bluuebunny/crossref_metadata_2025_split huggingface dataset:
Faith and Reason: A Response to Duncan Pritchard
Authors: Ceglie Roberto di 
Published: January 2017

AbstractIn a recent essay Duncan Pritchard argues that there is no fundamental epistemological distinction between religious belief and ordinary or non-religious belief. Both of them – so he maintains in the footsteps of Wittgenstein's On certainty – are ultimately grounded on a-rational commitments, namely, commitments unresponsive to rational criteria. I argue that, while this view can be justified theologically, it cannot be advanced philosophically as Pritchard assumes.I offer an account of Aquinas's reflection on faith and reason to show that the theologian – not the philosopher – is entitled to deal with a-rational commitments, because the truths of faith can be seen as simply intellectual – like the rational statements considered by the philosopher – but also as decisions made by way of divine grace. I also suggest that Pritchard's thesis may be re-proposed on a new basis, if Aquinas's theological stance were reinterpreted so as to point out unexpected connections between theology and philosophy.
Monitoring selective logging with Landsat satellite imagery reveals that protected forests in Western Siberia experience greater harvest than non-protected forests
Authors: SHCHUR ALEXANDER , BRAGINA EUGENIA , SIEBER ANIKA , PIDGEON ANNA M. , RADELOFF VOLKER C. 
Published: January 2017

SUMMARYWhen timber harvesting is an important source of local income and forest resources are declining, even forests that are designated as protected areas may become vulnerable. Therefore, regular monitoring of forest disturbance is necessary to enforce the protection of forest ecosystems. However, mapping forest disturbance with satellite imagery can be complicated if the majority of the harvesting is selective logging and not clearcuts. Our goal was to map both selective logging and clearcuts within and outside of protected areas in Western Siberia, a region with a highly developed timber industry. Combining summer and winter imagery allowed us to accurately estimate not only clearcuts, but also selective logging. Winter Landsat images substantially improved our classification and resulted in a highly accurate forest disturbance map (97.5% overall accuracy and 86% user accuracy for the rarest class, clearcuts). Selective logging and stripcuts were the dominant disturbance types, accounting for 96.3% of all forest disturbances, versus 3.7% for clearcuts. The total annual forest disturbance rate (i.e. disturbance rate for clearcuts, stripcuts and selective logging together) was 0.53%, but total forest disturbance within protected areas was greater than in non-protected forest (0.66% versus 0.50%, respectively), and so was the annual rate of selective logging (i.e. without clearcuts, 0.37% versus 0.25%, respectively). Our results highlight that monitoring only clearcuts without assessing selective logging might result in significant underestimation of forest disturbance. Also, when timber harvesting is important for the local economy and when protected areas have valuable timber resources that have already been depleted elsewhere, then additional protection may be necessary in order to maintain natural forests within protected areas. We suggest that this is the situation in our study area in Western Siberia right now and is likely the situation in many other parts of the globe as well.
Intravitreally-administered dopamine D2-like (and D4), but not D1-like, receptor agonists reduce form-deprivation myopia in tree shrews
Authors: WARD ALEXANDER H. , SIEGWART JOHN T. , FROST MICHAEL R. , NORTON THOMAS T. 
Published: January 2017

