bluuebunny/crossref_metadata_2025_split huggingface dataset:
The glutamate/cystine xCT antiporter antagonizes glutamine metabolism and reduces nutrient flexibility
Authors: Shin Chun-Shik , Mishra Prashant , Watrous Jeramie D. , Carelli Valerio , D’Aurelio Marilena , Jain Mohit , Chan David C. 
Published: April 2017

AbstractAs noted by Warburg, many cancer cells depend on the consumption of glucose. We performed a genetic screen to identify factors responsible for glucose addiction and recovered the two subunits of the xCT antiporter (system xc−), which plays an antioxidant role by exporting glutamate for cystine. Disruption of the xCT antiporter greatly improves cell viability after glucose withdrawal, because conservation of glutamate enables cells to maintain mitochondrial respiration. In some breast cancer cells, xCT antiporter expression is upregulated through the antioxidant transcription factor Nrf2 and contributes to their requirement for glucose as a carbon source. In cells carrying patient-derived mitochondrial DNA mutations, the xCT antiporter is upregulated and its inhibition improves mitochondrial function and cell viability. Therefore, although upregulation of the xCT antiporter promotes antioxidant defence, it antagonizes glutamine metabolism and restricts nutrient flexibility. In cells with mitochondrial dysfunction, the potential utility of xCT antiporter inhibition should be further tested.
A mouse tissue transcription factor atlas
Authors: Zhou Quan , Liu Mingwei , Xia Xia , Gong Tongqing , Feng Jinwen , Liu Wanlin , Liu Yang , Zhen Bei , Wang Yi , Ding Chen , Qin Jun 
Published: April 2017

AbstractTranscription factors (TFs) drive various biological processes ranging from embryonic development to carcinogenesis. Here, we employ a recently developed concatenated tandem array of consensus TF response elements (catTFRE) approach to profile the activated TFs in 24 adult and 8 fetal mouse tissues on proteome scale. A total of 941 TFs are quantitatively identified, representing over 60% of the TFs in the mouse genome. Using an integrated omics approach, we present a TF network in the major organs of the mouse, allowing data mining and generating knowledge to elucidate the roles of TFs in various biological processes, including tissue type maintenance and determining the general features of a physiological system. This study provides a landscape of TFs in mouse tissues that can be used to elucidate transcriptional regulatory specificity and programming and as a baseline that may facilitate understanding diseases that are regulated by TFs.
Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer
Authors: Dhawan Andrew , Nichol Daniel , Kinose Fumi , Abazeed Mohamed E. , Marusyk Andriy , Haura Eric B. , Scott Jacob G. 
Published: April 2017

AbstractDrug resistance remains an elusive problem in cancer therapy, particularly for novel targeted therapies. Much work is focused upon the development of an arsenal of targeted therapies, towards oncogenic driver genes such as ALK-EML4, to overcome the inevitable resistance that develops over time. Currently, after failure of first line ALK TKI therapy, another ALK TKI is administered, though collateral sensitivity is not considered. To address this, we evolved resistance in an ALK rearranged non-small cell lung cancer line (H3122) to a panel of 4 ALK TKIs, and performed a collateral sensitivity analysis. All ALK inhibitor resistant cell lines displayed significant cross-resistance to all other ALK inhibitors. We then evaluated ALK-inhibitor sensitivities after drug holidays of varying length (1–21 days), and observed dynamic patterns of resistance. This unpredictability led us to an expanded search for treatment options, where we tested 6 further anti-cancer agents for collateral sensitivity among resistant cells, uncovering possibilities for further treatment, including cross-sensitivity to standard cytotoxic therapies, as well as Hsp90 inhibitors. Taken together, these results imply that resistance to targeted therapy in non-small cell lung cancer is highly dynamic, and also one where there are many opportunities to re-establish sensitivities where there was once resistance. Drug resistance in cancer inevitably emerges during treatment; particularly with novel targeted therapies, designed to inhibit specific molecules. A clinically-relevant example of this phenomenon occurs in ALK-positive non-small cell lung cancer, where targeted therapies are used to inhibit the ALK-EML4 fusion protein. A potential solution to this may lie in finding drug sensitivities in the resistant population, termed collateral sensitivities, and then using these as second-line agents. This study shows how the evolution of resistance in ALK-positive lung cancer is a dynamic process through time, one in which patterns of drug resistance and collateral sensitivity change substantially, and therefore one where temporal regimens, such as drug cycling and drug holidays may have great benefit.
Post-Surgery Glioma Growth Modeling from Magnetic Resonance Images for Patients with Treatment
Authors: Elazab Ahmed , Bai Hongmin , Abdulazeem Yousry M. , Abdelhamid Talaat , Zhou Sijie , Wong Kelvin K. L. , Hu Qingmao 
Published: April 2017

