway Scope in comparison with the Macintosh laryngoscope for nasotracheal intubation in paediatric patients. For this, 108 patients were enrolled in an open-label, randomized controlled trial. Patients were randomly allocated to one of three groups based on use of the Macintosh laryngoscope, McGrath video laryngoscope, or Pentax Airway Scope. Time to intubation, the intubation difficulty, and the quality of navigation were compared among groups. The median nasotracheal intubation time [interquartile range] in the Macintosh group (33.5 [28.3–39.8] s) was significantly shorter than those of the McGrath (39.0 [32.0–43.0] s) and Pentax groups (43.0 [35.0–52.0] s). The difficulty of nasotracheal intubation was similar among all groups. When navigating and aligning the tube from the oropharynx into the glottic inlet, the cuff inflation method was required in significantly fewer patients for the Macintosh group (11.1%) than for the McGrath (48.6%) and Pentax (51.4%) groups. Thus, compared to the McGrath video laryngoscope and Pentax Airway Scope, the Macintosh laryngoscope allowed shorter nasotracheal intubation times and better facilitated tracheal navigation, requiring less use of the cuff inflation method to navigate the tracheal tube into the glottic inlet.
Variations in the immune and metabolic response of proactive and reactive Sparus aurata under stimulation with Vibrio anguillarum vaccine
Authors: Vargas R. , Balasch J. C. , Brandts I. , Reyes-López F. , Tort L. , Teles M. 
Published: November 2018

AbstractEnvironmental insults, such as exposure to pathogens, modulate the behavioural coping style of animals to stressors, and repeated exposure to stressful environments may lead to species-specific infection phenotypes. To analyse the influence of stress behavioural phenotypes on immune and metabolic performance, gilthead sea bream (Sparus aurata L.) were first screened for proactive and reactive coping styles. Once characterized, both behavioural phenotypes fish groups were bath vaccinated with bacterin from Vibrio anguillarum, an opportunistic widespread pathogen of fish. Gills and liver were sampled at 0 (control group), 1, 3 and 7 days post-vaccination. Immune-, oxidative stress- and metabolic-related transcripts (il1β, tnfα, igm, gpx1, sod, cat, lpl, ghr1 and ghr2), metabolic endpoints (glucose, cholesterol and triglycerides), hepatic health indicators (aspartate aminotransferase, alanine transaminase and alkaline phosphatase), oxidative stress status (esterase activity, total antioxidant capacity and total oxidative status) and stress biomarkers (cortisol) were determined. Present results indicate that screening for coping styles in the gilthead sea bream segregated the two distinct phenotypes as expected: proactive and reactive. Results also indicate that under bath vaccination proactive fish show high immune response and lower metabolism, whereas reactive fish show low immune and higher metabolic responses.
Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Authors: Du Zhonghua , Jia Lin , Wang Yichen , Wang Cong , Wen Xue , Chen Jingcheng , Zhu Yanbo , Yu Dehai , Zhou Lei , Chen Naifei , Zhang Shilin , Celik Ilkay , Ay Ferhat , Gao Sujun , Zhang Songling , Li Wei , Hoffman Andrew R. , Cui Jiuwei , Hu Ji-Fan 
Published: November 2018

AbstractPluripotent stem cells hold great investigative potential for developmental biology and regenerative medicine. Recent studies suggest that long noncoding RNAs (lncRNAs) may function as key regulators of the maintenance and the lineage differentiation of stem cells. However, the underlying mechanisms by which lncRNAs affect the reprogramming process of somatic cells into pluripotent cells remain largely unknown. Using fibroblasts and induced pluripotent stem cells (iPSCs) at different stages of reprogramming, we performed RNA transcriptome sequencing (RNA-Seq) to identify lncRNAs that are differentially-expressed in association with pluripotency. An RNA reverse transcription-associated trap sequencing (RAT-seq) approach was then utilized to generate a database to map the regulatory element network for lncRNA candidates. Integration of these datasets can facilitate the identification of functional lncRNAs that are associated with reprogramming. Identification of lncRNAs that regulate pluripotency may lead to new strategies for enhancing iPSC induction in regenerative medicine.
Anthropomorphic breast model repository for research and development of microwave breast imaging technologies
Authors: Omer Muhammad , Fear Elise 
Published: November 2018

