bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change
Authors: Li Hong-Lei , Wang Wei , Mortimer Peter E. , Li Rui-Qi , Li De-Zhu , Hyde Kevin D. , Xu Jian-Chu , Soltis Douglas E. , Chen Zhi-Duan 
Published: September 2015

AbstractNitrogen is fundamental to all life forms and is also one of the most limiting of nutrients for plant growth. Several clades of angiosperms have developed symbiotic relationships with actinorhizal bacteria that fix atmospheric nitrogen and increase access to this nutrient. However, the evolutionary patterns of actinorhizal nitrogen-fixing symbioses remain unclear to date. Furthermore the underlying environmental pressures that led to the gain of symbiotic actinorhizal nitrogen fixation have never been investigated. Here, we present the most comprehensive genus-level phylogenetic analysis of the nitrogen-fixing angiosperms based on three plastid loci. We found that actinorhizal nitrogen-fixing species are distributed in nine distinct lineages. By dating the branching events, we determined that seven actinorhizal nitrogen-fixing lineages originated during the Late Cretaceous and two more emerged during the Eocene. We put forward a hypothesis that multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms may have been associated with increased global temperatures and high levels of atmospheric carbon dioxide during these two time periods, as well as the availability of open habitats with high light conditions. Our nearly complete genus-level time-tree for the nitrogen-fixing clade is a significant advance in understanding the evolutionary and ecological background of this important symbiosis between plants and bacteria.
Peptide dimer structure in an Aβ(1–42) fibril visualized with cryo-EM
Authors: Schmidt Matthias , Rohou Alexis , Lasker Keren , Yadav Jay K. , Schiene-Fischer Cordelia , Fändrich Marcus , Grigorieff Nikolaus 
Published: September 2015

Significance
β-Amyloid (Aβ) fibrils are formed from Aβ peptide and are a hallmark feature of Alzheimer’s disease (AD). Despite their involvement in AD, much remains unclear about the formation of these aggregates and their structures at the molecular level. We have obtained a 3D image of a fibril formed from the Aβ(1–42) peptide isoform using electron cryomicroscopy and built a partial atomic model based on these data. We show that the core of the fibril is formed by two peptide C termini, explaining why aggregation inhibitors are most potent when targeting the C terminus. Our model explains how addition of C-terminal amino acids may stabilize peptide interaction and how fibril stability is affected by mutations leading to familial AD.
Hyperglycemia impairs left–right axis formation and thereby disturbs heart morphogenesis in mouse embryos
Authors: Hachisuga Masahiro , Oki Shinya , Kitajima Keiko , Ikuta Satomi , Sumi Tomoyuki , Kato Kiyoko , Wake Norio , Meno Chikara 
Published: September 2015

SignificanceEpidemiological studies have revealed that pregestational diabetes mellitus increases the risk for congenital anomalies, including congenital heart defects (CHDs). Despite the importance of preventing diabetes-related congenital malformations, however, the underlying pathogenic mechanisms have remained largely unknown. Pregestational diabetes mellitus is associated specifically with CHDs accompanied by heterotaxia. We have now examined left–right (L–R) axis formation in embryos of diabetic female mice as well as in mouse embryos exposed to high-glucose concentrations in culture. We found that high-glucose levels prevent establishment of the L–R axis required for heart morphogenesis and the L–R asymmetry of visceral organs. Such a mechanism may thus explain, at least in part, the CHDs and accompanying heterotaxia in the offspring of diabetic mothers.
Impact of human mobility on the emergence of dengue epidemics in Pakistan
Authors: Wesolowski Amy , Qureshi Taimur , Boni Maciej F. , Sundsøy Pål Roe , Johansson Michael A. , Rasheed Syed Basit , Engø-Monsen Kenth , Buckee Caroline O. 
Published: September 2015

Significance
Dengue virus has rapidly spread into new human populations due to human travel and changing suitability for the mosquito vector, causing severe febrile illness and significant mortality. Accurate predictive models identifying changing vulnerability to dengue outbreaks are necessary for epidemic preparedness and containment of the virus. Here we show that an epidemiological model of dengue transmission in travelers, based on mobility data from ∼40 million mobile phone subscribers and climatic information, predicts the geographic spread and timing of epidemics throughout the country. We generate fine-scale dynamic risk maps with direct application to dengue containment and epidemic preparedness.
Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals “aging factors” and mechanism of lifespan asymmetry
Authors: Yang Jing , McCormick Mark A. , Zheng Jiashun , Xie Zhengwei , Tsuchiya Mitsuhiro , Tsuchiyama Scott , El-Samad Hana , Ouyang Qi , Kaeberlein Matt , Kennedy Brian K. , Li Hao 
Published: September 2015

