bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluctuating fitness shapes the clone-size distribution of immune repertoires
Authors: Desponds Jonathan , Mora Thierry , Walczak Aleksandra M. 
Published: December 2015

SignificanceReceptors on the surface of lymphocytes specifically recognize foreign pathogens. The diversity of these receptors sets the range of infections that can be detected and fought off. Recent experiments show that, despite the many differences between these receptors in different cell types and species, their distribution of diversity is a strikingly reproducible power law. By introducing effective models of repertoire dynamics that include environmental and antigenic fluctuations affecting lymphocyte growth or “fitness,” we show that a temporally fluctuating fitness is responsible for the observed heavy tail distribution. These models are general and describe the dynamics of various cell types in different species. They allow for the classification of the functionally relevant repertoire dynamics from the features of the experimental distributions.
Metabolic connectivity mapping reveals effective connectivity in the resting human brain
Authors: Riedl Valentin , Utz Lukas , Castrillón Gabriel , Grimmer Timo , Rauschecker Josef P. , Ploner Markus , Friston Karl J. , Drzezga Alexander , Sorg Christian 
Published: December 2015

Significance
Noninvasive brain imaging of humans identifies prominent networks related to sensory and cognitive functions in the resting state; however, the signaling hierarchy and directionality among these networks remain largely unknown. Integrating simultaneously recorded measures for network identification and regional energy metabolism, we propose metabolic connectivity mapping (MCM) as a novel measure to reveal signaling directionality in the human brain. Comparing simple “eyes closed” and “eyes open” conditions in healthy subjects, MCM revealed stable bidirectional signaling among visual cortices and top-down signaling from parietal control regions. Additional top-down signaling from a salience network occurs only during the eyes open condition. We propose MCM as a measure for investigating signaling directions among brain networks in healthy and diseased brains.
Benefits of mercury controls for the United States
Authors: Giang Amanda , Selin Noelle E. 
Published: December 2015

Significance
Mercury is a globally transported pollutant with potent neurotoxic effects for both humans and wildlife. This study introduces an assessment method to estimate the potential human health-related economic benefits of global and domestic mercury control policies. It finds that for the US population as a whole, global mercury controls could lead to approximately twice the benefits of domestic action by 2050. This result is robust to several uncertainties and variabilities along the emissions-to-impacts path, although we find that those consuming locally caught freshwater fish in the United States could benefit more from domestic action.
Feature-based face representations and image reconstruction from behavioral and neural data
Authors: Nestor Adrian , Plaut David C. , Behrmann Marlene 
Published: December 2015

Significance
The present work establishes a novel approach to the study of visual representations. This approach allows us to estimate the structure of human face space as encoded by high-level visual cortex, to extract image-based facial features from this structure, and to use such features for the purpose of facial image reconstruction. The derivation of visual features from empirical data provides an important step in elucidating the nature and the specific content of face representations. Further, the integrative character of this work sheds new light on the existing concept of face space by rendering it instrumental in image reconstruction. Last, the robustness and generality of our reconstruction approach is established by its ability to handle both neuroimaging and psychophysical data.
Sustainable proliferation of liposomes compatible with inner RNA replication
Authors: Tsuji Gakushi , Fujii Satoshi , Sunami Takeshi , Yomo Tetsuya 
Published: December 2015

Significance
The reconstitution of liposomal growth and division compatible with replication of genetic information are required for the development of model cell growth. The growth dynamics of liposomes and their internal reactions should be synchronized to maintain the whole system. In this report, we demonstrate the concurrent incorporation of nutrients and membranes into RNA-containing liposomes using a modified freeze–thaw technique. The fusion and fission of liposomes, RNA replication, and distribution to daughter liposomes were observed compatibly. Finally, the sustainable proliferation of RNA-containing liposomes was observed by iteratively supplying nutrients for 10 cycles. We propose the use of this culturable liposome as an advanced recursive model of a liposomal protocell.
Systematic study of constitutive cyclooxygenase-2 expression: Role of NF-κB and NFAT transcriptional pathways
Authors: Kirkby Nicholas S. , Chan Melissa V. , Zaiss Anne K. , Garcia-Vaz Eliana , Jiao Jing , Berglund Lisa M. , Verdu Elena F. , Ahmetaj-Shala Blerina , Wallace John L. , Herschman Harvey R. , Gomez Maria F. , Mitchell Jane A. 
Published: December 2015