AbstractA repository of anthropomorphic numerical breast models is made available for the scientific community to support research and development of microwave imaging technologies for diagnostic and therapeutic applications. These models are constructed from magnetic resonance imaging (MRI) scans acquired at our university hospital. Our 3D breast modelling method is used to translate the MRI scans into 3D models representing the geometry and microwave-frequency properties of tissues in the breast. The reconstructed models demonstrate anatomical realism, reconfigurable complexity, and flexibility to adapt to simulations of various microwave imaging techniques and prototype systems. With these models, realistic and rigorous test scenarios can be defined in simulations to support feasibility analysis, performance verification and design improvements of developing microwave imaging techniques, prior to testing on experimental systems. A repository of breast models is created which includes breasts of varying classification – fatty, scattered, heterogeneous, and dense. In addition, the models include brief documentation to facilitate researchers in selecting a model by matching its features with their requirements.
Generation and quality control of lipidomics data for the alzheimer’s disease neuroimaging initiative cohort
Authors: Barupal Dinesh Kumar , Fan Sili , Wancewicz Benjamin , Cajka Tomas , Sa Michael , Showalter Megan R. , Baillie Rebecca , Tenenbaum Jessica D. , Louie Gregory ,   Alzheimer’s Disease Neuroimaging Initiative,   Alzheimer’s Disease Metabolomics Consortium, Kaddurah-Daouk Rima , Fiehn Oliver 
Published: November 2018

AbstractAlzheimer’s disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository athttp://adni.loni.usc.edu/
Sinusoidal charging of Li‐ion battery based on frequency detection algorithm by pole placement control method
Authors: Vazini Hossein , Asadi Mehdi , Karimadini Mohammad , Hajisadeghian Hossein 
Published: November 2018

This study presents a control system to track the sinusoidal ripple current (SRC) of lithium (Li)‐ion batteries. In this method, a combination of a DC and a sinusoidal ripple current is injected to the battery. By choosing the appropriate frequency, the minimum AC impedance of the battery is obtained. This study, the impact of temperature has been considered as a protection criterion in the proposed charge algorithm, also a state‐space model of the charger system has been developed, and finally a pole placement controller has been proposed to control charging current. To evaluate the design, a laboratory setup has been implemented to obtain experimental results from a 1 kW Li‐ion battery pack. Also, simulations have been carried out by Simulink/MATLAB. The proposed pole placement control method for tracking of SRC and the optimal frequency detection algorithm have been designed and tested on a practical 10 Ah Li iron phosphate battery pack in different charge modes. In addition, results of the conventional proportional–integrator (PI) controller have been compared with the proposed controller. Both simulation and experimental results show the effectiveness of the proposed algorithm and control system to track SRC reference current in all frequencies.
3‐min all‐out effort on cycle ergometer is valid to estimate the anaerobic capacity by measurement of blood lactate and excess post‐exercise oxygen consumption
Authors: Zagatto Alessandro Moura , Redkva Paulo Eduardo , de Poli Rodrigo Araújo Bonetti , González Joel Abraham Martinez , Brandani Jeniffer Zanetti , Penedo Thiago , Bertuzzi Rômulo Cássio De Moraes 
Published: November 2018

AbstractThe purpose of this study was to investigate the use of a single 3‐min all‐out maximal effort to estimate anaerobic capacity (AC) through the lactate and excess post‐exercise oxygen consumption (EPOC) response methods on a cycle ergometer. Eleven physically active men (age = 28.1 ± 4.0 yrs, height = 175.1 ± 4.2 cm, body mass = 74.8 ± 11.9 kg and ⩒O2max = 40.7 ± 7.3 mL kg−1 min−1), participated in the study and performed: i) five submaximal efforts, ii) a supramaximal effort at 115% of intensity of ⩒O2max, and iii) a 3‐min all‐out maximal effort. Anaerobic capacity was estimated using the supramaximal effort through conventional maximal accumulated oxygen deficit (MAOD) and also through the sum of oxygen equivalents from the glycolytic (fast component of excess post‐exercise oxygen consumption) and phosphagen pathways (blood lactate accumulation) , while during the 3‐min all‐out maximal effort the anaerobic capacity was estimated using the procedure. There were no significant differences between the three methods (p > 0.05). Additionally, the anaerobic capacity estimated during the 3‐min all‐out effort was significantly correlated with the MAOD (r = 0.74; p = 0.009) and methods (r = 0.65; p = 0.029). Therefore, it is possible to conclude that the 3‐min all‐out effort is valid to estimate anaerobic capacity in physically active men during a single cycle ergometer effort.
Long-term outcomes of pneumonectomy, back-table lung preservation, double-sleeve resection and reimplantation for advanced central lung cancer: the Oto procedure
Authors: Tanaka Shin , Sugimoto Seiichiro , Soh Junichi , Oto Takahiro 
Published: November 2018