Significance
In this work, we took a proteome-centric view to analyze the cell division and lifespan asymmetry between mother and daughter cells in budding yeast. Using a flow cytometry-based, high-throughput approach, we quantified the partitioning of the proteome and identified 74 mother-enriched and 60 daughter-enriched proteins. Functional analysis of these proteins suggests mechanisms of asymmetric partitioning at an organelle/suborganelle level. We found that mother-enriched proteins are much more likely to becoming aging factors than those proteins chosen at random. The proposed mechanism, as supported by our single-cell observations, is that these proteins accumulate in old mother cells to a high level that becomes lifespan-limiting. Our work sheds new light on the mechanisms of asymmetric cell division and aging.
Topological patterns in two-dimensional gel electrophoresis of DNA knots
Authors: Michieletto Davide , Marenduzzo Davide , Orlandini Enzo 
Published: September 2015

SignificanceGel electrophoresis is a ubiquitous biophysical technique. It consists of dragging charged biopolymers through a porous gel, by applying an electric field. Because the migration speed depends on topology, this method can be used to classify DNA knots. Currently, electrophoresis relies on empirical observations, and its theoretical understanding is limited. No theory can explain why knot mobility under strong fields depends nonmonotonically on complexity. Our study reveals a possible reason: Although complex knots have a smaller size, and hence move faster through the gel, they can become severely entangled with the gel, causing longer pauses. Our results can improve the design of future electrophoresis experiments.
RNA transcription modulates phase transition-driven nuclear body assembly
Authors: Berry Joel , Weber Stephanie C. , Vaidya Nilesh , Haataja Mikko , Brangwynne Clifford P. 
Published: September 2015

Significance
Living cells contain various membraneless organelles whose size and assembly appear to be governed by equilibrium thermodynamic phase separation. However, the dynamics of this process are poorly understood. Here, we quantify the assembly dynamics of liquid-phase nuclear bodies and find that they can be explained by classical models of phase separation and coarsening. In addition, active nonequilibrium processes, particularly rRNA transcription, can locally modulate thermodynamic parameters to stabilize nucleoli. Our findings demonstrate that the classical phase separation mechanisms long associated with nonliving condensed matter can mediate organelle assembly in living cells, whereas chemical activity may serve to regulate these processes in response to developmental or environmental conditions.
NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor
Authors: O’Connor Casey , White Kate L. , Doncescu Nathalie , Didenko Tatiana , Roth Bryan L. , Czaplicki Georges , Stevens Raymond C. , Wüthrich Kurt , Milon Alain 
Published: September 2015

Significance
The human kappa opioid receptor (KOR) is implicated in addiction, pain, reward, mood, cognition, and perception. Activation of KOR by the neuropeptide dynorphin is critical in mediating analgesia and tolerance. Our solution NMR study of dynorphin (1–13) provided quantitative data on a KOR-bound conformation. Analysis of the peptide structure and dynamics revealed a central helical turn bounded on both sides by flexibly disordered peptide segments. Future drug development will benefit from knowledge of the dynorphin structure bound to its human receptor.
Ritual drinks in the pre-Hispanic US Southwest and Mexican Northwest
Authors: Crown Patricia L. , Gu Jiyan , Hurst W. Jeffrey , Ward Timothy J. , Bravenec Ardith D. , Ali Syed , Kebert Laura , Berch Marlaina , Redman Erin , Lyons Patrick D. , Merewether Jamie , Phillips David A. , Reed Lori S. , Woodson Kyle 
Published: September 2015

Significance
This article presents the results of a large-scale National Science Foundation-funded study of organic residues from archaeological sites in the US Southwest/Mexican Northwest. It reveals widespread use of two different caffeinated plants, cacao and holly, as the basis for drinks used in communal, ritual gatherings. This is the largest study of its kind, both in terms of numbers of samples and in terms of temporal/spatial scope. It is the first to argue for holly beverage consumption in the US Southwest/Mexican Northwest. The combined evidence for cacao and holly beverage consumption has implications for our understanding of distant resource acquisition and shared cultural practices in North America.
SHAPE directed RNA folding
Authors: Lorenz Ronny , Luntzer Dominik , Hofacker Ivo L. , Stadler Peter F. , Wolfinger Michael T. 
Published: September 2015

