bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer
Authors: Wenric Stephane , ElGuendi Sonia , Caberg Jean-Hubert , Bezzaou Warda , Fasquelle Corinne , Charloteaux Benoit , Karim Latifa , Hennuy Benoit , Frères Pierre , Collignon Joëlle , Boukerroucha Meriem , Schroeder Hélène , Olivier Fabrice , Jossa Véronique , Jerusalem Guy , Josse Claire , Bours Vincent 
Published: December 2017

AbstractNon-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that are complementary and overlapping to those of either protein-coding (PCT) or non-coding transcripts. Several ncNATs were described as regulating protein coding gene expression on the same loci, and they are expected to act more frequently in cis compared to other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired adjacent non-malignant tissues were analyzed by strand-specific RNA sequencing. To highlight ncNATs potentially playing a role in protein coding gene regulations that occur in breast cancer, three different data analysis methods were used: differential expression analysis of ncNATs between tumor and non-malignant tissues, differential correlation analysis of paired ncNAT/PCT between tumor and non-malignant tissues, and ncNAT/PCT read count ratio variation between tumor and non-malignant tissues. Each of these methods yielded lists of ncNAT/PCT pairs that were enriched in survival-associated genes. This work highlights ncNAT lists that display potential to affect the expression of protein-coding genes involved in breast cancer pathology.
Ratiometric Mass Spectrometry for Cell Identification and Quantitation Using Intracellular “Dual-Biomarkers”
Authors: Chen Xiaoming , Wo Fangjie , Chen Jiang , Tan Jie , Wang Tao , Liang Xiao , Wu Jianmin 
Published: December 2017

AbstractThis study proposed an easy-to-use method for cell identification and quantitation by ratiometric matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Two pairs of MS peaks in the molecular fingerprint of cells were selected as intracellular dual-biomarkers due to the stability and specificity of their ratio values in different types of hepatocellular cancer (HCC) cell lines. Five types of HCC cells can be thereafter differentiated based on these two pairs of intracellular peptides/proteins. Two types of HCC cells, Huh7 and LM3 were co-cultured as a model to test whether the method is feasible for cell quantitation. The results indicated that the ratiometric peak intensity of the two pair biomarkers exhibits linear relationship with the proportion of Huh7 cells. Furthermore, tumor heterogeneity was simulated by subcutaneously injecting the co-cultured cells into nude mice. The cell type and proportion in the section of grown tumor tissue can be discriminated using the ratiometric MALDI imaging approach. LC-MS/MS detection revealed that one of the biomarker pairs belongs to thymosin family, β4 and β10. The ratiometric MS spectral approach using intracellular dual-biomarkers might become a pervasive strategy for high-throughput cell identification and quantitation, which is vital in tumor heterogeneity study, clinical diagnosis and drug screening.
Probing the growth and melting pathways of a decagonal quasicrystal in real-time
Authors: Han Insung , Xiao Xianghui , Shahani Ashwin J. 
Published: December 2017

AbstractHow does a quasicrystal grow? Despite the decades of research that have been dedicated to this area of study, it remains one of the fundamental puzzles in the field of crystal growth. Although there has been no lack of theoretical studies on quasicrystal growth, there have been very few experimental investigations with which to test their various hypotheses. In particular, evidence of the in situ and three-dimensional (3D) growth of a quasicrystal from a parent liquid phase is lacking. To fill-in-the-gaps in our understanding of the solidification and melting pathways of quasicrystals, we performed synchrotron-based X-ray imaging experiments on a decagonal phase with composition of Al-15at%Ni-15at%Co. High-flux X-ray tomography enabled us to observe both growth and melting morphologies of the 3D quasicrystal at temperature. We determined that there is no time-reversal symmetry upon growth and melting of the decagonal quasicrystal. While quasicrystal growth is predominantly dominated by the attachment kinetics of atomic clusters in the liquid phase, melting is instead barrier-less and limited by buoyancy-driven convection. These experimental results provide the much-needed benchmark data that can be used to validate simulations of phase transformations involving this unique phase of matter.
Observation of deformation twinning and martensitic transformation during nanoindentation of a transformation-induced plasticity steel
Authors: Xiong Zhiping , Casillas Gilberto , Saleh Ahmed A. , Cui Shaogang , Pereloma Elena V. 
Published: December 2017