AbstractWe examined the effect of intravitreal injections of D1-like and D2-like dopamine receptor agonists and antagonists and D4 receptor drugs on form-deprivation myopia (FDM) in tree shrews, mammals closely related to primates. In eleven groups (n= 7 per group), we measured the amount of FDM produced by monocular form deprivation (FD) over an 11-day treatment period. The untreated fellow eye served as a control. Animals also received daily 5µL intravitreal injections in the FD eye. The reference group received 0.85% NaCl vehicle. Four groups received a higher, or lower, dose of a D1-like receptor agonist (SKF38393) or antagonist (SCH23390). Four groups received a higher, or lower, dose of a D2-like receptor agonist (quinpirole) or antagonist (spiperone). Two groups received the D4 receptor agonist (PD168077) or antagonist (PD168568). Refractions were measured daily; axial component dimensions were measured on day 1 (before treatment) and day 12. We found that in groups receiving the D1-like receptor agonist or antagonist, the development of FDM and altered ocular component dimensions did not differ from the NaCl group. Groups receiving the D2-like receptor agonist or antagonist at the higher dose developed significantly less FDM and had shorter vitreous chambers than the NaCl group. The D4 receptor agonist, but not the antagonist, was nearly as effective as the D2-like agonist in reducing FDM. Thus, using intravitreally-administered agents, we did not find evidence supporting a role for the D1-like receptor pathway in reducing FDM in tree shrews. The reduction of FDM by the dopamine D2-like agonist supported a role for the D2-like receptor pathway in the control of FDM. The reduction of FDM by the D4 receptor agonist, but not the D4 antagonist, suggests an important role for activation of the dopamine D4 receptor in the control of axial elongation and refractive development.
A “Black Cult” in Early Medieval China: Iranian-Zoroastrian Influence in the Northern Dynasties
Authors: CHEN SANPING , MAIR VICTOR H 
Published: January 2017

AbstractThrough an analysis of Chinese theophoric names - a genre that emerged in the early medieval period largely under heavy Iranian-Sogdian influence - we suggest that there was a contemporary ‘black worship’ or ‘black cult’ in northern China that has since vanished. The followers of this ‘black cult’ ranged from common people living in ethnically mixed frontier communities to the ruling echelons of the Northern Dynasties. By tapping into the fragmentary pre-Islamic Iranian-Sogdian data, we link this ‘black cult’ to the now nearly forgotten ancient Iranic worship of the Avestan family of heroes centered around Sāma. This religio-cultural exchange prompts an examination of the deliberate policy by the ethnic rulers of the Northern Dynasties to attract Central Asian immigrants for political reasons, a precursor to the Semu, the Mongols’ ‘assistant conquerors’ in the Yuan dynasty.
RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression
Authors: Niu Ningning , Xiang Jian-Feng , Yang Qin , Wang Lijun , Wei Zhanying , Chen Ling-Ling , Yang Li , Zou Weiguo 
Published: January 2017

AbstractProtein translation regulation has essential roles in inflammatory responses, cancer initiation and the pathogenesis of several neurodegenerative disorders. However, the role of the regulation of protein translation in mammalian skeleton development has been rarely elaborated. Here we report that the lack of the RNA-binding protein sterile alpha motif domain containing protein 4 (SAMD4) resulted in multiple developmental defects in mice, including delayed bone development and decreased osteogenesis. Samd4-deficient mesenchymal progenitors exhibit impaired osteoblast differentiation and function. Mechanism study demonstrates that SAMD4 binds the Mig6 mRNA and inhibits MIG6 protein synthesis. Consistent with this, Samd4-deficient cells have increased MIG6 protein level and knockdown of Mig6 rescues the impaired osteogenesis in Samd4-deficient cells. Furthermore, Samd4-deficient mice also display chondrocyte defects, which is consistent with the regulation of MIG6 protein level by SAMD4. These findings define SAMD4 as a previously unreported key regulator of osteoblastogenesis and bone development, implying that regulation of protein translation is an important mechanism governing skeletogenesis and that control of protein translation could have therapeutic potential in metabolic bone diseases, such as osteoporosis.
Erratum: Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis
Authors: Sonnenschein Eva C , Nielsen Kristian F , D’Alvise Paul , Porsby Cisse H , Melchiorsen Jette , Heilmann Jens , Kalatzis Panos G , López-Pérez Mario , Bunk Boyke , Spröer Cathrin , Middelboe Mathias , Gram Lone 
Published: January 2017

Abstract
Correction to: The ISME Journal (2016) 11, 569–583; doi:10.1038/ismej.2016.111; published online 23 August 2016 The affiliation listed for Boyke Bunk and Cathrin Spröer was incorrectly listed as ‘Helmholtz Centre for Infection Research, Braunschweig, Germany’. The correct affiliation is ‘Leibniz-Institute DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany’.
Refined Ordovician timescale reveals no link between asteroid breakup and biodiversification
Authors: Lindskog A. , Costa M. M. , Rasmussen C.M.Ø. , Connelly J. N. , Eriksson M. E. 
Published: January 2017