Abstract
Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure.
Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA.
Contact: michael.wolfinger@univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of a new γ-ray-emitting narrow-line Seyfert 1 galaxy, at redshift ∼1
Authors: Yao Su , Yuan Weimin , Zhou Hongyan , Komossa S. , Zhang Jin , Qiao Erlin , Liu Bifang 
Published: September 2015

Abstract
We report on the identification of a new γ-ray-emitting narrow-line Seyfert 1 (NLS1) galaxy, SDSS J122222.55+041315.7, which increases the number of known objects of this remarkable but rare type of active galactic nuclei to seven. Its optical spectrum, obtained in the Sloan Digital Sky Survey-Baryon Oscillation Spectroscopic Survey, reveals a broad H β emission line with a width (FWHM) of 1734 ± 104 km s−1. This, along with strong optical Fe ii multiplets [R4570 = 0.9] and a weak [O iii] λ5007 emission line, makes the object a typical NLS1. On the other hand, the source exhibits a high radio brightness temperature, rapid infrared variability, and a flat X-ray spectrum extending up to ∼200 keV. It is associated with a luminous γ-ray source detected significantly with Fermi/LAT. Correlated variability with other wavebands has not yet been tested. The spectral energy distribution can be well modelled by a one-zone leptonic jet model. This new member is by far the most distant γ-ray-emitting NLS1, at a redshift of z = 0.966.
Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription
Authors: Tosoni Elena , Frasson Ilaria , Scalabrin Matteo , Perrone Rosalba , Butovskaya Elena , Nadai Matteo , Palù Giorgio , Fabris Dan , Richter Sara N. 
Published: September 2015

AbstractFolding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy.
Contextual Influences and Strategies for Dissemination and Implementation in Mental Health
Authors: Benjamin Wolk Courtney , Powell Byron J. , Beidas Rinad S. 
Published: September 2015

Abstract
Implementation science has emerged to bridge the gap between research and practice. A number of conceptual frameworks have been developed to advance implementation research and illuminate the contextual influences that can facilitate or impede the implementation of evidence-based practices. Contextual factors that may be important in the dissemination and implementation of evidence-based practice may occur at the system-, organizational-, and provider-levels. System-level barriers may include external policies, incentives, and peer pressure. Organizational-level factors that are important in implementation include organizational culture and climate and implementation climate. At the individual provider-level, barriers may occur around provider attitudes, knowledge, and self-efficacy. Finally, additional barriers such as client-level factors and characteristics of the intervention itself can exist. Implementation strategies have been developed that can be used to overcome contextual barriers when attempting to implement evidence-based practices into new settings. Several exemplar implementation strategies are discussed, including the Availability, Responsiveness, and Continuity intervention, Community Development Team model, and Interagency Collaborative Team Model.
Why Not a Woman of Color?
Authors: Sanbonmatsu Kira 
Published: September 2015

Abstract
This review seeks to broaden the study of women candidates and minority women’s candidacies, specifically by focusing on the intersection of gender and race in statewide executive officeholding. Scholarly neglect of this topic risks naturalizing the dearth of women of color in statewide executive positions, sending the message that it is understandable that women lack access to those offices and/or that such offices aren’t realistically obtainable. Using data from the Center for American Women and Politics, the article assesses the status of women of color in statewide offices, examines state and party patterns in their presence as candidates and officeholders, and suggests directions for future research. Due to the low number of women of color who have ever achieved statewide office, the article combines women across racial/ethnic backgrounds into the category “women of color” to make an analysis feasible; however, future scholars could examine differences among women.
Strategic Responses to the Boston Marathon Bombing
Authors: Dugan Laura , Fisher Daren G. 
Published: September 2015

Abstract
The explosions on April 15, 2013 during the Patriot’s Day Marathon in Boston mark the first major terrorist attack in the United States since 9/11 and the first time since 1996 that terrorists targeted a major US sporting event. This chapter reviews events before and after the bombing to explore strategies to reduce risk and harm at sporting events without compromising the ideals of freedom and human capacity inherent to all sports. The chapter first presents the background of the Tsarnaev brothers and the challenges they faced. It then describes what is known of their plans for the day of the Marathon and the pursuit by law enforcement after the attack. It details the tactical and technological advances that helped law enforcement successfully end the crisis and arrest the surviving perpetrator. Finally, it discusses prevention and harm reduction measures that have since been adopted in major sporting events.
Identification and Characterization of GAL-021 as a Novel Breathing Control Modulator
Authors: Golder Francis J. , Dax Scott , Baby Santhosh M. , Gruber Ryan , Hoshi Toshinori , Ideo Courtney , Kennedy Andrew , Peng Sean , Puskovic Veljko , Ritchie David , Woodward Richard , Wardle Robert L. , Van Scott Michael R. , Mannion James C. , MacIntyre D. Euan 
Published: September 2015

AbstractAbstract
Intravenously administered GAL-021 attenuated opiate-induced respiratory depression in rats and nonhuman primates without affecting morphine analgesia in rats. GAL-021 ventilatory stimulation in rats was attenuated by carotid sinus nerve transection. GAL-021 ventilatory stimulation was attenuated in mice lacking the pore-forming α-subunit of the KCa1.1 channel.

