bluuebunny/crossref_metadata_2025_split huggingface dataset:
mRNA-binding protein tristetraprolin is essential for cardiac response to iron deficiency by regulating mitochondrial function
Authors: Sato Tatsuya , Chang Hsiang-Chun , Bayeva Marina , Shapiro Jason S. , Ramos-Alonso Lucia , Kouzu Hidemichi , Jiang Xinghang , Liu Ting , Yar Sumeyye , Sawicki Konrad T. , Chen Chunlei , Martínez-Pastor María Teresa , Stumpo Deborah J. , Schumacker Paul T. , Blackshear Perry J. , Ben-Sahra Issam , Puig Sergi , Ardehali Hossein 
Published: June 2018

Significance
Iron deficiency is the most common nutrient deficiency, yet cardiomyopathy rarely develops in these patients. We solved this paradox and identified a protective mechanism involving the mRNA-binding protein tristetraprolin (TTP), which adjusts mitochondrial function in response to iron deficiency. Mice lacking TTP in their hearts were phenotypically normal at baseline but developed spontaneous cardiomyopathy under iron deficiency and exhibited increased reactive oxygen species (ROS)-mediated damage in their hearts. We further demonstrate that down-regulation of specific iron-containing mitochondrial complexes by TTP is the mechanism preventing the formation of dysfunctional mitochondria, subsequent ROS production, and cellular damage. In summary, we show that activation of TTP is part of a required pathway protecting critical organ function when iron becomes scarce.
Policy distortions, farm size, and the overuse of agricultural chemicals in China
Authors: Wu Yiyun , Xi Xican , Tang Xin , Luo Deming , Gu Baojing , Lam Shu Kee , Vitousek Peter M. , Chen Deli 
Published: June 2018

Significance
Overuse of agricultural chemicals has resulted in enormous damages to environmental quality and human health in China. Reducing the use of agricultural chemicals to an optimal level is a crucial challenge for the sustainable development of agriculture. We demonstrate that small farm size (in China, typically ∼0.1 ha for each parcel) is strongly related to overuse of agricultural chemicals. Farm size increases with economic development in many other countries, but this is not observed in China due to national policies. Increasing farm size by removing policy distortions would substantially decrease both the use of agricultural chemicals and their environmental impact, while increasing rural income in China.
Antibody selection using clonal cocultivation of
Escherichia coli
and eukaryotic cells in miniecosystems
Authors: Zheng Tianqing , Xie Jia , Yang Zhuo , Tao Pingdong , Shi Bingbing , Douthit Lacey , Wu Peng , Lerner Richard A. 
Published: June 2018

Significance
We constructed a library of miniecosystems that can translate the information from antibody phage display directly into signals of biological function, thereby allowing for rapid selection of antibodies with the function of interest. Compared with the conventional phage display platform that can only isolate antibodies based on their binding affinity toward antigens, our new method bypasses the step of affinity-based selection, and the selection is based purely on the activity of antibodies in a biological system without concern for their relative affinity for antigens. This new method bridges the gap, which has existed for almost three decades, between affinity- and activity-based antibody selection for phage display of combinatorial antibody libraries, thus advancing antibody drug discovery.
Tolerance of bitter stimuli and attenuation/accumulation of their bitterness in humans
Authors: Mura Emi , Yagi Minako , Yokota Kohei , Seto Eri , Matsumiya Kentaro , Matsumura Yasuki , Hayashi Yukako 
Published: June 2018

ABSTRACT
Some components of bitterness make key flavor contributions to promote the palatability of foods, whereas other components are recognized as aversive signals to avoid consuming harmful substances. These contradictory behaviors suggest that humans tolerate tastes of bitterants based on certain criteria. Here, we investigated human taste tolerance and sensory cues leading to diverse taste tolerance of bitter compounds. Tolerance of eight bitter compounds, which are typically contained in foods, was evaluated by measuring detection and rejection thresholds. The results revealed that the level of tolerance of each compound was variable, and some compounds showed an acceptable concentration regarding the suprathreshold intensity. Tolerance did not depend on the nutritive value or attenuation and accumulation characteristics of bitterness and bitter taste receptors. These results suggest that the criteria controlling tolerance of bitter compounds may be derived from a complex relationship between the taste quality and cognitive process.
Final report on supplementary comparison EURAMET.M.P-S14 of hydraulic gauge pressure standards from 50 MPa to 1000 MPa
Authors: Könemann J , Sabuga W , Pražák D , Rabault T , Wüthrich C 
Published: June 2018

