bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detrimental role of the EP1 prostanoid receptor in blood-brain barrier damage following experimental ischemic stroke
Authors: Frankowski Jan C. , DeMars Kelly M. , Ahmad Abdullah S. , Hawkins Kimberly E. , Yang Changjun , Leclerc Jenna L. , Doré Sylvain , Candelario-Jalil Eduardo 
Published: December 2015

AbstractCyclooxygenase-2 (COX-2) is activated in response to ischemia and significantly contributes to the neuroinflammatory process. Accumulation of COX-2-derived prostaglandin E2 (PGE2) parallels the substantial increase in stroke-mediated blood-brain barrier (BBB) breakdown. Disruption of the BBB is a serious consequence of ischemic stroke and is mainly mediated by matrix metalloproteinases (MMPs). This study aimed to investigate the role of PGE2 EP1 receptor in neurovascular injury in stroke. We hypothesized that pharmacological blockade or genetic deletion of EP1 protects against BBB damage and hemorrhagic transformation by decreasing the levels and activity of MMP-3 and MMP-9. We found that post-ischemic treatment with the EP1 antagonist, SC-51089, or EP1 genetic deletion results in a significant reduction in BBB disruption and reduced hemorrhagic transformation in an experimental model of transient focal cerebral ischemia. These neurovascular protective effects of EP1 inactivation are associated with a significant reduction in MMP-9/-3, less peripheral neutrophil infiltration and a preservation of tight junction proteins (ZO-1 and occludin) composing the BBB. Our study identifies the EP1 signaling pathway as an important link between neuroinflammation and MMP-mediated BBB breakdown in ischemic stroke. Targeting the EP1 receptor could represent a novel approach to diminish the devastating consequences of stroke-induced neurovascular damage.
Low temperature solution process-based defect-induced orange-red light emitting diode
Authors: Biswas Pranab , Baek Sung-Doo , Hoon Lee Sang , Park Ji-Hyeon , Jeong Lee Su , Il Lee Tae , Myoung Jae-Min 
Published: December 2015

AbstractWe report low-temperature solution-processed p-CuO nanorods (NRs)/n-ZnO NRs heterojunction light emitting diode (LED), exploiting the native point defects of ZnO NRs. ZnO NRs were synthesized at 90 °C by using hydrothermal method while CuO NRs were synthesized at 100 °C by using microwave reaction system. The electrical properties of newly synthesized CuO NRs revealed a promising p-type nature with a hole concentration of 9.64 × 1018 cm−3. The current-voltage characteristic of the heterojunction showed a significantly high rectification ratio of 105 at 4 V with a stable current flow. A broad orange-red emission was obtained from the forward biased LED with a major peak at 610 nm which was attributed to the electron transition from interstitial zinc to interstitial oxygen point defects in ZnO. A minor shoulder peak was also observed at 710 nm, corresponding to red emission which was ascribed to the transition from conduction band of ZnO to oxygen vacancies in ZnO lattice. This study demonstrates a significant progress toward oxide materials based, defect-induced light emitting device with low-cost, low-temperature methods.
Phosphorus Concentrations in Sequentially Fractionated Soil Samples as Affected by Digestion Methods
Authors: do Nascimento Carlos A. C. , Pagliari Paulo H. , Schmitt Djalma , He Zhongqi , Waldrip Heidi 
Published: December 2015

AbstractSequential fractionation has helped improving our understanding of the lability and bioavailability of P in soil. Nevertheless, there have been no reports on how manipulation of the different fractions prior to analyses affects the total P (TP) concentrations measured. This study investigated the effects of sample digestion, filtration and acidification on the TP concentrations determined by ICP-OES in 20 soil samples. Total P in extracts were either determined without digestion by ICP-OES, or ICP-OES following block digestion, or autoclave digestion. The effects of sample filtration and acidification on undigested alkaline extracts prior to ICP-OES were also evaluated. Results showed that, TP concentrations were greatest in the block-digested extracts, though the variability introduced by the block-digestion was the highest. Acidification of NaHCO3 extracts resulted in lower TP concentrations, while acidification of NaOH randomly increased or decreased TP concentrations. The precision observed with ICP-OES of undigested extracts suggests this should be the preferred method for TP determination in sequentially extracted samples. Thus, observations reported in this work would be helpful in appropriate sample handling for P determination, thereby improving the precision of P determination. The results are also useful for literature data comparison and discussion when there are differences in sample treatments.
Simulation of avascular tumor growth by agent-based game model involving phenotype-phenotype interactions
Authors: Chen Yong , Wang Hengtong , Zhang Jiangang , Chen Ke , Li Yumin 
Published: December 2015

