bluuebunny/crossref_metadata_2025_split huggingface dataset:
IHC-based subcellular quantification provides new insights into prognostic relevance of FLIP and procaspase-8 in non-small-cell lung cancer
Authors: Hutchinson Ryan A , Coleman Helen G , Gately Kathy , Young Vincent , Nicholson Siobhan , Cummins Robert , Kay Elaine , Hynes Sean O , Dunne Philip D , Senevirathne Seedevi , Hamilton Peter W , McArt Darragh G , Longley Daniel B 
Published: September 2017

AbstractIn this study, we developed an image analysis algorithm for quantification of two potential apoptotic biomarkers in non-small-cell lung cancer (NSCLC): FLIP and procaspase-8. Immunohistochemical expression of FLIP and procaspase-8 in 184 NSCLC tumors were assessed. Individual patient cores were segmented and classified as tumor and stroma using the Definiens Tissue Studio. Subsequently, chromogenic expression of each biomarker was measured separately in the nucleus and cytoplasm and reported as a quantitative histological score. The software package pROC was applied to define biomarker thresholds. Cox proportional hazards analysis was applied to generate hazard ratios (HRs) and associated 95% CI for survival. High cytoplasmic expression of tumoral (but not stromal) FLIP was associated with a 2.5-fold increased risk of death in lung adenocarcinoma patients, even when adjusted for known confounders (HR 2.47, 95% CI 1.14–5.35). Neither nuclear nor cytoplasmic tumoral procaspase-8 expression was associated with overall survival in lung adenocarcinoma patients; however, there was a significant trend (P for trend=0.03) for patients with adenocarcinomas with both high cytoplasmic FLIP and high cytoplasmic procaspase-8 to have a multiplicative increased risk of death. Notably, high stromal nuclear procaspase-8 expression was associated with a reduced risk of death in lung adenocarcinoma patients (adjusted HR 0.31, 95% CI 0.15–0.66). On further examination, the cells with high nuclear procaspase-8 were found to be of lymphoid origin, suggesting that the better prognosis of patients with tumors with high stromal nuclear procaspase-8 is related to immune infiltration, a known favorable prognostic factor. No significant associations were detected in analysis of lung squamous cell carcinoma patients. Our results suggest that cytoplasmic expression of FLIP in the tumor and nuclear expression of procaspase-8 in the stroma are prognostically relevant in non-small-cell adenocarcinomas but not in squamous cell carcinomas of the lung.
Regulation of hnRNPA1 by microRNAs controls the miR-18a–K-RAS axis in chemotherapy-resistant ovarian cancer
Authors: Rodriguez-Aguayo Cristian , Monroig Paloma del C , Redis Roxana S , Bayraktar Emine , Almeida Maria I , Ivan Cristina , Fuentes-Mattei Enrique , Rashed Mohammed H , Chavez-Reyes Arturo , Ozpolat Bulent , Mitra Rahul , Sood Anil K , Calin George A , Lopez-Berestein Gabriel 
Published: September 2017