The EURAMET.M.P-S14 supplementary comparison was organized for the purpose of determination of the degree of equivalence of the national standards for static high-pressure measurement over the range 0.05 GPa to 1 GPa. A collection of eight selected high-pressure transducers with different ranges was used as a transfer standard. Five National Metrology Institutes (NMIs) from EURAMET participated in this comparison—PTB (Germany), SMU (Slovakia), CMI (Czech Republic), LNE (France), METAS (Switzerland), and all participants reported independent traceability chains to the SI. The measurements were provided at prescribed reference pressure and temperature conditions. The comparison reference value (CRV) and its uncertainty were determined separately at each pressure point, pressure transducer and particular conditions (up- and downward pressure measurement and pressure range). All the CRV results were summarised to determine the degree of equivalence for each laboratory at each pressure. The calculated degrees of equivalence show all the laboratories to be consistent at all pressures. METAS has measured, but withdrawn its results at (600, 700 and 800) MPa. Moreover, SMU withdrew their results as well. The uncertainties of the laboratories' measurements were, in many cases, much higher than the uncertainties of the laboratories' standards, which indicate problems in calibration of high pressure transducers at high pressures.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis
Authors: Lee Jungwoo , Oh Sejoon , Sael Lee 
Published: June 2018

AbstractMotivationGiven multi-platform genome data with prior knowledge of functional gene sets, how can we extract interpretable latent relationships between patients and genes? More specifically, how can we devise a tensor factorization method which produces an interpretable gene factor matrix based on functional gene set information while maintaining the decomposition quality and speed?ResultsWe propose GIFT, a Guided and Interpretable Factorization for Tensors. GIFT provides interpretable factor matrices by encoding prior knowledge as a regularization term in its objective function. We apply GIFT to the PanCan12 dataset (TCGA multi-platform genome data) and compare the performance with P-Tucker, our baseline method without prior knowledge constraint, and Silenced-TF, our naive interpretable method. Results show that GIFT produces interpretable factorizations with high scalability and accuracy. Furthermore, we demonstrate how results of GIFT can be used to reveal significant relations between (cancer, gene sets, genes) and validate the findings based on literature evidence.Availability and implementationThe code and datasets used in the paper are available at https://github.com/leesael/GIFT.Supplementary informationSupplementary data are available at Bioinformatics online.
Cross-Sectional Association of Frailty and Arterial Stiffness in Community-Dwelling Older Adults: The Framingham Heart Study
Authors: Orkaby Ariela R , Lunetta Kathryn L , Sun Fangui J , Driver Jane A , Benjamin Emelia J , Hamburg Naomi M , Mitchell Gary F , Vasan Ramachandran S , Murabito Joanne M 
Published: June 2018

Abstract

Background
Frailty is a risk factor for cardiovascular disease (CVD). Underlying mechanisms to explain the connection between frailty and CVD are unclear. We sought to examine the association between frailty and arterial stiffness, a precursor of hypertension and CVD.

Methods
We conducted a cross-sectional analysis of community-dwelling Framingham Heart Study Offspring and Omni participants ≥60 years of age examined in 2005–2008. Frailty was defined primarily according to the Fried physical phenotype definition, which identifies nonfrail, prefrail, and frail individuals. Arterial stiffness was assessed using carotid–femoral pulse wave velocity (CFPWV). Generalized linear regression was used to examine the association between frailty level and CFPWV (modeled as −1000/CFPWV in msec/m, then transformed back to the original scale, m/s), adjusted for age, sex, cohort, mean arterial pressure, heart rate, height, and smoking.

