bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collaborative and Reproducible Research: Goals, Challenges, and Strategies
Authors: Langer Steve G. , Shih George , Nagy Paul , Landman Bennet A. 
Published: February 2018

Abstract
Combining imaging biomarkers with genomic and clinical phenotype data is the foundation of precision medicine research efforts. Yet, biomedical imaging research requires unique infrastructure compared with principally text-driven clinical electronic medical record (EMR) data. The issues are related to the binary nature of the file format and transport mechanism for medical images as well as the post-processing image segmentation and registration needed to combine anatomical and physiological imaging data sources. The SiiM Machine Learning Committee was formed to analyze the gaps and challenges surrounding research into machine learning in medical imaging and to find ways to mitigate these issues. At the 2017 annual meeting, a whiteboard session was held to rank the most pressing issues and develop strategies to meet them. The results, and further reflections, are summarized in this paper.
The concomitant use of lapatinib and paracetamol - the risk of interaction
Authors: Karbownik Agnieszka , Szałek Edyta , Sobańska Katarzyna , Grabowski Tomasz , Klupczynska Agnieszka , Plewa Szymon , Wolc Anna , Magiera Magdalena , Porażka Joanna , Kokot Zenon J. , Grześkowiak Edmund 
Published: February 2018

Summary
Lapatinib is a tyrosine kinase inhibitor used for the treatment of breast cancer. Paracetamol is an analgesic commonly applied to patients with mild or moderate pain and fever. Cancer patients are polymedicated, which involves high risk of drug interactions during therapy. The aim of the study was to assess the interaction between lapatinib and paracetamol in rats. The rats were divided into three groups of eight animals in each. One group received lapatinib + paracetamol (IL + PA), another group received lapatinib (IIL), whereas the last group received paracetamol (IIIPA). A single dose of lapatinib (100 mg/kg b.w.) and paracetamol (100 mg/kg b.w.) was administered orally. Plasma concentrations of lapatinib, paracetamol and its metabolites – glucuronide and sulphate, were measured with the validated HPLC-MS/MS method and HPLC-UV method, respectively. The pharmacokinetic parameters of both drugs were calculated using non-compartmental methods. The co-administration of lapatinib and paracetamol increased the area under the plasma concentration-time curve (AUC) and the maximum concentration (Cmax) of lapatinib by 239.6% (p = 0.0030) and 184% (p = 0.0011), respectively. Lapatinib decreased the paracetamol AUC0-∞ by 48.8% and Cmax by 55.7%. In the IL + PA group the Cmax of paracetamol glucuronide was reduced, whereas the Cmax of paracetamol sulphate was higher than in the IIIPA group. Paracetamol significantly affected the enhanced plasma exposure of lapatinib. Additionally, lapatinib reduced the concentrations of paracetamol. The co-administration of lapatinib decreased the paracetamol glucuronidation but increased the sulphation. The findings of this study may be of clinical relevance to
patients requiring analgesic therapy.
Image dataset of ophiuroid and other deep sea benthic organisms in 2015 extracted from the survey off Sanriku, Japan, by the research following the Great East Japan Earthquake 2011
Authors: Yamakita Takehisa , Yokooka Hiroyuki , Fujiwara Yoshihiro , Kawato Masaru , Tsuchida Shinji , Ishibashi Shojiro , Kurokawa Tadayuki , Fujikura Katsunori 
Published: February 2018