Significance
Nonsteroidal antiinflammatory drugs (NSAIDs) work by inhibiting cyclooxygenase-2 (COX-2) induced at sites of inflammation. They are among the most widely used drugs worldwide, but their cardiovascular side effects are a major concern for patients, regulators, and industry. NSAID side effects are mediated by inhibition of constitutively expressed COX-2 present in discrete regions, including the kidney. However, the pathways driving constitutive COX-2 remain poorly understood. The work presented here defines these pathways and importantly shows constitutive COX-2 expression in the kidney occurs through pathways distinct to those driving COX-2 in inflammation. These data therefore highlight the potential that targeting COX-2 at the transcriptional level may provide a way to dissociate antiinflammatory benefits of NSAIDs from their treatment-limiting cardiovascular side effects.
Long-acting cocaine hydrolase for addiction therapy
Authors: Chen Xiabin , Xue Liu , Hou Shurong , Jin Zhenyu , Zhang Ting , Zheng Fang , Zhan Chang-Guo 
Published: December 2015

Significance
It is essential for a truly effective addiction medication to block the drug's physiological effects effectively without affecting normal functions of the brain and other critical organs such as the heart and while still preventing relapse during abstinence. Most popularly used pharmacological approaches to addiction treatment, including all currently available addiction therapies, either affect normal functions of brain receptors/transporters or are unable to prevent relapse. The long-acting enzyme approach may provide a novel, truly promising therapy capable of effectively blocking the physiological and toxic effects of cocaine without affecting normal functions of the brain and other critical organs and prevent relapse during abstinence. New insights obtained in this study also may be valuable in guiding development of other therapeutic proteins.
Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome
Authors: Cassidy Lara M. , Martiniano Rui , Murphy Eileen M. , Teasdale Matthew D. , Mallory James , Hartwell Barrie , Bradley Daniel G. 
Published: December 2015

Significance
Modern Europe has been shaped by two episodes in prehistory, the advent of agriculture and later metallurgy. These innovations brought not only massive cultural change but also, in certain parts of the continent, a change in genetic structure. The manner in which these transitions affected the islands of Ireland and Britain on the northwestern edge of the continent remains the subject of debate. The first ancient whole genomes from Ireland, including two at high coverage, demonstrate that large-scale genetic shifts accompanied both transitions. We also observe a strong signal of continuity between modern day Irish populations and the Bronze Age individuals, one of whom is a carrier for the C282Y hemochromatosis mutation, which has its highest frequencies in Ireland today.
HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein
Authors: Chen Jianbo , Rahman Sheikh Abdul , Nikolaitchik Olga A. , Grunwald David , Sardo Luca , Burdick Ryan C. , Plisov Sergey , Liang Edward , Tai Sheldon , Pathak Vinay K. , Hu Wei-Shau 
Published: December 2015

Significance
Dimerization of the RNA genome is a key event in HIV-1 virion assembly and has a strong impact in viral replication and evolution. Packaging the dimeric genome allows frequent recombination to rescue genetic information in damaged RNAs and to generate variants that can evade the host immune response or resist antiviral treatments. Furthermore, genome packaging is regulated by recognition of dimeric RNA. Our studies demonstrate that HIV-1 RNAs dimerize not in the cytoplasm but on the plasma membrane, often early during the assembly process, and that Gag protein is required for maintenance of the RNA dimer. These studies address the timing, location, and partners involved in RNA dimerization, an important process for HIV-1 replication.
Ecology-driven stereotypes override race stereotypes
Authors: Williams Keelah E. G. , Sng Oliver , Neuberg Steven L. 
Published: December 2015

SignificanceEcological features shape people’s goals, strategies, and behaviors. Our research suggests that social perceivers possess a lay understanding of ecology’s influence on behavior, resulting in ecology-driven stereotypes. Moreover, because race is confounded with ecology in the United States, Americans’ stereotypes about racial groups may actually reflect their stereotypes about these groups’ presumed home ecologies. In a series of studies, we demonstrate that (i) individuals possess ecology-driven stereotypes; (ii) these stereotypes are not derivative of race stereotypes; and (iii) the application of race stereotypes to targets is greatly diminished when more immediate cues to home ecology are present. These findings have important implications for the conceptualization of race stereotypes, as well as for reducing the application of pernicious stereotypes to individuals.
Delineating the continuum of marine ecosystem-based management: a US fisheries reference point perspective
Authors: Dolan Tara E. , Patrick Wesley S. , Link Jason S. 
Published: December 2015