Results
Of 2,171 participants (55% women, 91% white), 45% were prefrail and 7% were frail. Mean ages were 67, 70, and 73 years, and adjusted CFPWV least squares means were 10.0 (95% CI, 9.9–10.1), 10.3 (10.2–10.5), and 10.5 m/s (10.1–11.0); p = .0002 for nonfrail, prefrail, and frail groups, respectively. Results were similar using the Rockwood cumulative deficit model of frailty, and in a sensitivity analysis adjusting for prevalent coronary heart disease and diabetes.

Conclusions
Prefrailty and frailty were associated with higher arterial stiffness in a cohort of community-dwelling older adults. Arterial stiffness may help explain the relationship between frailty and CVD.
Formation of a Malin 1 analogue in IllustrisTNG by stimulated accretion
Authors: Zhu Qirong , Xu Dandan , Gaspari Massimo , Rodriguez-Gomez Vicente , Nelson Dylan , Vogelsberger Mark , Torrey Paul , Pillepich Annalisa , Zjupa Jolanta , Weinberger Rainer , Marinacci Federico , Pakmor Rüdiger , Genel Shy , Li Yuexing , Springel Volker , Hernquist Lars 
Published: June 2018

ABSTRACT
The galaxy Malin 1 contains the largest stellar disc known but the formation mechanism of this structure has been elusive. In this paper, we report a Malin 1 analogue in the 100 Mpc IllustrisTNG simulation and describe its formation history. At redshift zero, this massive galaxy, having a maximum circular velocity Vmax of 430 km s−1, contains a 100 kpc gas/stellar disc with morphology similar to Malin 1. The simulated galaxy reproduces well many observed features of Malin 1’s vast disc, including its stellar ages, metallicities, and gas rotation curve. We trace the extended disc back in time and find that a large fraction of the cold gas at redshift zero originated from the cooling of hot halo gas, triggered by the merger of a pair of intruding galaxies. Our finding provides a novel way to form large galaxy discs as extreme as Malin 1 within the current galaxy formation framework.
Optimizing Outcome Prediction Scores in Patients Undergoing Endovascular Thrombectomy for Large Vessel Occlusions Using Collateral Grade on Computed Tomography Angiography
Authors: Ryu Chang-Woo , Kim Byung Moon , Kim Hyug-Gi , Heo Ji Hoe , Nam Hyo Suk , Kim Dong Joon , Kim Young Dae ,   collateral-based resetting of endovascular treatment for acute stroke; CoSETS investigators
Published: June 2018

Abstract

BACKGROUND
Although several outcome prediction scores incorporated with pretreatment variables have been developed for acute ischemic stroke (AIS) patients, there is not currently a prediction score that includes pretreatment imaging that can show salvageable brain tissue.

OBJECTIVE
To evaluate whether addition of the collateral grade on computed tomography angiography to previously published prediction scores could increase accuracy of clinical outcome prediction in endovascular thrombectomy (EVT) for AIS.

METHODS
This study used a retrospective multicenter registry for patients undergoing EVT for anterior circulation large vessel occlusion. Three previously published outcome prediction scores (Houston intra-arterial therapy 2, HIAT2; totaled health risks in vascular events, THRIVE; and Pittsburgh response to endovascular therapy, PRE scores) were tested in this study. Using 482 deprivation cohorts, areas under the receiver operating characteristic curves (AUC-ROCs) were compared between prediction scores with/without collateral grades in predicting the poor outcomes (modified Rankin Scale 4-6 at 3-mo follow-up) after EVT. We developed modified prediction scores by adding the collateral grade, and their advancement of outcome prediction was validated using 208 independent validation cohorts.

RESULTS
AUC-ROCs of HIAT2, THRIVE, and PRE scores that incorporated with collateral grade were superior in predicting poor outcomes when compared to that of the unmodified scores (P < 0.001). In modified prediction models, 3, 3, and 10 points were added for poor collateral grade to HIAT2, THRIVE, and PRE score. Modified models outperformed unmodified models in testing of the validation cohorts (P < 0.001).