AbstractFor the first time, deformation twinning and martensitic transformation were observed in retained austenite in a low-alloyed transformation-induced plasticity steel using nanoindentation in conjunction with electron backscattering diffraction and transmission electron microscopy. Dislocation glide, martensite formation and deformation twinning were correlated to pop-ins and deviation from linearity in the load-displacement curve. Deformation twinning was found to enhance the stability of retained austenite. This observation furthers our understanding of RA stability during straining of low-alloyed multiphase TRIP steel.
The response of an arboreal mammal to livestock grazing is habitat dependant
Authors: Neilly Heather , Schwarzkopf Lin 
Published: December 2017

AbstractInappropriate livestock grazing is implicated in the decline of vertebrate fauna species globally. Faunal responses to grazing can interact with the vegetation community in which they occur. We measured the response of an arboreal marsupial, the common brushtail possum (Trichosurus vulpecula vulpecula) to different cattle grazing strategies and vegetation types, and examined whether micro-habitat selection is driving this response. We hypothesised that where arboreal habitat is intact, brushtail possums would be resistant to the impacts of heavy grazing. We conducted a mark-recapture survey among four grazing treatments and in two vegetation types (Box and Ironbark), at a 20-year grazing trial in northern Australia. We found that brushtail possums were resistant to the impact of heavy grazing in both vegetation types, but preferred the heavy grazing treatment in the Box vegetation type. Complex arboreal habitat and low ground cover was preferred, and high grass cover and low tree species richness avoided. Most individuals exclusively used one vegetation type, with few using both, suggesting a ‘matrix’ vegetation between the Box and Ironbark may be creating a movement barrier. Vegetation type should provide a context for determining the benefits to arboreal wildlife of adopting a particular grazing management strategy.
Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection
Authors: Song Deping , Peng Qi , Chen Yanjun , Zhou Xinrong , Zhang Fanfan , Li Anqi , Huang Dongyan , Wu Qiong , Ye Yu , He Houjun , Wang Leyi , Tang Yuxin 
Published: December 2017

AbstractPorcine epidemic diarrhea virus (PEDV) is a devastating cause of diarrhea in pigs worldwide. Most of studies have focused on molecular and pathogenic characterization of PEDV, whereas there were limited studies in understanding the role of gut microbiota (GM) in viral-associated diarrhea. Here, using the Illumina MiSeq platform, we examined and compared the impact of PEDV infection on the GM of sows and their piglets less than 10 days old. Our results showed that PEDV caused alternations in the structure and abundance of GM from levels of phylum to genus, and even species. For sows, a significant decrease of observed species was found in diarrheal sows than that in healthy sows (p < 0.05). The unweighted and weighted UniFrac distances also revealed considerable segregations of GM structure among healthy, asymptomatic, and diarrheal sows. For piglets, Bacteroidetes, the dominant bacteria in healthy piglets, were replaced by Firmicutes in asymptomatic and diarrheal piglets. The abundances of Fusobacteria and Proteobacteria were also remarkably increased in asymptomatic piglets and diarrheal piglets when compared to those of the healthy piglets. Our findings demonstrated that PEDV infection caused severe perturbations of GM, reduced probiotic bacteria, and enriched pathogenic bacteria.
ENSO relationship to summer rainfall variability and its potential predictability over Arabian Peninsula region
Authors: Abid Muhammad Adnan , Almazroui Mansour , Kucharski Fred , O’Brien Enda , Yousef Ahmed Elsayed 
Published: December 2017