AbstractThe regulation of microRNA (miRNA) biogenesis, function and degradation involves a range of mechanisms, including interactions with RNA-binding proteins. The potential contribution of regulatory miRNAs to the expression of these RNA interactor proteins that could control other miRNAs expression is still unclear. Here we demonstrate a regulatory circuit involving oncogenic and tumor-suppressor miRNAs and an RNA-binding protein in a chemotherapy-resistant ovarian cancer model. We identified and characterized miR-15a-5p and miR-25-3p as negative regulators of hnRNPA1 expression, which is required for the processing of miR-18a-3p, an inhibitor of the K-RAS oncogene. The inhibition of miR-25-3p and miR-15a-5p decreased the proliferation, motility, invasiveness and angiogenic potential and increased apoptosis when combined with docetaxel. Alteration of this regulatory circuit causes poor overall survival outcome in ovarian cancer patients. These results highlight miR-15a-5p and miR-25-3p as key regulators of miR-18a-3p expression and its downstream target K-RAS, through direct modulation of hnRNPA1 expression. Our results demonstrate the therapeutic potential of inhibiting miR-25-3p and miR-15a-5p and the use of miR-18a-3p/KRAS ratio as a prominent outcome prognostic factor.
The Apostasia genome and the evolution of orchids
Authors: Zhang Guo-Qiang , Liu Ke-Wei , Li Zhen , Lohaus Rolf , Hsiao Yu-Yun , Niu Shan-Ce , Wang Jie-Yu , Lin Yao-Cheng , Xu Qing , Chen Li-Jun , Yoshida Kouki , Fujiwara Sumire , Wang Zhi-Wen , Zhang Yong-Qiang , Mitsuda Nobutaka , Wang Meina , Liu Guo-Hui , Pecoraro Lorenzo , Huang Hui-Xia , Xiao Xin-Ju , Lin Min , Wu Xin-Yi , Wu Wan-Lin , Chen You-Yi , Chang Song-Bin , Sakamoto Shingo , Ohme-Takagi Masaru , Yagi Masafumi , Zeng Si-Jin , Shen Ching-Yu , Yeh Chuan-Ming , Luo Yi-Bo , Tsai Wen-Chieh , Van de Peer Yves , Liu Zhong-Jian 
Published: September 2017

AbstractConstituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica4, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information
Authors: Luo Yunan , Zhao Xinbin , Zhou Jingtian , Yang Jinglin , Zhang Yanqing , Kuang Wenhua , Peng Jian , Chen Ligong , Zeng Jianyang 
Published: September 2017

AbstractThe emergence of large-scale genomic, chemical and pharmacological data provides new opportunities for drug discovery and repositioning. In this work, we develop a computational pipeline, called DTINet, to predict novel drug–target interactions from a constructed heterogeneous network, which integrates diverse drug-related information. DTINet focuses on learning a low-dimensional vector representation of features, which accurately explains the topological properties of individual nodes in the heterogeneous network, and then makes prediction based on these representations via a vector space projection scheme. DTINet achieves substantial performance improvement over other state-of-the-art methods for drug–target interaction prediction. Moreover, we experimentally validate the novel interactions between three drugs and the cyclooxygenase proteins predicted by DTINet, and demonstrate the new potential applications of these identified cyclooxygenase inhibitors in preventing inflammatory diseases. These results indicate that DTINet can provide a practically useful tool for integrating heterogeneous information to predict new drug–target interactions and repurpose existing drugs.
Hydrogen bonds to Au atoms in coordinated gold clusters
Authors: Bakar Md. Abu , Sugiuchi Mizuho , Iwasaki Mitsuhiro , Shichibu Yukatsu , Konishi Katsuaki 
Published: September 2017

AbstractIt is well known that various transition elements can form M···H hydrogen bonds. However, for gold, there has been limited decisive experimental evidence of such attractive interactions. Herein we demonstrate an example of spectroscopically identified hydrogen bonding interaction of C–H units to Au atoms in divalent hexagold clusters ([Au6]2+) decorated by diphosphine ligands. X-ray crystallography reveals substantially short Au–H/Au–C distances to indicate the presence of attractive interactions involving unfunctionalized C–H moieties. Solution 1H and 13C NMR signals of the C–H units appear at considerably downfield regions, indicating the hydrogen-bond character of the interactions. The Au···H interactions are critically involved in the ligand-cluster interactions to affect the stability of the cluster framework. This work demonstrates the uniqueness and potential of partially oxidised Au cluster moieties to participate in non-covalent interaction with various organic functionalities, which would expand the scope of gold clusters.
Low Frequency Magnetic Fields Induce Autophagy-associated Cell Death in Lung Cancer through miR-486-mediated Inhibition of Akt/mTOR Signaling Pathway
Authors: Xu Yujun , Wang Yizhong , Yao Anran , Xu Zhen , Dou Huan , Shen Sunan , Hou Yayi , Wang Tingting 
Published: September 2017