AbstractReaction diffusion is the most common growth modelling methodology due to its simplicity and consistency with the biological tumor growth process. However, current extensions of the reaction diffusion model lack one or more of the following: efficient inclusion of treatments’ effects, taking into account the viscoelasticity of brain tissues, and guaranteed stability of the numerical solution. We propose a new model to overcome the aforementioned drawbacks. Guided by directional information derived from diffusion tensor imaging, our model relates tissue heterogeneity with the absorption of the chemotherapy, adopts the linear-quadratic term to simulate the radiotherapy effect, employs Maxwell-Weichert model to incorporate brain viscoelasticity, and ensures the stability of the numerical solution. The performance is verified through experiments on synthetic and real MR images. Experiments on 9 MR datasets of patients with low grade gliomas undergoing surgery with different treatment regimens are carried out and validated using Jaccard score and Dice coefficient. The growth simulation accuracies of the proposed model are in ranges of [0.673 0.822] and [0.805 0.902] for Jaccard scores and Dice coefficients, respectively. The accuracies decrease up to 4% and 2.4% when ignoring treatment effects and the tensor information, while brain viscoelasticity has no significant impact on the accuracies.
Importance of surface topography on pulsed laser-induced damage threshold of Sapphire crystals
Authors: Bussière Benoît , Sanner Nicolas , Sentis Marc , Utéza Olivier 
Published: April 2017

AbstractWe measure the laser-induced damage threshold (LIDT) fluence under single shot at the surface of Sapphire samples prepared following the standards of two methods yielding to different surface finish and used in optical and laser industry. We use AFM microscopy to measure the roughness parameter Ra and power spectral density (PSD) of the sample surface. We show that the quality of surface topography resulting from surface preparation affects the damage threshold of Sapphire crystals exposed to femtosecond, picosecond, and nanosecond laser conditions at visible and near-infrared wavelengths. We observe a higher resistance to laser damage or macroscopic modification when the surface finish presents a smooth and regular topography. We indeed measure a 1.4 to 2 times increase of the LIDT fluence in femtosecond and picosecond regimes and up to 5 times with nanosecond pulses. Using simple damage model and PSD data, we correlate the LIDT reduction of Sapphire samples of lower quality of surface finish with the high-frequency tail component of their PSD distribution corresponding to striations of the width of a fraction of the laser wavelength. This study emphasizes the importance of detailed assessment of surface topography for laser damage evaluation and understanding and for indicating directions of improvement.
Continuous daylight in the high-Arctic summer supports high plankton respiration rates compared to those supported in the dark
Authors: Mesa Elena , Delgado-Huertas Antonio , Carrillo-de-Albornoz Paloma , García-Corral Lara S. , Sanz-Martín Marina , Wassmann Paul , Reigstad Marit , Sejr Mikael , Dalsgaard Tage , Duarte Carlos M. 
Published: April 2017