AbstractThis is the first large image dataset and occurrence records of marine organisms in the Northwest Pacific off Tohoku, Japan. This area suffered by Great East Japan Earthquake 2011 and continental shelf and slope off of this area considered one of the most productive areas both for fishery and primary production in the world because of the complex mixture of the Kuroshio Current, Oyashio Current, and Tsugaru Warm Current. We compiled 3415 images of animals, stones, and sediments. Most of the images are of dominant species of Ophiuroidea (brittle stars), with 789 and 1421 images captured in two areas of different depth. These images are cropped from downward camera images collected during two dives in 2015 using remotely operated vehicles in a deeper area (670–800 m deep) off Kamaishi (cruise id KY15‐08; dive no. HPD1812) and a shallower area (280 m deep) off Minami Sanriku town (cruise id NT15‐E04; dive no. CRB17). The attribute of each image is listed in the subsequent comma delimited (csv) text file and the observed occurrence of each organisms was also converted into the text format used in Japan Ocean Biogeographic Information System Center (J‐OBIS), which is comparable with Darwin Core 2.0. Basically, we recorded the higher taxonomic levels (e.g., order and class) that could be specified with certainty and added a list of potential species as an appendix. For better understanding the broad‐scale impact of the earthquake along the continental shelf and slope, it is necessary to extract occurrence data of organisms from biological surveys. Gathering image or video data is appropriate for this purpose because most underwater surveys simultaneously record images and/or videos. This dataset will add the information of the status after 4 years of the disaster. These image data are also considered as training image data set for automatic extraction of organisms.
Influences on mammals frequency of use of small bridges and culverts along the Qinghai–Tibet railway, China
Authors: Wang Yun , Guan Lei , Chen Jiding , Kong Yaping 
Published: February 2018

AbstractUnderstanding the use of small bridges and culverts by wildlife to cross the Qinghai–Tibet railway will aid in the design of wildlife crossing structures for similar transportation infrastructure. From 2014 to 2016, 36 infrared cameras were placed inside 14 small bridges and 11 culverts along the Qinghai–Tibet railway to determine the structures’ effectiveness as wildlife passages. Thirteen species of mammals were found to use the small bridges and culverts to cross the railway. The crossing rates for all mammals were significantly higher for small bridges than for culverts. Tibetan antelope (Pantholops hodgsonii), Tibetan gazelle (Procapra picticaudata), kiang (Equus kiang), and wild yak (Bos mutus) preferred small bridges over culverts to cross the railway. In contrast, mountain weasel (Mustela altaica) and Asian badger (Meles leucurus) preferred culverts to cross the railway. The crossing rates of all mammals, particularly Tibetan gazelle and woolly hare, were positively influenced by structure width. Structure height had a positive influence on wild yak, but structure length had a negative influence on kiang. The distance to the highway had a positive influence on the crossing rates of all mammals, particularly wild yak and woolly hare. Human use of the structures had no influence on the crossings of most mammals except for common wolf. We suggest that road design schemes include large and open crossing structures to benefit most species with limitations on human activities near wildlife passages.
Contributions to a Mathematical Analysis of the English Verb-phrase
Authors: Lambek Joachim 
Published: February 2018

Ideally, the grammar of a language should tell us whkh sequences of words form sentences and which sequences don’t. It is doubtful whether any existing grammar achieves this end for one of the natural languages, such as English, Russian or Chinese. However, logicians have constructed certain artificial languages (e. g. the prepositional calculus) together with a set of rules which distinguish between sentences (or well-formed formulas, as logicians prefer to call them) and non-sentences. While it is premature to attempt a complete description of English, partial grammars have been constructed.In this paper we shall consider a fragment of English containing the namesJohnandJane, the verbsmust, work, call, have, be, the adverbtoday, the conjunctionsbutandwhileand a few other words of the same types. We also admit inflected forms such asworks, worked, working, etc. We shall attempt to-decide which sequences of these word-forms are sentences and which are not. Our grammar, if successful, must tell us that “John must have been calling Jane today” is a sentence, and that “John has must call Jane” is not a sentence. However, we may as well admit that many sentences will escape our net, owing to the fact that certain constructions, e. g. the gerund, will not be considered here.
Russian / j /
Authors: Hamp Eric P. 
Published: February 2018

James O. St. Clair-Sobell has touched on many interesting points in his “Notes on Spelling Pronunciation with Special Reference to Modern Standard Russian”, Canadian Slavonic Papers I (1956) : 66-75. The purpose of the present brief note is simply to rectify, as I think, what must be an analytical oversight in his discussion (70-71) of intervocalic / j /.St. Clair-Sobell cites the statements of Isačenko and Shaxmatov to the effect that intervocalic / j / ‘lapses’ in certain environments. He continues : ‘But the “presence” of the intervocalic j is indicated by the quality of the preceding vowel and also by the quality of the following unstressed vowel.’ He then goes on to say (71) that many phoneticians and orthoëpists seem to have missed this dropping of the / j / , and that ‘in affected, that is, in spelling pronunciation the j is heard or it is imagined that the j is heard.’
Notes on Montreal English
Authors: Hamilton Donald E. 
Published: February 2018