AbstractThe El Niño Southern Oscillation (ENSO) phenomenon is considered to be responsible for rainfall predictability in many regions. Some of its regional teleconnections, such as over the Arabian Peninsula in boreal summer (June–August) season, are not well studied. Therefore, in this paper, the relationship between the summer seasonal mean rainfall and ENSO is analyzed with the aid of a 15-member ensemble of simulations using the Saudi-King Abdulaziz University (KAU) Atmospheric Global Climate Model (AGCM) for the period 1981–2015. The southwestern peninsula rainfall is linked to the Sea Surface Temperature (SST) anomalies in the central-eastern pacific region. This relationship is established through an atmospheric teleconnection which shows upper-level convergence anomalies over the southern Arabian Peninsula compensating the central-eastern Pacific upper-level divergence anomalies for the warm ENSO phase, and vice-versa for the cold Phase. The upper-level convergence over the southern Arabian Peninsula leads to sinking motion, low-level divergence and consequently to reduced rainfall in the warm phase, while reverse happens in the cold phase. The correlation coefficient between the observed area-averged Niño3.4 index and a Southwestern Arabian Peninsula Rainfall Index (SARI) is −0.43 (statistically significant at 95%). Overall, model shows a potential predictability (PP) of 0.53 for the SARI region. Predictability during El Niño is higher than during La Niña events. This is not only because of a stronger signal, but also noise reduction contributes to the increase of PP in El Niño compared to that of La Niña years.
Single-Word Speech Intelligibility in Children and Adults With Down Syndrome
Authors: Wild Alyssa , Vorperian Houri K. , Kent Ray D. , Bolt Daniel M. , Austin Diane 
Published: December 2017

PurposeA single-word identification test was used to study speech production in children and adults with Down syndrome (DS) to determine the developmental pattern of speech intelligibility with an emphasis on vowels.MethodSpeech recordings were collected from 62 participants with DS aged 4–40 years and 25 typically developing participants aged 4–7 years. Panels of 5 adult lay listeners transcribed the speech recordings orthographically, and their responses were scored in comparison with the speakers' target words.ResultsSpeech intelligibility in persons with DS improved with age, especially between the ages of 4 and 16 years. Whereas consonants contribute to intelligibility, vowels also played an important role in reduced intelligibility with an apparent developmental difference in low versus high vowels, where the vowels /æ/ and/ɑ/ developed at a later age than /i/ and /u/. Interspeaker variability was large, with male individuals being generally less intelligible than female individuals and some adult men having very low intelligibility.ConclusionResults show age-related patterns in speech intelligibility in persons with DS and identify the contribution of dimensions of vowel production to intelligibility. The methods used clarify the phonetic basis of reduced intelligibility, with implications for assessment and treatment.
Herscheland SCUBA-2 observations of dust emission in a sample ofPlanckcold clumps
Authors: Juvela Mika , He Jinhua , Pattle Katherine , Liu Tie , Bendo George , Eden David J. , Fehér Orsolya , Michel Fich , Fuller Gary , Hirano Naomi , Kim Kee-Tae , Li Di , Liu Sheng-Yuan , Malinen Johanna , Marshall Douglas J. , Paradis Deborah , Parsons Harriet , Pelkonen Veli-Matti , Rawlings Mark G. , Ristorcelli Isabelle , Samal Manash R. , Tatematsu Ken’ichi , Thompson Mark , Traficante Alessio , Wang Ke , Ward-Thompson Derek , Wu Yuefang , Yi Hee-Weon , Yoo Hyunju 
Published: December 2017

Context.Analysis of all-skyPlancksubmillimetre observations and the IRAS 100μm data has led to the detection of a population of Galactic cold clumps. The clumps can be used to study star formation and dust properties in a wide range of Galactic environments.Aims.Our aim is to measure dust spectral energy distribution (SED) variations as a function of the spatial scale and the wavelength.Methods.We examined the SEDs at large scales using IRAS,Planck, andHerscheldata. At smaller scales, we compared JCMT/SCUBA-2 850μm maps withHerscheldata that were filtered using the SCUBA-2 pipeline. Clumps were extracted using the Fellwalker method, and their spectra were modelled as modified blackbody functions.Results.According to IRAS andPlanckdata, most fields have dust colour temperaturesTC~ 14–18 K and opacity spectral index values ofβ= 1.5–1.9. The clumps and cores identified in SCUBA-2 maps haveT~ 13 K and similarβvalues. There are some indications of the dust emission spectrum becoming flatter at wavelengths longer than 500μm. In fits involvingPlanckdata, the significance is limited by the uncertainty of the corrections for CO line contamination. The fits to the SPIRE data give a medianβvalue that is slightly above 1.8. In the joint SPIRE and SCUBA-2 850μm fits, the value decreases toβ~ 1.6. Most of the observedT-βanticorrelation can be explained by noise.Conclusions.The typical submillimetre opacity spectral indexβof cold clumps is found to be ~1.7. This is above the values of diffuse clouds, but lower than in some previous studies of dense clumps. There is only tentative evidence of aT-βanticorrelation andβdecreasing at millimetre wavelengths.
CHANG-ES
Authors: Krause Marita , Irwin Judith , Wiegert Theresa , Miskolczi Arpad , Damas-Segovia Ancor , Beck Rainer , Li Jiang-Tao , Heald George , Müller Peter , Stein Yelena , Rand Richard J. , Heesen Volker , Walterbos Rene A. M. , Dettmar Ralf-Jürgen , Vargas Carlos J. , English Jayanne , Murphy Eric J. 
Published: December 2017