AbstractPlankton respiration rate is a major component of global CO2 production and is forecasted to increase rapidly in the Arctic with warming. Yet, existing assessments in the Arctic evaluated plankton respiration in the dark. Evidence that plankton respiration may be stimulated in the light is particularly relevant for the high Arctic where plankton communities experience continuous daylight in spring and summer. Here we demonstrate that plankton community respiration evaluated under the continuous daylight conditions present in situ, tends to be higher than that evaluated in the dark. The ratio between community respiration measured in the light (Rlight) and in the dark (Rdark) increased as the 2/3 power of Rlight so that the Rlight:Rdark ratio increased from an average value of 1.37 at the median Rlight measured here (3.62 µmol O2 L−1 d−1) to an average value of 17.56 at the highest Rlight measured here (15.8 µmol O2 L−1 d−1). The role of respiratory processes as a source of CO2 in the Arctic has, therefore, been underestimated and is far more important than previously believed, particularly in the late spring, with 24 h photoperiods, when community respiration rates are highest.
Ultra-weak photon emission as a dynamic tool for monitoring oxidative stress metabolism
Authors: Burgos Rosilene Cristina Rossetto , Schoeman Johannes Cornelius , Winden Lennart Jan van , Červinková Kateřina , Ramautar Rawi , Van Wijk Eduard P. A. , Cifra Michal , Berger Ruud , Hankemeier Thomas , Greef Jan van der 
Published: April 2017

AbstractIn recent years, excessive oxidative metabolism has been reported as a critical determinant of pathogenicity in many diseases. The advent of a simple tool that can provide a physiological readout of oxidative stress would be a major step towards monitoring this dynamic process in biological systems, while also improving our understanding of this process. Ultra-weak photon emission (UPE) has been proposed as a potential tool for measuring oxidative processes due to the association between UPE and reactive oxygen species. Here, we used HL-60 cells as anin vitromodel to test the potential of using UPE as readout for dynamically monitoring oxidative stress after inducing respiratory burst. In addition, to probe for possible changes in oxidative metabolism, we performed targeted metabolomics on cell extracts and culture medium. Lastly, we tested the effects of treating cells with the NADPH oxidase inhibitor diphenyleneiodonium chloride (DPI). Our results show that UPE can be used as readout for measuring oxidative stress metabolism and related processes.
Distributed atomic quantum information processing via optical fibers
Authors: Luo Ming-Xing , Li Hui-Ran , Wang Xiaojun 
Published: April 2017

AbstractThe qudit system may offer great flexibilities for quantum information processing. We investigate the possibility of realizing elementary quantum gates between two high-dimensional atoms in distant cavities coupled by an optical fiber. We show that highly reliable special swap gate is achievable by different detuning. The numerical simulation shows that the proposed elementary gate is robust against the atomic spontaneous decay, photon leakage of cavities and optical fibers by choosing the experimental parameters appropriately.
A predation cost to bold fish in the wild
Authors: Hulthén Kaj , Chapman Ben B. , Nilsson P. Anders , Hansson Lars-Anders , Skov Christian , Brodersen Jakob , Vinterstare Jerker , Brönmark Christer 
Published: April 2017

AbstractStudies of predator-mediated selection on behaviour are critical for our understanding of the evolution and maintenance of behavioural diversity in natural populations. Consistent individual differences in prey behaviour, especially in the propensity to take risks (“boldness”), are widespread in the animal kingdom. Theory predicts that individual behavioural types differ in a cost-benefit trade-off where bolder individuals benefit from greater access to resources while paying higher predation-risk costs. However, explicitly linking predation events to individual behaviour under natural conditions is challenging and there is currently little data from the wild. We assayed individual behaviour and electronically tagged hundreds of fish (roach,Rutilus rutilus) before releasing them into their lake of origin, thereby exposing them to predation risk from avian apex predators (cormorants,Phalacrocorax carbo). Scanning for regurgitated tags at the cormorant roosting site provided data on individual predation events. We found that fish with higher boldness have a greater susceptibility to cormorant predation compared to relatively shy, risk-averse individuals. Our findings hereby provide unique and direct evidence of behavioural type-dependent predation vulnerability in the wild, i.e. that there is a predation cost to boldness, which is critical for our understanding of the evolution and maintenance of behavioural diversity in natural populations.
Structural alterations in the prefrontal cortex mediate the relationship between Internet gaming disorder and depressed mood
Authors: Choi Jihye , Cho Hyun , Kim Jin-Young , Jung Dong Jin , Ahn Kook Jin , Kang Hang-Bong , Choi Jung-Seok , Chun Ji-Won , Kim Dai-Jin 
Published: April 2017