The following notes are based on findings obtained in a pilot study of the speech of English-speaking residents of Montreal, which was carried out from 1957 to 1958. The data was obtained by circulating a questionnaire designed to elicit information on vocabulary, pronunciation, and grammar and syntax. In general, the choice of items for inclusion in this questionnaire was restricted to those which illustrate differences between British and American usage. In the vocabulary section, a further restriction was made in that no items pertaining exclusively to rural life were included.With respect to the selection of informants there were several deviations from the established methods of linguistic surveys. In most surveys it is usual to insist that informants belong to families which have been established in the area under investigation for several generations, and that they speak no other language but English.
Quelques Traits phonétiques d'une Paroisse Gaspésienne
Authors: Gendron Jean-Denis 
Published: February 2018

L'enquête linguistique, faite durant l'été de 1954 sur la côte sud de la Gaspésie, à Bonaventure, s'insère dans un groupe d'enquêtes dont le but est d'établir un Atlas linguistique de la région gaspésienne.Comme on a déjà décrit cette région dans ses grandes lignes et signalé sa richesse en matéiaux linguistiques, nous nous contenterons, dans cet article, de faire les remarques générales qui s'imposent sur la paroisse qui nous intéresse, et de donner un bref aperçu phonétique des matériaux recueillis.Bonaventure, une des plus vieilles paroisses de la côte sud de la Gaspésie, fut fondée vers 1774 par des Acadiens en quête de terres nouvelles où habiter. Depuis lors, ceux-ci se sont multipliés au point de former l'agglomération la plus considérable du comté, et ce, presque sans apport d'immigrants étrangers.
Revisiting the Revised Hierarchical Model: Evidence for concept mediation in backward translation
Authors: WU ZHAOHONG , JUFFS ALAN 
Published: February 2018

A claim fundamental to the revised hierarchical model (Kroll & Stewart, 1994) was that concepts did not mediate backward translation, based on their findings of a category interference effect in forward translation in relatively fluent bilinguals but no category effect in backward translation. This study hypothesized that there was a category facilitation effect in L2-to-concept, which counterbalanced the category interference effect in concept-to-L1, resulting in an overall L2-to-L1 null category effect.In a novel English word-pair semantic comparison task, participants were presented with a sequence of English word-pairs, and judged which word's real-world referent was bigger in size. Results found a significant category facilitation effect in both L2-to-concept for young Chinese adults and L1-to-concept for young English adults when increasing the number of trials. The findings help explain why Kroll and Stewart's finding of an overall L2-to-L1 null category effect cannot be evidence against concept mediation in backward translation.
Kant’s Transcendental Deduction and the Unity of Space and Time
Authors: Roche Andrew F. 
Published: February 2018

AbstractOn one reading of Kant’s account of our original representations of space and time, they are, in part, products of the understanding or imagination. On another, they are brute, sensible givens, entirely independent of the understanding. In this article, while I agree with the latter interpretation, I argue for a version of it that does more justice to the insights of the former than others currently available. I claim that Kant’s Transcendental Deduction turns on the representations of space and time as determinate, enduring particulars, whose unity is both given and a product of synthesis.
Giant intrinsic chiro-optical activity in planar dielectric nanostructures
Authors: Zhu Alexander Y , Chen Wei Ting , Zaidi Aun , Huang Yao-Wei , Khorasaninejad Mohammadreza , Sanjeev Vyshakh , Qiu Cheng-Wei , Capasso Federico 
Published: February 2018