AbstractEcosystem management (EM) suffers from linguistic uncertainty surrounding the definition of “EM” and how it can be operationalized. Using fisheries management as an example, we clarify how EM exists in different paradigms along a continuum, starting with a single-species focus and building towards a more systemic and multi-sector perspective. Focusing on the specification of biological and other systemic reference points (SRPs) used in each paradigm and its related regulatory and governance structures, we compare and contrast similarities among these paradigms. We find that although EM is a hierarchical continuum, similar SRPs can be used throughout the continuum, but the scope of these reference points are broader at higher levels of management. This work interprets the current state of the conversation, and may help to clarify the levels of how EM is applied now and how it can be applied in the future, further advancing its implementation.
An overview of global research effort in fisheries science
Authors: Aksnes Dag W. , Browman Howard I. 
Published: December 2015

AbstractWe used bibliometric indicators to characterize recent (2010–2013) research activity in fisheries science with the objective of garnering insights into how this increased effort has been directed. Specifically, we provide an overview of the primary literature on fisheries research, including which countries are the largest contributors (USA, China, Japan, Australia, Canada, and Norway), and an assessment of the citation impact of the research conducted by different countries. The countries with the highest impact were the UK, Norway, Germany, France, Canada, and Italy. We further assessed the research topics that are most commonly studied and attempt to understand what drives that. During the past three decades, research appears to have shifted from a focus on species-related questions to processes. An analysis of how publication output is distributed at the level of fish species indicates that a small number of species (e.g. Atlantic salmon, rainbow trout, and Atlantic cod) account for a disproportionate volume of the total research effort. Interestingly, publication output is not correlated with the commercial importance of a species. Although fisheries management is purportedly based upon scientific research, our analysis reveals that hardly any research at all is conducted on several of the (commercially) most important species, at least as measured by articles appearing in international scientific journals.
Is There a Role for Decompression Alone for Treating Symptomatic Degenerative Lumbar Spondylolisthesis?
Authors: Joaquim Andrei F. , Milano Jeronimo B. , Ghizoni Enrico , Patel Alpesh A. 
Published: December 2015

Background Context:
A posterior decompression with an instrumented fusion is one of the most common surgical procedures performed for treating symptomatic spinal stenosis associated with degenerative spondylolisthesis (DS). However, some patients may benefit from a decompression alone, avoiding complications related to instrumentation and fusion.

Objective:
To identify the characteristics of patients with symptomatic DS who may be successfully treated with an isolated decompression.

Study Design:
A systematic literature review of studies including patients who underwent decompression without instrumentation for treatment of DS.

Methods:
A systematic review of the Medline database was performed. Retrospective and prospective studies of patients with DS who underwent a decompression were included, as well as studies comparing decompression with instrumented decompression. All the articles were classified according to their level of evidence.

Results:
Thirteen studies met all inclusion and exclusion criteria. We identified several characteristics that may be associated with a less favorable outcome after a decompression alone: a facet angle >50 degrees, a disk space of >6.5 mm, presence of low back pain rather than lower extremity symptoms, presence of hypermobility in the listhetic level on dynamic radiographs (>1.25 to 2 mm), and resection of the posterior elements. The majority of the studies comparing decompression alone to decompression and instrumented fusion included in our review suggested similar clinical outcomes with both procedures; however, with long-term follow-up, fusion may provide better outcomes. Decompression with a noninstrumented fusion is also a good alternative to improve symptoms in selected patients, potentially decreasing the risk of reoperation compared with an instrumented fusion.

Conclusions:
Satisfactory clinical outcome can be achieved with an isolated decompression in selected patients, avoiding the additional risks and costs of instrumentation and spinal fusion. Noninstrumented fusion is also an interesting alternative to instrumented fusion for well-selected patients to decrease complications related to instrumentation.
Initiator tRNA Genes Template the 3’CCA End at High Frequencies in Bacteria
Authors: Ardell David H. , Hou Ya-Ming 
Published: December 2015

ABSTRACTWhile the CCA sequence at the mature 3’ end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In bacteria, tRNA genes template CCA sporadically. In order to understand variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in the tRNAdb-CE database. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Preferential retention of CCA in initiator tRNA genes evolved multiple times during reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We suggest that cotranscriptional synthesis of initiator tRNA CCA 3’ ends can complement inefficient processing of initiator tRNA precursors, “bootstrap” rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursors. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli.
The Fisher-Wright model with deterministic seed bank and selection
Authors: Koopmann Bendix , Müeller Johannes , Tellier Aurélien , Živković Daniel 
Published: December 2015