AbstractAll tumors, both benign and metastatic, undergo an avascular growth stage with nutrients supplied by the surrounding tissue. This avascular growth process is much easier to carry out in more qualitative and quantitative experiments starting from tumor spheroidsin vitrowith reliable reproducibility. Essentially, this tumor progression would be described as a sequence of phenotypes. Using agent-based simulation in a two-dimensional spatial lattice, we constructed a composite growth model in which the phenotypic behavior of tumor cells depends on not only the local nutrient concentration and cell count but also the game among cells. Our simulation results demonstrated that in silico tumors are qualitatively similar to those observed in tumor spheroid experiments. We also found that the payoffs in the game between two living cell phenotypes can influence the growth velocity and surface roughness of tumors at the same time. Finally, this current model is flexible and can be easily extended to discuss other situations, such as environmental heterogeneity and mutation.
Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses
Authors: Yang Szu-Chi , Lin Huan-Chun , Liu Tzu-Ming , Lu Jen-Tang , Hung Wan-Ting , Huang Yu-Ru , Tsai Yi-Chun , Kao Chuan-Liang , Chen Shih-Yuan , Sun Chi-Kuang 
Published: December 2015

AbstractVirus is known to resonate in the confined-acoustic dipolar mode with microwave of the same frequency. However this effect was not considered in previous virus-microwave interaction studies and microwave-based virus epidemic prevention. Here we show that this structure-resonant energy transfer effect from microwaves to virus can be efficient enough so that airborne virus was inactivated with reasonable microwave power density safe for the open public. We demonstrate this effect by measuring the residual viral infectivity of influenza A virus after illuminating microwaves with different frequencies and powers. We also established a theoretical model to estimate the microwaves power threshold for virus inactivation and good agreement with experiments was obtained. Such structure-resonant energy transfer induced inactivation is mainly through physically fracturing the virus structure, which was confirmed by real-time reverse transcription polymerase chain reaction. These results provide a pathway toward establishing a new epidemic prevention strategy in open public for airborne virus.
Sensitivity and specificity of Cobas TaqMan MTB real-time polymerase chain reaction for culture-proven Mycobacterium tuberculosis: meta-analysis of 26999 specimens from 17 Studies
Authors: Horita Nobuyuki , Yamamoto Masaki , Sato Takashi , Tsukahara Toshinori , Nagakura Hideyuki , Tashiro Ken , Shibata Yuji , Watanabe Hiroki , Nagai Kenjiro , Nakashima Kentaro , Ushio Ryota , Ikeda Misako , Sakamaki Kentaro , Yoshiyama Takashi , Kaneko Takeshi 
Published: December 2015

AbstractSince 2010, studies on the diagnostic accuracy of COBAS TaqMan MTB (CTM) have been frequently reported with an unignorable discrepancy. The key inclusion criterion for this systematic review was original studies that could provide sufficient data for calculating the sensitivity and the specificity of CTM for M tuberculosis (TB) or M tuberculosis complex. The reference test was Mycobacterium culture. We used bivariate model for meta-analyses. Of the 201 candidate articles, we finally identified 17 eligible articles.Concerning the respiratory specimens, 1900 culture positive specimens and 20983 culture negative specimens from 15 studies were assessed. This provided the summary estimate sensitivity of 0.808 (95% CI 0.758–0.850) and the summary estimate specificity of 0.990 (95% CI 0.981–0.994). The area under curve was 0.956. The diagnostic odds ratio was 459 (95% CI 261–805, I2 26%). For the smear positive respiratory specimens, the sensitivity was 0.952 (95% CI 0.926–0.969) and the specificity was 0.916 (95% CI 0.797–0.968). For the smear negative respiratory specimens, the sensitivity and the specificity were 0.600 (95% CI 0.459–0.726) and 0.989 (95% CI 0.981–0.993), respectively. The diagnostic accuracy was poorer for the non-respiratory specimens, than for the respiratory specimens, but was acceptable. We believe that the information obtained from this study will aid physicians’ decision making.
Simple surface engineering of polydimethylsiloxane with polydopamine for stabilized mesenchymal stem cell adhesion and multipotency
Authors: Chuah Yon Jin , Koh Yi Ting , Lim Kaiyang , Menon Nishanth V. , Wu Yingnan , Kang Yuejun 
Published: December 2015