AbstractThe strong optical chirality arising from certain synthetic metamaterials has important and widespread applications in polarization optics, stereochemistry and spintronics. However, these intrinsically chiral metamaterials are restricted to a complicated three-dimensional (3D) geometry, which leads to significant fabrication challenges, particularly at visible wavelengths. Their planar two-dimensional (2D) counterparts are limited by symmetry considerations to operation at oblique angles (extrinsic chirality) and possess significantly weaker chiro-optical responses close to normal incidence. Here, we address the challenge of realizing strong intrinsic chirality from thin, planar dielectric nanostructures. Most notably, we experimentally achieve near-unity circular dichroism with ~90% of the light with the chosen helicity being transmitted at a wavelength of 540 nm. This is the highest value demonstrated to date for any geometry in the visible spectrum. We interpret this result within the charge-current multipole expansion framework and show that the excitation of higher-order multipoles is responsible for the giant circular dichroism. These experimental results enable the realization of high-performance miniaturized chiro-optical components in a scalable manner at optical frequencies.
A GABAergic cell type in the lateral habenula links hypothalamic homeostatic and midbrain motivation circuits with sex steroid signaling
Authors: Zhang Limei , Hernández Vito S. , Swinny Jerome D. , Verma Anil K. , Giesecke Torsten , Emery Andrew C. , Mutig Kerim , Garcia-Segura Luis M. , Eiden Lee E. 
Published: February 2018

AbstractThe lateral habenula (LHb) has a key role in integrating a variety of neural circuits associated with reward and aversive behaviors. There is limited information about how the different cell types and neuronal circuits within the LHb coordinate physiological and motivational states. Here, we report a cell type in the medial division of the LHb (LHbM) in male rats that is distinguished by: (1) a molecular signature for GABAergic neurotransmission (Slc32a1/VGAT) and estrogen receptor (Esr1/ERα) expression, at both mRNA and protein levels, as well as the mRNA for vesicular glutamate transporter Slc17a6/VGLUT2, which we term the GABAergic estrogen-receptive neuron (GERN); (2) its axonal projection patterns, identified by in vivo juxtacellular labeling, to both local LHb and to midbrain modulatory systems; and (3) its somatic expression of receptors for vasopressin, serotonin and dopamine, and mRNA for orexin receptor 2. This cell type is anatomically located to receive afferents from midbrain reward (dopamine and serotonin) and hypothalamic water and energy homeostasis (vasopressin and orexin) circuits. These afferents shared the expression of estrogen synthase (aromatase) and VGLUT2, both in their somata and axon terminals. We demonstrate dynamic changes in LHbM VGAT+ cell density, dependent upon gonadal functional status, that closely correlate with motivational behavior in response to predator and forced swim stressors. The findings suggest that the homeostasis and reward-related glutamatergic convergent projecting pathways to LHbMC employ a localized neurosteroid signaling mechanism via axonal expression of aromatase, to act as a switch for GERN excitation/inhibition output prevalence, influencing depressive or motivated behavior.
Plasma exosomes induced by remote ischaemic preconditioning attenuate myocardial ischaemia/reperfusion injury by transferring miR-24
Authors: Minghua Wen , Zhijian Gong , Chahua Huang , Qiang Liang , Minxuan Xu , luqiao Wang , Weifang Zhang , Peng Lu , Biming Zhan , Lingling Yu , Zhenzhen Wang , Jianqing Xu , Huihui Bao , Xiaozhong Wang , Xiaoshu Cheng 
Published: February 2018

AbstractRemote ischaemic preconditioning (RIPC) is well known to protect the myocardium against ischaemia/reperfusion injury (IRI). Exosomes are small extracellular vesicles that have become the key mediators of intercellular communication. Various studies have confirmed that circulating exosomes mediate RIPC. However, the underlying mechanisms for RIPC-induced exosome-mediated cardioprotection remain elusive. In our study, we found that the expression level of miR-24 was higher in exosomes derived from the plasma of rats subjected to RIPC than in exosomes derived from the plasma of control rats in vivo. The rat plasma exosomes could be taken up by H9c2 cells. In addition, miR-24 was present in RIPC-induced exosomes and played a role in reducing oxidative stress-mediated injury and decreasing apoptosis by downregulating Bim expression in H2O2-treated H9c2 cells in vitro. In vivo, miR-24 in RIPC-induced exosomes reduced cardiomyocyte apoptosis, attenuated the infarct size and improved heart function. Furthermore, the apoptosis-reducing effect of miR-24 was counteracted by miR-24 antagomirs or inhibitors both in vitro and in vivo. Therefore, we provided evidence that RIPC-induced exosomes could reduce apoptosis by transferring miR-24 in a paracrine manner and that miR-24 in the exosomes plays a central role in mediating the protective effects of RIPC.
Kupffer cell-derived TNF-α promotes hepatocytes to produce CXCL1 and mobilize neutrophils in response to necrotic cells
Authors: Su Li , Li Na , Tang Hua , Lou Ziyang , Chong Xiaodan , Zhang Chenxi , Su Jiacan , Dong Xin 
Published: February 2018