AbstractLow frequency magnetic fields (LF-MFs) can affect cell proliferation in a cell-type and intensity-dependent way. Previous study has reported the anti-tumor effect of LF-MFs in lung cancers. Our previous study also optimized the intensity and duration of LF-MFs to effectively inhibit the proliferation of lung cancer cells. However, the anti-tumor mechanism of LF-MFs remains unclear, which limit the clinical application of LF-MFs in anti-tumor therapy. Here, in a well-established Lewis Lung Cancer (LLC) mouse model, we found that LF-MFs inhibit tumor growth and induce an autophagic cell death in lung cancer. We also found that LF-MFs could up-regulate the expression level of miR-486, which was involved in LF-MFs activated cell autophagy. Furthermore, we found B-cell adaptor for phosphatidylinositol 3-kinase (BCAP) is a direct target of miR-486. miR-486 inhibit AKT/mTOR signaling through inhibiting expression of BCAP. Moreover, a decreased expression of miR-486 and an increased expression of BCAP were found in tumor tissues of lung cancer patients. Taken together, this study proved that LF-MFs can inhibit lung cancers through miR-486 induced autophagic cell death, which suggest a clinical application of LF-MFs in cancer treatment.
The common variants implicated in microstructural abnormality of first episode and drug-naïve patients with schizophrenia
Authors: Ren H. Y. , Wang Q. , Lei W. , Zhang C. C. , Li Y. F. , Li X. J. , Li M. L. , Deng W. , Huang C. H. , Du F. , Zhao L. S. , Wang Y. C. , Ma X. H. , Hu X. , Li T. 
Published: September 2017

AbstractBoth post-mortem and neuroimaging studies have identified abnormal white matter (WM) microstructure in patients with schizophrenia. However, its genetic underpinnings and relevant biological pathways remain unclear. In order to unravel the genes and the pathways associated with abnormal WM microstructure in schizophrenia, we recruited 100 first-episode, drug-naïve patients with schizophrenia and 140 matched healthy controls to conduct genome-wide association analysis of fractional anisotropy (FA) value measured using diffusing tensor imaging (DTI), followed by multivariate association study and pathway enrichment analysis. The results showed that one intergenic SNP (rs11901793), which is 20 kb upstream of CXCR7 gene on chromosome 2, was associated with the total mean FA values with genome-wide significance (p = 4.37 × 10−8), and multivariate association analysis identified a strong association between one region-specific SNP (rs10509852), 400 kb upstream of SORCS1 gene on chromosome 10, and the global trait of abnormal WM microstructure (p = 1.89 × 10−7). Furthermore, one pathway that is involved in cell cycle regulation, REACTOME_CHROMOSOME _MAINTENANCE, was significantly enriched by the genes that were identified in our study (p = 1.54 × 10−17). In summary, our study provides suggestive evidence that abnormal WM microstructure in schizophrenia is associated with genes that are likely involved in diverse biological signals and cell-cycle regulation although further replication in a larger independent sample is needed.
How do the hierarchical levels of premises affect category-based induction: diverging effects from the P300 and N400
Authors: Lei Yi , Liang Xiuling , Lin Chongde 
Published: September 2017

AbstractAlthough a number of studies have explored the time course of category-based induction, little is known about how the hierarchical levels (superordinate, basic, subordinate) of premises affect category-based induction. The EEG data were recorded when nineteen healthy human participants were performing a simplified category-based induction task. The ERP results showed that: in the subordinate conclusion condition, the basic premise elicited a larger N400, versus the superordinate promise; in the basic conclusion condition, the superordinate promise elicited a larger P300 relative to both the basic premise and subordinate premise; in the superordinate conclusion condition, however, no difference was found between different promise. Furthermore, the process that reasoning from a higher level to a lower level evoked a larger P300, compared to it did in the reverse direction. The divergent evidence suggested that category-based induction at superordinate, basic, and subordinate levels might be affected by various factors, such as abstract level, direction, and distance between premise and conclusion, which yielded new insights into the neural underpinnings of category-based induction with different inductive strengths.
Command Electro-Optical Switching of Photoaligned Liquid Crystal on Photopatterned Graphene
Authors: Varanytsia Andrii , Chien Liang-Chy 
Published: September 2017