AbstractPolydimethylsiloxane (PDMS) has been extensively exploited to study stem cell physiology in the field of mechanobiology and microfluidic chips due to their transparency, low cost and ease of fabrication. However, its intrinsic high hydrophobicity renders a surface incompatible for prolonged cell adhesion and proliferation. Plasma-treated or protein-coated PDMS shows some improvement but these strategies are often short-lived with either cell aggregates formation or cell sheet dissociation. Recently, chemical functionalization of PDMS surfaces has proved to be able to stabilize long-term culture but the chemicals and procedures involved are not user- and eco-friendly. Herein, we aim to tailor greener and biocompatible PDMS surfaces by developing a one-step bio-inspired polydopamine coating strategy to stabilize long-term bone marrow stromal cell culture on PDMS substrates. Characterization of the polydopamine-coated PDMS surfaces has revealed changes in surface wettability and presence of hydroxyl and secondary amines as compared to uncoated surfaces. These changes in PDMS surface profile contribute to the stability in BMSCs adhesion, proliferation and multipotency. This simple methodology can significantly enhance the biocompatibility of PDMS-based microfluidic devices for long-term cell analysis or mechanobiological studies.
Variation of a Persistent Primitive Hypoglossal Artery (PPHA) as Incidental Finding in the Diagnostic Clarification of Cerebral Vasculopathy Associated with Intracranial Vasculitis
Authors: Marques L. , Preiß M. , Börm W. , Müller-Hülsbeck S. , Hopf-Jensen S. 
Published: December 2015

AbstractWe present a very rare variation of a persistent primitive hypoglossal artery (PPHA) arising from the internal carotid artery, detected during a diagnostic angiography. A 50-year-old female patient was admitted with an atypical intracranial hematoma in the left frontal lobe. Catheter angiography revealed intracranial vasculopathy with segmental stenoses, a small aneurysm of the right internal carotid artery bifurcation and a “string of beads” appearance of the left carotid artery, consistent with fibromuscular disease. On the left side, a vertebral artery ending in the posterior inferior cerebellar artery (PICA) was detected, whereas on the right side the vertebral artery was aplastic. During selective angiography of the right common carotid artery, a persistent hypoglossal artery was seen supplying the basilar artery. The literature of persistent embryonal carotid-vertebrobasilar anastomosis and their anatomical variations is discussed with respect to clinical importance for ischemia, interventional procedures, and surgery.
Computational complexity of ecological and evolutionary spatial dynamics
Authors: Ibsen-Jensen Rasmus , Chatterjee Krishnendu , Nowak Martin A. 
Published: December 2015

Significance
An important question in evolution is: how does population structure affect the outcome of the evolutionary process? The theory of evolution in structured population has provided an impressive range of results, but an understanding of the computational complexity of even simple questions was missing. We prove that some fundamental problems in ecology and evolution can be precisely characterized by well-established computational complexity classes. This implies that the problems cannot be answered by simple equations. For example, there cannot be simple formulas for the fixation probability of a mutant given frequency-dependent selection in a structured population. We also show that, for example, calculating the molecular clock of neutral evolution in structured populations admit efficient algorithmic solutions.
Global phosphorus retention by river damming
Authors: Maavara Taylor , Parsons Christopher T. , Ridenour Christine , Stojanovic Severin , Dürr Hans H. , Powley Helen R. , Van Cappellen Philippe 
Published: December 2015