Aim.The vertical halo scale height is a crucial parameter to understand the transport of cosmic-ray electrons (CRE) and their energy loss mechanisms in spiral galaxies. Until now, the radio scale height could only be determined for a few edge-on galaxies because of missing sensitivity at high resolution.Methods.We developed a sophisticated method for the scale height determination of edge-on galaxies. With this we determined the scale heights and radial scale lengths for a sample of 13 galaxies from the CHANG-ES radio continuum survey in two frequency bands.Results.The sample average values for the radio scale heights of the halo are 1.1 ± 0.3 kpc inC-band and 1.4 ± 0.7 kpc inL-band. From the frequency dependence analysis of the halo scale heights we found that the wind velocities (estimated using the adiabatic loss time) are above the escape velocity. We found that the halo scale heights increase linearly with the radio diameters. In order to exclude the diameter dependence, we defined a normalized scale heighth˜which is quite similar for all sample galaxies at both frequency bands and does not depend on the star formation rate or the magnetic field strength. However,h˜shows a tight anticorrelation with the mass surface density.Conclusions.The sample galaxies with smaller scale lengths are more spherical in the radio emission, while those with larger scale lengths are flatter. The radio scale height depends mainly on the radio diameter of the galaxy. The sample galaxies are consistent with an escape-dominated radio halo with convective cosmic ray propagation, indicating that galactic winds are a widespread phenomenon in spiral galaxies. While a higher star formation rate or star formation surface density does not lead to a higher wind velocity, we found for the first time observational evidence of a gravitational deceleration of CRE outflow, e.g. a lowering of the wind velocity from the galactic disk.
The feasibility of colorectal endoscopic submucosal dissection for the treatment of residual or recurrent tumor localized in therapeutic scar tissue
Authors: Kobayashi Ryosuke , Hirasawa Kingo , Ikeda Ryosuke , de Fukuchi Takeh , Ishii Yasuaki , Kaneko Hiroaki , Makazu Makomo , Sato Chiko , Maeda Shin 
Published: December 2017

Abstract
Background and study aims Endoscopic submucosal dissection (ESD) is used to treat superficial colorectal tumors. Previous studies have reported the efficacy of ESD for treating residual or local recurrent colorectal tumors. This study sought to evaluate the efficacy of ESD in treating these lesions and to assess factors that prevent successful ESD.
Methods This retrospective study assessed 25 cases of residual or local recurrent lesions that were previously treated using EMR (18 lesions), TEM (5 lesions), ESD (1 lesion) or surgery (1 lesion), and 459 primary lesions treated using ESD between April 2008 and September 2015. Clinicopathological characteristics, treatment outcome and adverse events were compared between groups with or without scar tissue. Factors related to perforation and a prolonged treatment time, which indicate the likelihood of technical difficulties, were identified using multiple logistic regression analysis.
Results In residual or local recurrent lesions groups, patients experienced more perforations (32 % vs 4 %, P < 0.001) and required a longer treatment time (117 min vs 61 min, P < 0.001) compared with the primary lesions group. Both groups showed a similar curative resection rate. Emergency surgery was not needed in any case. Multiple logistic regression analysis indicated that tumor location and therapeutic scar tissue were high risk factors for perforation, and that large tumor size and therapeutic scar tissue were high risk factors for prolonged treatment time.
Conclusions ESD for residual or local recurrent colorectal tumors is a technically challenging, but effective and minimally invasive treatment. When performed carefully with sufficient proficiency, it is a useful treatment option.
Low yield for non-targeted biopsies of the stomach and esophagus during elective esophagogastroduodenoscopy
Authors: Dougherty Michael , Santoiemma Phillip , Weber Andrew , Metz David , Yang Yu-Xiao 
Published: December 2017