Abstract
The technique of pneumonectomy, back-table lung preservation, double-sleeve resection and reimplantation of basal segments (the Oto procedure) has been proposed as a useful technique for the management of locally advanced central lung cancer with short-term follow-up. We report the long-term outcomes of 5 consecutive patients who underwent the Oto procedure.
Percutaneous coronary intervention in cancer patients: a report of the prevalence and outcomes in the United States
Authors: Potts Jessica E , Iliescu Cezar A , Lopez Mattei Juan C , Martinez Sara C , Holmvang Lene , Ludman Peter , De Belder Mark A , Kwok Chun Shing , Rashid Muhammad , Fischman David L , Mamas Mamas A 
Published: November 2018

Abstract

Aims
This study aims to examine the temporal trends and outcomes in patients who undergo percutaneous coronary intervention (PCI) with a previous or current diagnosis of cancer, according to cancer type and the presence of metastases.

Methods and results
Individuals undergoing PCI between 2004 and 2014 in the Nationwide Inpatient Sample were included in the study. Multivariable analyses were used to determine the association between cancer diagnosis and in-hospital mortality and complications. 6 571 034 PCI procedures were included and current and previous cancer rates were 1.8% and 5.8%, respectively. Both rates increased over time and the four most common cancers were prostate, breast, colon, and lung cancer. Patients with a current lung cancer had greater in-hospital mortality (odds ratio (OR) 2.81, 95% confidence interval (95% CI) 2.37–3.34) and any in-hospital complication (OR 1.21, 95% CI 1.10–1.36), while current colon cancer was associated with any complication (OR 2.17, 95% CI 1.90–2.48) and bleeding (OR 3.65, 95% CI 3.07–4.35) but not mortality (OR 1.39, 95% CI 0.99–1.95). A current diagnosis of breast was not significantly associated with either in-hospital mortality or any of the complications studied and prostate cancer was only associated with increased risk of bleeding (OR 1.41, 95% CI 1.20–1.65). A historical diagnosis of lung cancer was independently associated with an increased OR of in-hospital mortality (OR 1.65, 95% CI 1.32–2.05).

Conclusions
Cancer among patients receiving PCI is common and the prognostic impact of cancer is specific both for the type of cancer, presence of metastases and whether the diagnosis is historical or current. Treatment of patients with a cancer diagnosis should be individualized and involve a close collaboration between cardiologists and oncologists.
Virulence factor-dependent basolateral invasion of choroid plexus epithelial cells by pathogenic Escherichia coli in vitro
Authors: Rose Rebekah , Häuser Svenja , Stump-Guthier Carolin , Weiss Christel , Rohde Manfred , Kim Kwang Sik , Ishikawa Hiroshi , Schroten Horst , Schwerk Christian , Adam Rüdiger 
Published: November 2018

Abstract
Escherichia coli is the most common Gram-negative causative agent of neonatal meningitis and E. coli meningitis is associated with high morbidity and mortality. Previous research has been carried out with regard to the blood–brain barrier and thereby unveiled an assortment of virulence factors involved in E. coli meningitis. Little, however, is known about the role of the blood–cerebrospinal fluid (CSF) barrier (BCSFB), in spite of several studies suggesting that the choroid plexus (CP) is a possible entry point for E. coli into the CSF spaces. Here, we used a human CP papilloma (HIBCPP) cell line that was previously established as valid model for the study of the BCSFB. We show that E. coli invades HIBCPP cells in a polar fashion preferentially from the physiologically relevant basolateral side. Moreover, we demonstrate that deletion of outer membrane protein A, ibeA or neuDB genes results in decreased cell infection, while absence of fimH enhances invasion, although causing reduced adhesion to the apical side of HIBCPP cells. Our findings suggest that the BCSFB might constitute an entry point for E. coli into the central nervous system, and HIBCPP cells are a valuable tool for investigating E. coli entry of the BCSFB.
Potential for managing life history diversity in a commercially exploited intermediate predator, the goldsinny wrasse (Ctenolabrus rupestris)
Authors: Olsen Esben Moland , Halvorsen Kim Tallaksen , Larsen Torkel , Kuparinen Anna 
Published: November 2018