AbstractAdaptive gaming use has positive effects, whereas depression has been reported to be prevalent in Internet gaming disorder (IGD). However, the neural correlates underlying the association between depression and Internet gaming remain unclear. Moreover, the neuroanatomical profile of the striatum in IGD is relatively less clear despite its important role in addiction. We found lower gray matter (GM) density in the left dorsolateral prefrontal cortex (DLPFC) in the IGD group than in the Internet gaming control (IGC) group and non-gaming control (NGC) group, and the GM density was associated with lifetime usage of Internet gaming, depressed mood, craving, and impulsivity in the gaming users. Striatal volumetric analysis detected a significant reduction in the right nucleus accumbens (NAcc) in the IGD group and its association with lifetime usage of gaming and depression. These findings suggest that alterations in the brain structures involved in the reward system are associated with IGD-related behavioral characteristics. Furthermore, the DLPFC, involved in cognitive control, was observed to serve as a mediator in the association between prolonged gaming and depressed mood. This finding may provide insight into an intervention strategy for treating IGD with comorbid depression.
Pronounced Plasticity Caused by Phase Separation and β-relaxation Synergistically in Zr–Cu–Al–Mo Bulk Metallic Glasses
Authors: Wang Tuo , Wang Lu , Wang Qinjia , Liu Yanhui , Hui Xidong 
Published: April 2017

AbstractBulk metallic glasses (BMGs) are known to have extraordinary merits such as ultrahigh strength and dynamic toughness etc. but tied to the detrimental brittleness, which has become a critical issue to the engineering application and understanding the glass nature. In this article, we report a new class of Zr-Cu-Al-Mo BMGs with extraordinary plastic strain above 20%. “Work-hardening” effect after yielding in a wide range of plastic deformation process has been detected for this kind of BMGs. Compositional heterogeneity, which can be classified into ZrMo- and Cu-rich zones, was differentiated in this kind of BMG. Pronounced humps have been observed on the high frequency kinetic spectrum in Mo containing BMGs, which is the indicator of β-relaxation transition. The underlying mechanism for the excellent plastic deforming ability of this class of BMGs is ascribed to the synergistic effects of soft ZrMo-rich glass formed through phase separation and abundant flow units which related to β-relaxation.
Changes in North Atlantic Oscillation drove Population Migrations and the Collapse of the Western Roman Empire
Authors: Drake B. Lee 
Published: April 2017

AbstractShifts in the North Atlantic Oscillation (NAO) from 1–2 to 0–1 in four episodes increased droughts on the Roman Empire’s periphery and created push factors for migrations. These climatic events are associated with the movements of the Cimbri and Teutones from 113–101 B.C., the Marcomanni and Quadi from 164 to 180 A.D., the Goths in 376 A.D., and the broad population movements of the Migration Period from 500 to 600 A.D. Weakening of the NAO in the instrumental record of the NAO have been associated with a shift to drought in the areas of origin for the Cimbri, Quadi, Visigoths, Ostrogoths, Huns, and Slavs. While other climate indices indicate deteriorating climate after 200 A.D. and cooler conditions after 500 A.D., the NAO may indicate a specific cause for the punctuated history of migrations in Late Antiquity. Periodic weakening of the NAO caused drought in the regions of origin for tribes in antiquity, and may have created a powerful push factor for human migration. While climate change is frequently considered as a threat to sustainability, its role as a conflict amplifier in history may be one of its largest impacts on populations.
On the pH Dependence of the Potential of Maximum Entropy of Ir(111) Electrodes
Authors: Ganassin Alberto , Sebastián Paula , Climent Víctor , Schuhmann Wolfgang , Bandarenka Aliaksandr S. , Feliu Juan 
Published: April 2017

AbstractStudies over the entropy of components forming the electrode/electrolyte interface can give fundamental insights into the properties of electrified interphases. In particular, the potential where the entropy of formation of the double layer is maximal (potential of maximum entropy, PME) is an important parameter for the characterization of electrochemical systems. Indeed, this parameter determines the majority of electrode processes. In this work, we determine PMEs for Ir(111) electrodes. The latter currently play an important role to understand electrocatalysis for energy provision; and at the same time, iridium is one of the most stable metals against corrosion. For the experiments, we used a combination of the laser induced potential transient to determine the PME, and CO charge-displacement to determine the potentials of zero total charge, (EPZTC). Both PME and EPZTC were assessed for perchlorate solutions in the pH range from 1 to 4. Surprisingly, we found that those are located in the potential region where the adsorption of hydrogen and hydroxyl species takes place, respectively. The PMEs demonstrated a shift by ~30 mV per a pH unit (in the RHE scale). Connections between the PME and electrocatalytic properties of the electrode surface are discussed.
First-principles design of nanostructured hybrid photovoltaics based on layered transition metal phosphates
Authors: Lentz Levi C. , Kolpak Alexie M. 
Published: April 2017