AbstractWe report command electro-optical switching on photolithographically-patterned graphene into a high-density electrode pattern for a high-transmission in-plane-switching (IPS) liquid crystal device. A highly-effective liquid crystal photoalignment method is used to maximize the field-driven optical contrast of a prototyped device. A non-contact and low-temperature photoalignment allows delicate surface treatment required for successful processing of graphene layer into an IPS electrode structure. Electro-optic performance of the graphene-based single pixel laboratory IPS prototype demonstrates the application potential of graphene for liquid crystal electro-optic devices with complex and high-definition electrode patterns.
Live-bearing without placenta: Physical estimation indicates the high oxygen-supplying ability of white shark uterus to the embryo
Authors: Tomita Taketeru , Nozu Ryo , Nakamura Masaru , Matsuzaki Shohei , Miyamoto Kei , Sato Keiichi 
Published: September 2017

AbstractOne of the mysteries of shark aplacental viviparity is the ability of the embryos to acquire oxygen from their mothers without a placental connection. It has been assumed that embryonic respiration in aplacental viviparous shark depends on oxygen from the uterine wall, although this hypothesis has not been confirmed quantitatively. Morphological observations of the uterine wall of white shark (Carcharodon carcharias) provided the first quantitative evidence to support the ability of the uterus to supply ample oxygen to the embryo of viviparous elasmobranchs. The uterine surface of the white shark is characterized by (1) uterine lamellae that develop perpendicular to the uterine wall, (2) uterine lamellae folded in an accordion-like fashion, and (3) numerous micro-ridges on the lamellar surface. These modifications result in increased uterine surface are to up to 56 folds compared to the uterus with a smooth surface. Histological observations revealed that the diffusion barrier of the uterine wall is approximately 12 µm. By using these values, the oxygen-diffusion capacity of 1 cm2of the uterine wall of white shark was estimated to be 63.6 nmol·min−1·torr−1. This value is 250–400 times greater than that observed in other aplacental viviparous sharks (Squalusspp.) and is comparable with that of fish gills.
Investigation of a spontaneous mutant reveals novel features of iron uptake in Shewanella oneidensis
Authors: Dong Ziyang , Guo Shupan , Fu Huihui , Gao Haichun 
Published: September 2017

AbstractShewanella oneidensisis among the first and the best studied bacteria capable of respiring minerals as terminal electron acceptors (EAs), including a variety of iron ores. This respiration process relies on a large number ofc-type cytochromes, whichper seare iron-containing proteins. Thus, iron plays an essential and special role in iron respiration ofS. oneidensis, prompting extensive investigations into iron physiology. Despite this, we still know surprisingly little about the components and characteristics of iron transport in this bacterium. Here, we report that TonB-dependent receptor PutA (SO_3033) is specific to the siderophore-mediated iron uptake. Although homologs of PutA are abundant, none of them can function as a replacement. In the absence of PutA,S. oneidensissuffers from an iron shortage, which leads to a severe defect in production of cytochromec. However, proteins requiring other types of cytochromes, such asbandd, do not appear to be significantly impacted. Intriguingly, lactate, but not other carbon sources that are routinely used to support growth, is able to promote iron uptake when PutA is missing. We further show that the lactate-mediated iron import is independent of lactate permeases. Overall, our results suggest that inS. oneidensisthe siderophore-dependent pathway plays a key role in iron uptake when iron is limited, but many alternative routes exist.
Large-scale Metabolomic Analysis Reveals Potential Biomarkers for Early Stage Coronary Atherosclerosis
Authors: Gao Xueqin , Ke Chaofu , Liu Haixia , Liu Wei , Li Kang , Yu Bo , Sun Meng 
Published: September 2017