CONCLUSION
The addition of the collateral grade to outcome prediction scores resulted in better prediction of poor outcome after EVT for AIS compared to the prediction scores alone.
INtraoperative photoDYnamic Therapy for GliOblastomas (INDYGO): Study Protocol for a Phase I Clinical Trial
Authors: Dupont Clément , Vermandel Maximilien , Leroy Henri-Arthur , Quidet Mathilde , Lecomte Fabienne , Delhem Nadira , Mordon Serge , Reyns Nicolas 
Published: June 2018

Abstract

BACKGROUND
Glioblastoma (GBM) is characterized by marked proliferation, major infiltration, and poor prognosis. Despite current treatments, including surgery, radiation oncology, and chemotherapy, the overall median survival is 15 mo and the progression-free survival is 7 to 8 mo. Because of systematic relapse of the tumor, the improvement of local control remains an issue. In this context, photodynamic therapy (PDT) may offer a new treatment modality for GBM.

OBJECTIVE
To assess the feasibility of intraoperative PDT early after surgical resection of GBM without unacceptable and unexpected toxicities.

METHODS
The INDYGO clinical trial (INtraoperative photoDYnamic Therapy for GliOblastomas) treatment will be carried out in addition to the current standard of care (SOC) of glioblastoma: maximum resection surgery followed by concomitant radio-chemotherapy and adjuvant chemotherapy. PDT treatment will be delivered during surgery early, after the fluorescence-guided resection. Immunological responses and biomarkers will also be investigated during the follow-up. A total of 10 patients will be recruited during this study.

EXPECTED OUTCOMES
Clinical follow-up after the SOC with PDT is expected to be similar (no significant difference) to the SOC alone.

DISCUSSION
This INDYGO trial assesses the feasibility of intraoperative 5-aminolevulinic acid PDT, a novel seamless approach to treat GBM. The technology is easily embeddable within the reference treatment at a low-incremental cost. The safety of this new treatment modality is a preliminary requirement before a multicenter randomized clinical trial can be further conducted to assess local control improvement by treating infiltrating and nonresected GBM cells.
The multifaceted abstract brain
Authors: Desai Rutvik H. , Reilly Megan , van Dam Wessel 
Published: June 2018

Abstract concepts play a central role in human behaviour and constitute a critical component of the human conceptual system. Here, we investigate the neural basis of four types of abstract concepts, examining their similarities and differences through neuroimaging meta-analyses. We examine numerical and emotional concepts, and two higher-order abstract processes, morality judgements and theory of mind. Three main findings emerge. First, representation of abstract concepts is more widespread than is often assumed. Second, representations of different types of abstract concepts differ in important respects. Each of the domains examined here was associated with some unique areas. Third, some areas were commonly activated across domains and included inferior parietal, posterior cingulate and medial prefrontal cortex. We interpret these regions in terms of their role in episodic recall, event representation and social–emotional processing. We suggest that different types of abstract concepts can be represented and grounded through differing contributions from event-based, interoceptive, introspective and sensory-motor representations. The results underscore the richness and diversity of abstract concepts, argue against single-mechanism accounts for representation of all types of abstract concepts and suggest mechanisms for their direct and indirect grounding.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Gender is not simply a matter of black and white, or is it?
Authors: Semin Gün R. , Palma Tomás , Acartürk Cengiz , Dziuba Aleksandra 
Published: June 2018

Based on research in physical anthropology, we argue that brightness marks the abstract category of gender, with light colours marking the female gender and dark colours marking the male gender. In a set of three experiments, we examine this hypothesis, first in a speeded gender classification experiment with male and female names presented in black and white. As expected, male names in black and female names in white are classified faster than the reverse gender-colour combinations. The second experiment relies on a gender classification task involving the disambiguation of very briefly appearing non-descript stimuli in the form of black and white ‘blobs’. The former are classified predominantly as male and the latter as female names. Finally, the processes driving light and dark object choices for males and females are examined by tracking the number of fixations and their duration in an eye-tracking experiment. The results reveal that when choosing for a male target, participants look longer and make more fixations on dark objects, and the same for light objects when choosing for a female target. The implications of these findings, which repeatedly reveal the same data patterns across experiments with Dutch, Portuguese and Turkish samples for the abstract category of gender, are discussed. The discussion attempts to enlarge the subject beyond mainstream models of embodied grounding.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Dynamic grounding of emotion concepts
Authors: Winkielman Piotr , Coulson Seana , Niedenthal Paula 
Published: June 2018