Background
The authors describe the preclinical pharmacological properties of GAL-021, a novel peripheral chemoreceptor modulator.

Methods
The ventilatory effects of GAL-021 were characterized using tracheal pneumotachometry (n = 4 to 6), plethysmography (n = 5 to 6), arterial blood gas analyses (n = 6 to 11), and nasal capnography (n = 3 to 4) in naive animals and those subjected to morphine-induced respiratory depression. Morphine analgesia in rats was evaluated by tail-flick test (n = 6). Carotid body involvement in GAL-021 ventilatory effects was assessed by comparing responses in intact and carotid sinus nerve–transected rats. Hemodynamic effects of GAL-021 were evaluated in urethane-anesthetized rats (n = 7). The pharmacological profile of GAL-021 in vitro was investigated using radioligand binding, enzyme inhibition, and cellular electrophysiology assays.

Results
GAL-021 given intravenously stimulated ventilation and/or attenuated opiate-induced respiratory depression in rats, mice, and nonhuman primates, without decreasing morphine analgesia in rats. GAL-021 did not alter mean arterial pressure but produced a modest increase in heart rate. Ventilatory stimulation in rats was attenuated by carotid sinus nerve transection. GAL-021 inhibited KCa1.1 in GH3 cells, and the evoked ventilatory stimulation was attenuated in Slo1
−/− mice lacking the pore-forming α-subunit of the KCa1.1 channel.

Conclusions
GAL-021 behaved as a breathing control modulator in rodents and nonhuman primates and diminished opioid-induced respiratory depression without compromising opioid analgesia. It acted predominantly at the carotid body, in part by inhibiting KCa1.1 channels. Its preclinical profile qualified the compound to enter clinical trials to assess effects on breathing control disorders such as drug (opioid)-induced respiratory depression and sleep apnea.
Gradually Increased Oxygen Administration Improved Oxygenation and Mitigated Oxidative Stress after Resuscitation from Severe Hemorrhagic Shock
Authors: Luo Xin , Yin Yujing , You Guoxing , Chen Gan , Wang Ying , Zhao Jingxiang , Wang Bo , Zhao Lian , Zhou Hong 
Published: September 2015

AbstractAbstract
Gradually increased oxygen administration improved systemic/tissue oxygenation and mitigated oxidative stress simultaneously after resuscitation from severe hemorrhagic shock.

Background
The optimal oxygen administration strategy during resuscitation from hemorrhagic shock (HS) is still controversial. Improving oxygenation and mitigating oxidative stress simultaneously seem to be contradictory goals. To maximize oxygen delivery while minimizing oxidative damage, the authors proposed the notion of gradually increased oxygen administration (GIOA), which entails making the arterial blood hypoxemic early in resuscitation and subsequently gradually increasing to hyperoxic, and compared its effects with normoxic resuscitation, hyperoxic resuscitation, and hypoxemic resuscitation in severe HS.

Methods
Rats were subjected to HS, and on resuscitation, the rats were randomly assigned to four groups (n = 8): the normoxic, the hyperoxic, the hypoxemic, and the GIOA groups. Rats were observed for an additional 1 h. Hemodynamics, acid–base status, oxygenation, and oxidative injury were observed and evaluated.

Results
Central venous oxygen saturation promptly recovered only in the hyperoxic and the GIOA groups, and the liver tissue partial pressure of oxygen was highest in the GIOA group after resuscitation. Oxidative stress in GIOA group was significantly reduced compared with the hyperoxic group as indicated by the reduced malondialdehyde content, increased catalase activity, and the lower histologic injury scores in the liver. In addition, the tumor necrosis factor-α and interleukin-6 expressions in the liver were markedly decreased in the GIOA group than in the hyperoxic and normoxic groups as shown by the immunohistochemical staining.

Conclusions
GIOA improved systemic/tissue oxygenation and mitigated oxidative stress simultaneously after resuscitation from severe HS. GIOA may be a promising strategy to improve resuscitation from HS and deserves further investigation.