AbstractThe damage-associated molecular pattern molecules (DAMPs) released by necrotic cells can trigger inflammatory response, which will facilitate the clearance of these dead cells. Neutrophil mobilization is a very important step for the dead cell clearance, however the detailed mechanisms for DAMPs induce neutrophil mobilization remains largely elusive. In this study, by using a necrotic cell-induced neutrophil mobilization mice model, we found that both neutrophil number and percentage rapidly (as early as 30 min) increased with necrotic cells but not live cell treatment. CXCL1 was rapidly increased in the serum and was responsible for the neutrophil mobilization when treated with necrotic cells. We further demonstrated that the hepatocytes in the liver were the main source of CXCL1 production in response to necrotic cells challenge. However, the hepatocytes did not express CXCL1 when incubating with necrotic cells alone. When Kupffer cells were ablated, the increased CXCL1 levels as well as neutrophil mobilization were abolished with necrotic cells challenge. Moreover, we clarified Kupffer cells-derived TNF-α activates the NF-κB pathway in hepatocytes and promote hepatocytes to express CXCL1. In summary, we showed that the liver is the main source for necrotic cell-induced CXCL1 production and neutrophil mobilization. Kupffer cells in the liver sense DAMPs and release TNF-α to activate the NF-κB pathway in hepatocytes. The interaction between Kupffer cells and hepatocytes is critical for CXCL1 production.
Dual extra-retinal origins of microglia in the model of retinal microglia repopulation
Authors: Huang Yubin , Xu Zhen , Xiong Shanshan , Qin Guangrong , Sun Fangfang , Yang Jian , Yuan Ti-Fei , Zhao Lei , Wang Ke , Liang Yu-Xiang , Fu Lin , Wu Tianzhun , So Kwok-Fai , Rao Yanxia , Peng Bo 
Published: February 2018

AbstractElucidating the origin of microglia is crucial for understanding their functions and homeostasis. Previous study has indicated that Nestin-positive progenitor cells differentiate into microglia and replenish the brain after depleting most brain microglia. Microglia have also shown the capacity to repopulate the retina after eliminating all retinal microglia. However, the origin(s) of repopulated retinal microglia is/are unknown. In this study, we aim to investigate the origins of repopulated microglia in the retina. Interestingly, we find that repopulated retinal microglia are not derived from Nestin-positive progenitor cells. Instead, they have two origins: the center-emerging microglia are derived from residual microglia in the optic nerve and the periphery-emerging microglia are derived from macrophages in the ciliary body/iris. Therefore, we have for the first time identified the extra-retinal origins of microglia in the adult mammalian retina by using a model of microglial repopulation, which may shed light on the target exploration of therapeutic interventions for retinal degenerative disorders.
VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation
Authors: Yue Yanan , Liu Jun , Cui Xiaolong , Cao Jie , Luo Guanzheng , Zhang Zezhou , Cheng Tao , Gao Minsong , Shu Xiao , Ma Honghui , Wang Fengqin , Wang Xinxia , Shen Bin , Wang Yizhen , Feng Xinhua , He Chuan , Liu Jianzhao 
Published: February 2018

AbstractN6-methyladenosine (m6A) is enriched in 3′untranslated region (3′UTR) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m6A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3′UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m6A enrichment in 3′UTR. Depletions of VIRMA and METTL3 induce 3′UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3′UTR of over 2800 mRNAs, 84% of which are modified with m6A and have increased m6A peak density in 3′UTR and near stop codon after CPSF5 knockdown. Together, our studies provide insights into m6A deposition specificity in 3′UTR and its correlation with alternative polyadenylation.