AbstractCoronary atherosclerosis (CAS) is the pathogenesis of coronary heart disease, which is a prevalent and chronic life-threatening disease. Initially, this disease is not always detected until a patient presents with seriously vascular occlusion. Therefore, new biomarkers for appropriate and timely diagnosis of early CAS is needed for screening to initiate therapy on time. In this study, we used an untargeted metabolomics approach to identify potential biomarkers that could enable highly sensitive and specific CAS detection. Score plots from partial least-squares discriminant analysis clearly separated early-stage CAS patients from controls. Meanwhile, the levels of 24 metabolites increased greatly and those of 18 metabolites decreased markedly in early CAS patients compared with the controls, which suggested significant metabolic dysfunction in phospholipid, sphingolipid, and fatty acid metabolism in the patients. Furthermore, binary logistic regression showed that nine metabolites could be used as a combinatorial biomarker to distinguish early-stage CAS patients from controls. The panel of nine metabolites was then tested with an independent cohort of samples, which also yielded satisfactory diagnostic accuracy (AUC = 0.890). In conclusion, our findings provide insight into the pathological mechanism of early-stage CAS and also supply a combinatorial biomarker to aid clinical diagnosis of early-stage CAS.
Underwater recordings of the whistles of bottlenose dolphins in Fremantle Inner Harbour, Western Australia
Authors: Marley Sarah A. , Erbe Christine , Kent Chandra P. Salgado 
Published: September 2017

AbstractDolphins use frequency-modulated whistles for a variety of social functions. Whistles vary in their characteristics according to context, such as activity state, group size, group composition, geographic location, and ambient noise levels. Therefore, comparison of whistle characteristics can be used to address numerous research questions regarding dolphin populations and behaviour. However, logistical and economic constraints on dolphin research have resulted in data collection biases, inconsistent analytical approaches, and knowledge gaps. This Data Descriptor presents an acoustic dataset of bottlenose dolphin (Tursiops aduncus) whistles recorded in the Fremantle Inner Harbour, Western Australia. Data were collected using an autonomous recorder and analysed using a range of acoustic measurements. Acoustic data review identified 336 whistles, which were subsequently measured for six key characteristics using Raven Pro software. Of these, 164 ‘high-quality’ whistles were manually measured to provide an additional five acoustic characteristics. Digital files of individual whistles and corresponding measurements make this dataset available to researchers to address future questions regarding variations within and between dolphin communities.
How Does Information Spread on Social Media Lead to Effective Change?
Authors: Varghese Thomas 
Published: September 2017

AbstractSocial media encompasses computer-mediated technologies that facilitate the creation and sharing of information, ideas, and other forms of expression via virtual communities and networks. The key, of course, is the ability and willingness for information to be shared. But why does some information spread on social media and not others? What factors translate social media awareness to action? In this article, we explore these themes using case studies, as well as tips on how you can utilize social media to effectively champion a cause.
Social Media: Changing the Paradigm for Surgical Education
Authors: Petrucci Andrea , Chand Manish , Wexner Steven 
Published: September 2017

AbstractThe role of social media (SoMe) in surgical education is emerging as a tool that augments and complements traditional learning. As SoMe usage has steadily increased in our personal and professional lives, it is no surprise that it has permeated into surgical education. Different SoMe sites offer distinct platforms from which knowledge can be transmitted, while catering to various learning styles. The purpose of this review is to outline the various SoMe platforms and their use in surgical education. Moreover, it will discuss their effectiveness in teaching and learning surgical knowledge and skills as well as other potential roles SoMe has to offer to improve surgical education.
Changing the Rules of the Game: How Do We Measure Success in Social Media?
Authors: Hogan Aisling , Winter Desmond 
Published: September 2017

AbstractOurs will be the generation proud to say we shifted the sands of educational deserts by open access and proliferation, seeding of data sharing, and watering grassroots research in resource-compromised environments. Universal “social” media is defining features of modern professional life that provide powerful modes of knowledge acquisition/sharing to that end. Altmetric and other measurements stratify academic communications according to this alternate, online media presence (not academic penetrance). Are they meaningless, self-absorbed integers, or reliable yardsticks of scientific and educational prowess? Far beyond this trite, patronizing question from the minds of outdated, terrified technophobes, the real impact of “social” media is not narcissistic solipsism. Instant dissemination of contemporary surgical controversies on a truly global level drives improved (or at least reflective) health care for all. While a numerical assignment of value according to views, “likes,” impressions, or “retweets” may seem meaningless to cynical, established academics, the impetus for universal improvement is self-evident. Electronic data and opinion sharing may not balance the inequity between low- and high-income countries, but it keeps it in perspective. The best way to shift desert sands is to blow on them constantly.