AbstractThe catastrophic disruption of the L chondrite parent body in the asteroid belt c. 470 Ma initiated a prolonged meteorite bombardment of Earth that started in the Ordovician and continues today. Abundant L chondrite meteorites in Middle Ordovician strata have been interpreted to be the consequence of the asteroid breakup event. Here we report a zircon U-Pb date of 467.50±0.28 Ma from a distinct bed within the meteorite-bearing interval of southern Sweden that, combined with published cosmic-ray exposure ages of co-occurring meteoritic material, provides a precise age for the L chondrite breakup at 468.0±0.3 Ma. The new zircon date requires significant revision of the Ordovician timescale that has implications for the understanding of the astrogeobiologic development during this period. It has been suggested that the Middle Ordovician meteorite bombardment played a crucial role in the Great Ordovician Biodiversification Event, but this study shows that the two phenomena were unrelated.
Mineral inclusions in diamonds may be synchronous but not syngenetic
Authors: Nestola Fabrizio , Jung Haemyeong , Taylor Lawrence A. 
Published: January 2017

AbstractIt is widely assumed that mineral inclusions and their host diamonds are ‘syngenetic’ in origin, which means that they formed simultaneously and from the same chemical processes. Mineral inclusions that, instead, were formed earlier with respect to diamonds are termed protogenetic. However, minerals can have the same age as the diamonds in that they become enclosed in and isolated from any further isotopic exchange. But this is termed ‘synchronous’ not ‘syngenetic’. Here we demonstrate conclusively the protogenesis of inclusions in diamonds, based upon data from an exceptional fragment of a diamond-bearing peridotite, its clinopyroxene and a gem-quality diamond. Clinopyroxenes in the xenolith had the same chemistry and crystallographic orientation as those for inclusions in the diamond. With our results with garnets, olivines and sulfides, we can state that a major portion of the mineral inclusions in non-coated, monocrystalline-lithospheric diamonds are protogenetic. Our discovery here presented has implications for all genetic aspects of diamond growth, including their ages.
Scalable high-precision tuning of photonic resonators by resonant cavity-enhanced photoelectrochemical etching
Authors: Gil-Santos Eduardo , Baker Christopher , Lemaître Aristide , Ducci Sara , Gomez Carmen , Leo Giuseppe , Favero Ivan 
Published: January 2017

AbstractPhotonic lattices of mutually interacting indistinguishable cavities represent a cornerstone of collective phenomena in optics and could become important in advanced sensing or communication devices. The disorder induced by fabrication technologies has so far hindered the development of such resonant cavity architectures, while post-fabrication tuning methods have been limited by complexity and poor scalability. Here we present a new simple and scalable tuning method for ensembles of microphotonic and nanophotonic resonators, which enables their permanent collective spectral alignment. The method introduces an approach of cavity-enhanced photoelectrochemical etching in a fluid, a resonant process triggered by sub-bandgap light that allows for high selectivity and precision. The technique is presented on a gallium arsenide nanophotonic platform and illustrated by finely tuning one, two and up to five resonators. It opens the way to applications requiring large networks of identical resonators and their spectral referencing to external etalons.
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies
Authors: Módos Dezső , Bulusu Krishna C. , Fazekas Dávid , Kubisch János , Brooks Johanne , Marczell István , Szabó Péter M. , Vellai Tibor , Csermely Péter , Lenti Katalin , Bender Andreas , Korcsmáros Tamás 
Published: January 2017