Emotion concepts are important. They help us to understand, experience and predict human behaviour. Emotion concepts also link the realm of the abstract with the realm of bodily experience and actions. Accordingly, the key question is how such concepts are created, represented and used. Embodied cognition theories hold that concepts are grounded in neural systems that produce experiential and motor states. Concepts are also contextually situated and thus engage sensorimotor resources in a dynamic, flexible way. Finally, on that framework, conceptual understanding unfolds in time, reflecting embodied as well as linguistic and cultural influences. In this article, we review empirical work on emotion concepts and show how it highlights their grounded, yet dynamic and context-sensitive nature. The conclusions are consistent with recent developments in embodied cognition that allow concepts to be linked to sensorimotor systems, yet be flexibly sensitive to current representational and action needs.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Boundaries to grounding abstract concepts
Authors: Pecher Diane , Zeelenberg René 
Published: June 2018

Grounded theories of cognition claim that concept representation relies on the systems for perception and action. The sensory-motor grounding of abstract concepts presents a challenge for these theories. Some accounts propose that abstract concepts are indirectly grounded via image schemas or situations. Recent research, however, indicates that the role of sensory-motor processing for concrete concepts may be limited, providing evidence against the idea that abstract concepts are grounded via concrete concepts. Hybrid models that combine language and sensory-motor experience may provide a more viable account of abstract and concrete representations. We propose that sensory-motor grounding is important during acquisition and provides structure to concepts. Later activation of concepts relies on this structure but does not necessarily involve sensory-motor processing. Language is needed to create coherent concepts from diverse sensory-motor experiences.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Metacognition and abstract concepts
Authors: Shea Nicholas 
Published: June 2018

The problem of how concepts can refer to or be about the non-mental world is particularly puzzling for abstract concepts. There is growing evidence that many characteristics beyond the perceptual are involved in grounding different kinds of abstract concept. A resource that has been suggested, but little explored, is introspection. This paper develops that suggestion by focusing specifically on metacognition—on the thoughts and feelings that thinkers have about a concept. One example of metacognition about concepts is the judgement that we should defer to others in how a given concept is used. Another example is our internal assessment of which concepts are dependable and useful, and which less so. Metacognition of this kind may be especially important for grounding abstract concepts.
This article is part of the theme issue ‘Varieties of abstract concepts: development, use and representation in the brain’.
Modulatory effects of dynamic fMRI-based neurofeedback on emotion regulation networks in adolescent females
Authors: Zich Catharina , Johnstone Nicola , Lührs Michael , Lisk Stephen , Haller Simone P W , Lipp Annalisa , Lau Jennifer Y F , Kadosh Kathrin Cohen 
Published: June 2018

ABSTRACTResearch has shown that difficulties with emotion regulation abilities in childhood and adolescence increase the risk for developing symptoms of mental disorders, e.g anxiety. We investigated whether functional magnetic resonance imaging (fMRI)-based neurofeedback (NF) can modulate brain networks supporting emotion regulation abilities in adolescent females.We performed three studies (total N=63). We first compared different NF implementations regarding their effectiveness of modulating prefrontal cortex (PFC)-amygdala functional connectivity (fc). Further we assessed the effects of fc-NF on neural measures, emotional/metacognitive measures and their associations. Finally, we probed the mechanism underlying fc-NF by examining concentrations of inhibitory and excitatory neurotransmitters.Results showed that NF implementations differentially modulate PFC-amygdala fc. Using the most effective NF implementation we observed important relationships between neural and emotional/metacognitive measures, such as practice-related change in fc was related with change in thought control ability. Further, we found that the relationship between state anxiety prior to the MRI session and the effect of fc-NF was moderated by GABA concentrations in the PFC and anterior cingulate cortex.To conclude, we were able to show that fc-NF can be used in adolescent females to shape neural and emotional/metacognitive measures underlying emotion regulation. We further show that neurotransmitter concentrations moderate fc-NF-effects.