AbstractThe performance of bulk organic and hybrid organic-inorganic heterojunction photovoltaics is often limited by high carrier recombination arising from strongly bound excitons and low carrier mobility. Structuring materials to minimize the length scales required for exciton separation and carrier collection is therefore a promising approach for improving efficiency. In this work, first-principles computations are employed to design and characterize a new class of photovoltaic materials composed of layered transition metal phosphates (TMPs) covalently bound to organic absorber molecules to form nanostructured superlattices. Using a combination of transition metal substitution and organic functionalization, the electronic structure of these materials is systematically tuned to design a new hybrid photovoltaic material predicted to exhibit very low recombination due to the presence of a local electric field and spatially isolated, high mobility, two-dimensional electron and hole conducting channels. Furthermore, this material is predicted to have a large open-circuit voltage of 1.7 V. This work suggests that hybrid TMPs constitute an interesting class of materials for further investigation in the search for achieving high efficiency, high power, and low cost photovoltaics.
Enterovirus D68 Subclade B3 Strain Circulating and Causing an Outbreak in the United States in 2016
Authors: Wang Guiqing , Zhuge Jian , Huang Weihua , Nolan Sheila M. , Gilrane Victoria L. , Yin Changhong , Dimitrova Nevenka , Fallon John T. 
Published: April 2017

AbstractIn 2014 the United States experienced a nationwide outbreak of Enterovirus D68 (EV-D68) infection. There were no confirmed cases of EV-D68 in 2015 and CDC was only aware of limited sporadic EV-D68 detection in the US in 2016. In this report, we analyzed 749 nasopharyngeal (NP) specimens collected in 2015 and 2016 from patients in the Lower Hudson Valley, New York using a previously validated EV-D68-specific rRT-PCR assay. EV-D68 was detected in none of 199 NP specimens collected in 2015, and in one of 108 (0.9%) samples from January to May and 159 of 442 (36.0%) samples from July to October 2016. Complete EV-D68 genome sequences from 22 patients in 2016 were obtained using a metagenomic next-generation sequencing assay. Comparative genome analysis confirmed that a new EV-D68 strain belonging to subclade B3, with 3.2–4.8% divergence in nucleotide from subclade B1 strains identified during the 2014 US outbreak, was circulating in the US in 2016 and caused an outbreak in the Lower Hudson Valley, New York with 160 laboratory-confirmed cases. Our data highlight the genetic variability and capacity in causing outbreak by diverse EV-D68 strains, and the necessity of awareness and more surveillance on their active circulation worldwide.
FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry
Authors: Akimoto Nayumi , Ara Takeshi , Nakajima Daisuke , Suda Kunihiro , Ikeda Chiaki , Takahashi Shingo , Muneto Reiko , Yamada Manabu , Suzuki Hideyuki , Shibata Daisuke , Sakurai Nozomu 
Published: April 2017

AbstractCurrently, in mass spectrometry-based metabolomics, limited reference mass spectra are available for flavonoid identification. In the present study, a database of probable mass fragments for 6,867 known flavonoids (FsDatabase) was manually constructed based on new structure- and fragmentation-related rules using new heuristics to overcome flavonoid complexity. We developed the FlavonoidSearch system for flavonoid annotation, which consists of the FsDatabase and a computational tool (FsTool) to automatically search the FsDatabase using the mass spectra of metabolite peaks as queries. This system showed the highest identification accuracy for the flavonoid aglycone when compared to existing tools and revealed accurate discrimination between the flavonoid aglycone and other compounds. Sixteen new flavonoids were found from parsley, and the diversity of the flavonoid aglycone among different fruits and vegetables was investigated.