AbstractEven targeted chemotherapies against solid cancers show a moderate success increasing the need to novel targeting strategies. To address this problem, we designed a systems-level approach investigating the neighbourhood of mutated or differentially expressed cancer-related proteins in four major solid cancers (colon, breast, liver and lung). Using signalling and protein–protein interaction network resources integrated with mutational and expression datasets, we analysed the properties of the direct and indirect interactors (first and second neighbours) of cancer-related proteins, not found previously related to the given cancer type. We found that first neighbours have at least as high degree, betweenness centrality and clustering coefficient as cancer-related proteins themselves, indicating a previously unknown central network position. We identified a complementary strategy for mutated and differentially expressed proteins, where the affect of differentially expressed proteins having smaller network centrality is compensated with high centrality first neighbours. These first neighbours can be considered as key, so far hidden, components in cancer rewiring, with similar importance as mutated proteins. These observations strikingly suggest targeting first neighbours as a novel strategy for disrupting cancer-specific networks. Remarkably, our survey revealed 223 marketed drugs already targeting first neighbour proteins but applied mostly outside oncology, providing a potential list for drug repurposing against solid cancers. For the very central first neighbours, whose direct targeting would cause several side effects, we suggest a cancer-mimicking strategy by targeting their interactors (second neighbours of cancer-related proteins, having a central protein affecting position, similarly to the cancer-related proteins). Hence, we propose to include first neighbours to network medicine based approaches for (but not limited to) anticancer therapies.
Utility of baseline, interim and end-of-treatment 18F-FDG PET/CT in extranodal natural killer/T-cell lymphoma patients treated with L-asparaginase/pegaspargase
Authors: Chang Yu , Fu Xiaorui , Sun Zhenchang , Xie Xinli , Wang Ruihua , Li Zhaoming , Zhang Xudong , Sheng Guangyao , Zhang Mingzhi 
Published: January 2017

AbstractPositron emission tomography-computed tomography (PET/CT) is widely used for initial staging and monitoring treatment responses in Hodgkin and diffuse large B-cell lymphoma. However, its prognostic value in extranodal natural killer (NK)/T-cell lymphoma (ENKL) remains unclear. Here, we conducted a retrospective study to determine the impact of PET/CT in ENKL. Fifty-two patients newly diagnosed with ENKL were enrolled. Baseline maximum standardized uptake values (SUVmax), whole-body metabolic tumor volume (WBMTV) and whole-body total lesion glycolysis (WBTLG) were recorded. Additionally, interim PET/CT (I-PET) and end-of-treatment PET/CT (E-PET) results were scored using a 5-point scale. Patients were divided into groups using baseline parameter cut-off values; significant differences were found in overall survival (OS) and progression-free survival (PFS) between the high and low WBMTV and WBTLG groups and in OS between the two SUVmax groups. Positive I-PET and E-PET results predicted inferior PFS and OS. A multivariate analysis showed that baseline WBTLG, I-PET and E-PET results were associated with PFS and OS, and baseline SUVmax was an independent predictor of OS. Thus, baseline WBTLG, I-PET and E-PET results are good predictors of PFS and OS in ENKL patients who received L-asparaginase/pegaspargase in their first-line treatment, and baseline SUVmax is a valuable tool for assessing OS.
The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression
Authors: Almassalha L. M. , Tiwari A. , Ruhoff P. T. , Stypula-Cyrus Y. , Cherkezyan L. , Matsuda H. , Dela Cruz M. A. , Chandler J. E. , White C. , Maneval C. , Subramanian H. , Szleifer I. , Roy H. K. , Backman V. 
Published: January 2017

AbstractMost of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.
Piperine regulates UCP1 through the AMPK pathway by generating intracellular lactate production in muscle cells
Authors: Kim Nami , Nam Miso , Kang Mi Sun , Lee Jung Ok , Lee Yong Woo , Hwang Geum-Sook , Kim Hyeon Soo 
Published: January 2017

AbstractThis study characterizes the human metabolic response to piperine, a curcumin extract, and the details of its underlying molecular mechanism. Using1H-NMR-based metabolome analysis, we showed the metabolic effect of piperine on skeletal muscle and found that piperine increased the level of intracellular lactate, an important metabolic intermediate that controls expression of several genes involved in mitochondrial activity. Piperine also induced the phosphorylation of AMP-activated protein kinase (AMPK) and its downstream target, acetyl-CoA carboxylase (ACC), while additionally stimulating glucose uptake in an AMPK dependent manner. Piperine also stimulates the p38 mitogen-activated protein kinase (p38 MAPK), an effect that was reversed by pretreatment with compound C, an AMPK inhibitor. Inhibition of p38 MAPK resulted in no piperine-induced glucose uptake. Increased level of lactate resulted in increased expression of mitochondrial uncoupling protein 1 (UCP1), which regulates energy expenditure, thermogenesis, and fat browning. Knock-down of AMPK blocked piperine-induced UCP1 up-regulation, demonstrating the required role of AMPK in this effect. Taken together, these results suggest that piperine leads to benign metabolic effects by activating the AMPK-p38 MAPK signaling pathway and UCP1 expression by activating intracellular lactate production in skeletal muscle.
Allosteric Inhibition of Phosphoenolpyruvate Carboxylases is Determined by a Single Amino Acid Residue in Cyanobacteria
Authors: Takeya Masahiro , Hirai Masami Yokota , Osanai Takashi 
Published: January 2017