SignificancePhosphorus is an essential nutrient for life. Humans have massively altered the global phosphorus cycle by increasing loading to river systems through fertilizer use, soil erosion, and wastewater discharges. River damming interacts with anthropogenic phosphorus enrichment by trapping a fraction of the phosphorus in reservoir sediments. We estimate that in 2000, 12% of the global river phosphorus load was retained in dam reservoirs. This fraction could increase to 17% by 2030, because of the construction of over 3,700 new dams. Although reservoirs represent a huge phosphorus sink, rising anthropogenic phosphorus emissions continue to outpace the addition of new retention capacity by river damming. The resulting growth in riverine phosphorus export likely contributes to the expanding eutrophication of surface waters worldwide.
AMPA receptor inhibition by synaptically released zinc
Authors: Kalappa Bopanna I. , Anderson Charles T. , Goldberg Jacob M. , Lippard Stephen J. , Tzounopoulos Thanos 
Published: December 2015

Significance
Ionotropic glutamate AMPA receptors (AMPARs) play a fundamental role in normal function and plasticity of the brain, and they are also involved in many brain disorders. Despite the central role of AMPARs in neurobiology, the modulation of synaptic AMPA responses by endogenous modulators remains not well understood. Here, in three synapses found in two different brain areas, we provide the first evidence, to our knowledge, that endogenous zinc is coreleased with glutamate and modulates the strength of synaptic AMPAR responses. Because in many neocortical areas more than 50% of excitatory presynaptic terminals contain zinc within their glutamatergic vesicles, our findings establish zinc as a general neuromodulator that allows for fine-tuning and plasticity of glutamatergic fast synaptic transmission in the brain.
Inequality, climate impacts on the future poor, and carbon prices
Authors: Dennig Francis , Budolfson Mark B. , Fleurbaey Marc , Siebert Asher , Socolow Robert H. 
Published: December 2015

Significance
Hundreds of published papers produce “optimal” trajectories of global emissions of carbon dioxide, and corresponding carbon prices, over this century, taking into account future damages inflicted by climate change. To our knowledge, in all instances the models ignore inequalities in economic variables beyond regional differences. Here, we introduce heterogeneous subregional populations (distributed by income) and explore how the optimal trajectories are affected by whether regional damage afflicts the poor predominantly. We find that when future damage falls especially hard on the poor, considerably greater global mitigation effort is optimal than when damage is proportional to income.
Predicting experimentally stable allotropes: Instability of penta-graphene
Authors: Ewels Christopher P. , Rocquefelte Xavier , Kroto Harold W. , Rayson Mark J. , Briddon Patrick R. , Heggie Malcolm I. 
Published: December 2015

Significance
We describe criteria that should be applied when evaluating whether theoretically proposed carbon allotropes may be experimentally isolated. We discuss the importance of energetic isomeric “funnels” centered on a stable allotropic form, the role of defects in catalyzing structural transformations to lower energy isomers, and chemical stability. This is demonstrated with literature examples such as C60 and B80. We apply these criteria to a recently proposed carbon allotrope, penta-graphene, demonstrating with the aid of density functional calculations that it will not be experimentally attainable. A second example, Haeckelites, are unlikely to be experimentally achievable when neutral but may be stabilized through significant charge transfer. The principals discussed here are general and can be applied to any theoretically proposed materials.
TMEM110 regulates the maintenance and remodeling of mammalian ER–plasma membrane junctions competent for STIM–ORAI signaling
Authors: Quintana Ariel , Rajanikanth Vangipurapu , Farber-Katz Suzette , Gudlur Aparna , Zhang Chen , Jing Ji , Zhou Yubin , Rao Anjana , Hogan Patrick G. 
Published: December 2015

Significance
Close appositions between the endoplasmic reticulum (ER) and the plasma membrane in mammalian cells have essential roles in cellular lipid metabolism and in cytoplasmic calcium signaling. Although recent investigations have yielded considerable insight into the structural basis for lipid transfer at ER–plasma membrane junctions, little is known about the proteins that organize junctions for calcium signaling. Our data show that the ER membrane protein transmembrane protein 110 (TMEM110) supports the maintenance of ER–plasma membrane junctions competent for calcium signaling and acts in concert with other proteins in the dynamic remodeling of the junctions during signaling.
Antiinfectives targeting enzymes and the proton motive force
Authors: Feng Xinxin , Zhu Wei , Schurig-Briccio Lici A. , Lindert Steffen , Shoen Carolyn , Hitchings Reese , Li Jikun , Wang Yang , Baig Noman , Zhou Tianhui , Kim Boo Kyung , Crick Dean C. , Cynamon Michael , McCammon J. Andrew , Gennis Robert B. , Oldfield Eric 
Published: December 2015