AbstractSmall-bodied wrasse species are important for structuring coastal marine ecosystems but are also increasingly harvested as parasite cleaners on farmed salmon. Identifying management regulations that will support long-term sustainability of wrasse fisheries is challenging, because there is still limited knowledge about the impacts of fisheries on the demography of these intermediate predators in their natural environments. To this end, we studied individual growth histories of goldsinny wrasse (Ctenolabrus rupestris) at a fine spatial scale across replicated marine protected areas (MPAs) and areas open to commercial harvesting on the Norwegian coast. The MPAs were established 1–7 years prior to our sampling. We detected significant fine-scale spatial variation in wrasse asymptotic body size, but found no consistent difference between MPAs and fished areas. Male wrasses reached larger asymptotic body sizes than females, whereas fyke nets captured individuals with larger asymptotic body sizes compared with baited traps. These are the two commonly used gear types in wrasse fisheries. An extended use of baited traps, along with slot-size limits, could therefore aid in protecting large-growing phenotypes such as nest-guarding males.
Cytidine deaminase enables Toll-like receptor 8 activation by cytidine or its analogs
Authors: Furusho Katsuhiro , Shibata Takuma , Sato Ryota , Fukui Ryutaro , Motoi Yuji , Zhang Yun , Saitoh Shin-ichiroh , Ichinohe Takeshi , Moriyama Masafumi , Nakamura Seiji , Miyake Kensuke 
Published: November 2018

Abstract
Toll-like receptor 8 (TLR8), a sensor for pathogen-derived single-stranded RNA (ssRNA), binds to uridine (Uri) and ssRNA to induce defense responses. We here show that cytidine (Cyd) with ssRNA also activated TLR8 in peripheral blood leukocytes (PBLs) and a myeloid cell line U937, but not in an embryonic kidney cell line 293T. Cyd deaminase (CDA), an enzyme highly expressed in leukocytes, deaminates Cyd to Uri. CDA expression enabled TLR8 response to Cyd and ssRNA in 293T cells. CDA deficiency and a CDA inhibitor both reduced TLR8 responses to Cyd and ssRNA in U937. The CDA inhibitor also reduced PBL response to Cyd and ssRNA. A Cyd analogue, azacytidine, is used for the therapy of myelodysplastic syndrome and acute myeloid leukemia. Azacytidine with ssRNA induced tumor necrosis factor-α expression in U937 and PBLs in a manner dependent on CDA and TLR8. These results suggest that CDA enables TLR8 activation by Cyd or its analogues with ssRNA through deaminating activity. Nucleoside metabolism might impact TLR8 responses in a variety of situations such as the treatment with nucleoside analogues.
Topological quantum states of matter in iron-based superconductors: from concept to material realization
Authors: Hao Ning , Hu Jiangping 
Published: November 2018

AbstractWe review recent progress in the exploration of topological quantum states of matter in iron-based superconductors. In particular, we focus on the non-trivial topology existing in the band structures and superconducting states of iron’s 3d orbitals. The basic concepts, models, materials and experimental results are reviewed. The natural integration between topology and high-temperature superconductivity in iron-based superconductors provides great opportunities to study topological superconductivity and Majorana modes at high temperature.
Starspots in contact and semi-detached binary systems
Authors: Kouzuma Shinjirou 
Published: November 2018

AbstractWe investigated the statistical properties of both cool and hot starspots in eclipsing binary stars. The starspot and binary parameters for contact and semi-detached systems were collected from literature, determined on the basis of synthetic light-curve analysis. We examined associations between these parameters. It was found that the cool spots in W-type binaries show properties similar to those of sunspots and starspots generated by dynamos, which differs from those of the cool spots in A-type binaries.The properties of hotspots also differ between the W- and A-type samples. From the physical properties of A- and W-type binaries, we infer that mass transfer is a dominant process for forming the hotspots in A-type binaries, and that both mass transfer and magnetic activity can contribute to the formation of the hotspots in W-type binaries. Our results also indicate that the hotspot size in the A-type sample is correlated with the temperature of spotted stars, orbital period, mass ratio, and fill-out factor.
Mifepristone Pretreatment for the Medical Management of Early Pregnancy Loss
Authors: Schreiber C.A. , Creinin M.D. , Atrio J. , Sonalkar S. , Ratcliffe S.J. , Barnhart K.T. 
Published: November 2018

(N Engl J Med. 2018;378:2161–2170)
First-trimester miscarriage, or early pregnancy loss, is the most common complication in pregnancy. It can frequently be identified before onset of symptoms, and many women prefer active management, which provides the ability to have some control over the situation. Current guidelines recommend the use of prostaglandin analogues to expedite the expulsion of nonviable pregnancy tissue, with a standard dose of 800 μg misoprostol administered vaginally. However, misoprostol has low efficacy among women with a closed cervical os. Although mifepristone, a 19-nor steroid, can help to prepare the myometrium and cervix for prostaglandin activity, its reported effectiveness ranges from 52% to 95%. The authors of the present study thus compared the efficacy of pretreatment with mifepristone followed by treatment with misoprostol with misoprostol use alone, for the management of early pregnancy loss in women with a closed cervical os.