Abstract
Background and study aims Biopsies of non-specific mucosal findings are often performed during esophagogastroduodenoscopy (EGD). We sought to determine the prevalence and clinical utility of non-targeted biopsies of the stomach and esophagus.
Patients and methods We conducted a retrospective review of 949 outpatient EGDs performed at a US tertiary referral center. Non-targeted biopsies of the stomach were defined as either “normal” or “mild” to “moderate” “erythema” or “inflammation” without other endoscopic features. Non-targeted biopsies of the esophagus and gastroesophageal junction (GEJ) were defined as endoscopically “normal” mucosa. The primary outcome was the proportion of non-targeted biopsies resulting in “definite management change.” Secondary outcomes included histopathologic diagnoses of Helicobacter pylori, intestinal metaplasia and esophageal eosinophilia.
Results Of 949 EGDs, 332 (35.0 %, 95 % CI 31.9 – 38.1 %) had a non-targeted biopsy taken at any site. Erythema in the gastric body and antrum was biopsied at a rate of 83 – 86 %, while biopsies of “normal”-appearing mucosa occurred at rates from 3 % (GEJ) to 15 % (body and antrum). The percentage of non-targeted biopsies that led to definite management change ranged from 5 % in the GEJ and esophagus to 9 % in the antrum, but did not significantly differ by mucosal appearance. Multivariable regression analyses suggested associations of language and age > 50 with management change from non-targeted gastric biopsy.
Conclusions Non-targeted biopsies of the stomach and esophagus led to definite management change in a small proportion of patients. Further studies are needed to identify patient and/or endoscopic characteristics and techniques to improve the yield of this practice.
“Clever ministrations”: regenerative beauty at the fin de siècle
Authors: Clark Jessica P. 
Published: December 2017

AbstractThis paper is the first to consider the role of late-nineteenth century British beauty culturists in establishing the respectability of anti-aging goods and services. It surveys self-published beauty texts, periodical press coverage, and advertisements to ask how female beauty providers positioned their businesses so as to enhance the reputation of their wares. These texts reveal that, by foregrounding the respectability, modernity, and novelty of regenerative techniques, British beauty culturists challenged existing narratives of commercial beautification, shifting feminine regeneration from the realm of vanity to necessity, from a question of moral character to commercial endeavor. However, these discursive strategies, not to mention the use of technology for the purpose of female bodily enhancement, were not welcomed by all. The paper subsequently turns to police court coverage and medical journals that criticized beauty “quacks” for reportedly duping unsuspecting female customers. The pursuit of duplicitous “beauty doctors” by unsatisfied customers and medical publications comes to the fore in a concluding profile of Anna Ruppert, a popular London-based beauty culturist who found herself charged under Ireland’s Pharmaceutical Act in 1893 for selling arsenical compounds. And yet, despite public scrutiny, the British press, consumers, and commercial providers increasingly embraced a more overt beauty culture that would prevail through the interwar period. This paper argues that this was due, in part, to discursive shifts advanced by fin de siècle beauty culturists, who paid the price for these interventions, existing as a liminal group straddling respectability and quackery.
Flavonoid glycosides in Malabar spinach Basella alba inhibit the growth of Spodoptera litura larvae
Authors: Aboshi Takako , Ishiguri Shiho , Shiono Yoshihito , Murayama Tetsuya 
Published: December 2017

Abstract
Basella alba is a perennial plant of the Basellaceae and is known by various common names including Malabar spinach. There are few insects that cause damage to B. alba. In this study, we examined the effect of B. alba leaves on the growth of Spodoptera litura larvae. B. alba leaves and a methanolic extract of the leaves inhibited the growth of S. litura larvae. Half of the larvae reared on the leaves died within 1 week. We found that two flavonoids, vitexin, and vitexin-2″-O-arabinofuranoside, were abundant in the methanol extract of leaves. When larvae were reared on purified vitexin or vitexin-2″-O-arabinofuranoside, their growth was significantly impaired compared with larvae reared on control spinach leaves. These results suggested that the flavonoid glycosides in B. alba leaves act as deterrents to S. litura larvae.