AbstractPhosphoenolpyruvate carboxylase (PEPC) is an important enzyme for CO2 fixation and primary metabolism in photosynthetic organisms including cyanobacteria. The kinetics and allosteric regulation of PEPCs have been studied in many organisms, but the biochemical properties of PEPC in the unicellular, non-nitrogen-fixing cyanobacterium Synechocystis sp. PCC 6803 have not been clarified. In this study, biochemical analysis revealed that the optimum pH and temperature of Synechocystis 6803 PEPC proteins were 7.3 and 30 °C, respectively. Synechocystis 6803 PEPC was found to be tolerant to allosteric inhibition by several metabolic effectors such as malate, aspartate, and fumarate compared with other cyanobacterial PEPCs. Comparative sequence and biochemical analysis showed that substitution of the glutamate residue at position 954 with lysine altered the enzyme so that it was inhibited by malate, aspartate, and fumarate. PEPC of the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 was purified, and its activity was inhibited in the presence of malate. Substitution of the lysine at position 946 (equivalent to position 954 in Synechocystis 6803) with glutamate made Anabaena 7120 PEPC tolerant to malate. These results demonstrate that the allosteric regulation of PEPC in cyanobacteria is determined by a single amino acid residue, a characteristic that is conserved in different orders.
NLRP3 inflammasome: Pathogenic role and potential therapeutic target for IgA nephropathy
Authors: Tsai Yu-Ling , Hua Kuo-Feng , Chen Ann , Wei Chyou-Wei , Chen Wen-Shiang , Wu Cheng-Yeu , Chu Ching-Liang , Yu Yung-Luen , Lo Chia-Wen , Ka Shuk-Man 
Published: January 2017

AbstractWe have previously showed that IL-1β is involved in the pathogenesis of both spontaneously occurring and passively induced IgA nephropathy (IgAN) models. However, the exact causal-relationship between NLRP3 inflammasome and the pathogenesis of IgAN remains unknown. In the present study, we showed that [1] IgA immune complexes (ICs) activated NLRP3 inflammasome in macrophages involving disruption of mitochondrial integrity and induction of mitochondrial ROS, bone marrow-derived dendritic cells (BMDCs) and renal intrinsic cells; [2] knockout of NLRP3 inhibited IgA ICs-mediated activation of BMDCs and T cells; and [3] knockout of NLRP3 or a kidney-targeting delivery of shRNA of NLRP3 improved renal function and renal injury in a mouse IgAN model. These results strongly suggest that NLRP3 inflammasome serves as a key player in the pathogenesis of IgAN partly through activation of T cells and mitochondrial ROS production and that a local, kidney-targeting suppression of NLRP3 be a therapeutic strategy for IgAN.
A visual processing advantage for young-adolescent deaf observers: Evidence from face and object matching tasks
Authors: Megreya Ahmed M. , Bindemann Markus 
Published: January 2017

AbstractIt is unresolved whether the permanent auditory deprivation that deaf people experience leads to the enhanced visual processing of faces. The current study explored this question with a matching task in which observers searched for a target face among a concurrent lineup of ten faces. This was compared with a control task in which the same stimuli were presented upside down, to disrupt typical face processing, and an object matching task. A sample of young-adolescent deaf observers performed with higher accuracy than hearing controls across all of these tasks. These results clarify previous findings and provide evidence for a general visual processing advantage in deaf observers rather than a face-specific effect.