Significance
Uncoupling agents might be expected to be generally cytotoxic, but many US Food and Drug Administration (FDA)-approved drugs do have activity as uncouplers, in addition to targeting enzymes. There is therefore interest in the discovery of antibiotics that have such multitarget activity. Here, we show that some FDA-approved drugs, such as clofazimine, clomiphene, and bedaquiline, with antiinfective activity act as uncouplers. Using molecular dynamics-based in silico screening, we also discovered that the brain cancer drug lead vacquinol is an uncoupler that inhibits an enzyme involved in the formation of tuberculosis (TB) virulence factors, in addition to killing TB bacteria. Our results indicate strong drug–membrane interactions, and that screening for combined enzyme inhibition plus uncoupler activity will lead to new antibiotic leads.
Reconciling divergent estimates of oil and gas methane emissions
Authors: Zavala-Araiza Daniel , Lyon David R. , Alvarez Ramón A. , Davis Kenneth J. , Harriss Robert , Herndon Scott C. , Karion Anna , Kort Eric Adam , Lamb Brian K. , Lan Xin , Marchese Anthony J. , Pacala Stephen W. , Robinson Allen L. , Shepson Paul B. , Sweeney Colm , Talbot Robert , Townsend-Small Amy , Yacovitch Tara I. , Zimmerle Daniel J. , Hamburg Steven P. 
Published: December 2015

Significance
Past studies reporting divergent estimates of methane emissions from the natural gas supply chain have generated conflicting claims about the full greenhouse gas footprint of natural gas. Top-down estimates based on large-scale atmospheric sampling often exceed bottom-up estimates based on source-based emission inventories. In this work, we reconcile top-down and bottom-up methane emissions estimates in one of the country’s major natural gas production basins using easily replicable measurement and data integration techniques. These convergent emissions estimates provide greater confidence that we can accurately characterize the sources of emissions, including the large impact that a small proportion of high-emitters have on total emissions and determine the implications for mitigation.
Improved Models for Predicting Walleye Abundance and Setting Safe Harvest Quotas in Northern Wisconsin Lakes
Authors: Hansen Gretchen J. A. , Hennessy Joseph M. , Cichosz Thomas A. , Hewett Steven W. 
Published: December 2015

Abstract
In Wisconsin, the management of Walleyes Sander vitreus relies on a set of log-linear regressions to predict Walleye abundance and to set safe harvest. The regression models predict mean Walleye abundance from lake area, but they ignore variability among years; they also predict equal Walleye populations in lakes with the same size and recruitment source. We evaluated three alternative models in terms of predictive accuracy and the risk of overharvest. We used 899 mark–recapture population estimates (collected between 1953 and 2013) from 219 lakes to develop and evaluate (1) a log-linear mixed-effects model that used all individual observations and estimated adult Walleye abundance from lake area and lake-specific deviations from the overall intercept; (2) a mixed-effects model that builds on model 1 by adding a linear fixed effect of sampling year; and (3) a mixed-effects model that builds on model 1 by adding a random year effect. Walleye abundance was positively correlated with lake area in all models and was negatively correlated with sampling year (when included). Alternative models improved predictive accuracy by 17–22% over the current regression model. Restricting data to those collected during the most recent 20 years improved model responsiveness to new data and reduced the value of including a linear time trend. When all data were used for model construction, the relative risk of overharvest was lowest under the mixed-effects model with a linear time trend; when the most recent 20 years of data were used, the risk was lowest under the mixed-effects model with a random year effect. Accounting for variability among years would allow harvest to track changing Walleye populations and would allow management to be more adaptive. We recommend using the mixed-effects model with a random year effect and restricting the data inputs to the most recent 20 years.
Received May 20, 2015; accepted September 17, 2015