AbstractSeed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. We compute the equilibrium solution of the site-frequency spectrum and derive the times to fixation of an allele with and without selection. Finally, it is demonstrated that seed banks enhance the effect of selection onto the site-frequency spectrum while slowing down the time until the mutation-selection equilibrium is reached.
Epigenetic Regulation of Vegetative Phase Change in Arabidopsis
Authors: Xu Mingli , Hu Tieqiang , Smith Michael R. , Poethig R. Scott 
Published: December 2015

AbstractVegetative phase change in flowering plants is regulated by a decrease in the level of miR156. The molecular mechanism of this temporally regulated decrease in miR156 expression is still unknown. Most of the miR156 in Arabidopsis thaliana shoots is produced by MIR156A and MIR156C. We found that the downregulation of these genes during vegetative phase change is associated with an increase in their level of histone H3 lysine 27 trimethylation (H3K27me3) and requires this chromatin modification. The increase in H3K27me3 at MIR156A/MIR156C is associated with an increase in the binding of PRC2 to these genes and is mediated redundantly by the E(z) homologs SWINGER and CURLY LEAF. The CHD3 chromatin remodeler PICKLE (PKL) promotes the addition of H3K27me3 to MIR156A/MIR156C but is not responsible for the temporal increase in this chromatin mark. PKL is bound to the promoters of MIR156A/MIR156C, where it promotes low levels of H3K27ac early in shoot development and stabilizes the nucleosome at the +1 position. These results suggest a molecular mechanism for the initiation and maintenance of vegetative phase change in plants.
Women's opinions on being weighed at routine antenatal visits
Authors: Brownfoot FC , Davey M‐A , Kornman L 
Published: December 2015

ObjectiveTo assess the opinions of pregnant women regarding their weight gain and to assess the level of satisfaction and anxiety provoked by being weighed in clinic.DesignQuestionnaires were given to women participating in a randomised controlled trial comparing routine weighing in the antenatal clinic with standard care.SettingA tertiary hospital antenatal clinic in Melbourne, Australia.PopulationIn all, 782 healthy pregnant women participated in the randomised controlled trial and 586 responded to the questionnaire.MethodsA questionnaire was offered to all participants at 36 weeks of gestation gauging their satisfaction with their weight gain during pregnancy. The intervention group was asked about their level of satisfaction and anxiety provoked by being weighed in clinic. The control group was asked whether they would have liked to be weighed in clinic. Both groups were questioned about the influences on their weight gain.ResultsWomen in both groups were satisfied with their weight gain during pregnancy. Seventy‐three percent of women in the intervention group were very comfortable with being weighed in clinic. Approximately half of those in the control group would have favoured being weighed. Twenty‐one percent of women said other people influenced their weight gain; mostly family members and two‐thirds of them encouraged weight gain. Less than half of the women in the study used weighing scales at home.ConclusionWomen were satisfied with being weighed antenatally and it did not cause anxiety. Pregnant women accepted the re‐introduction of weighing in the antenatal clinic.Tweetable abstractWomen are satisfied with being weighed antenatally and it does not cause anxiety.
Effect of Taurine on Hemodiafiltration in Patients With Chronic Heart Failure
Authors: Shiohira Shunji , Komatsu Mizuki , Okazaki Masayuki , Naganuma Toshiaki , Kawaguchi Hiroshi , Nitta Kosaku , Tsuchiya Ken 
Published: December 2015

AbstractTaurine, an important factor in the living body, is essential for cardiovascular function and development and function of skeletal muscle, retina and central nervous system. In the present study, its effect on cardiovascular function was specifically taken into consideration. In hemodiafiltration (HDF) patients, the effect of taurine on patients with chronic heart failure (CHF), in whom dry weight was difficult to control, was evaluated. All patients who were subjected to regular HDF for 4 h three times per week at Joban hospital were included in this study. Patients with chronic heart failure, in whom dry weight was difficult to control (N = 4), were included in the evaluation of clinical status. X‐ray and echocardiography were determined before and after taurine treatment. Almost all patients were taking nitric acid, warfarin, anti‐platelet agents and vasopressors. Because vital signs were unstable in chronic heart failure, all cases withheld antihypertensive drugs during HDF. For unstable vital signs during HDF, pulmonary congestion was chronically recognized. After taurine was started, vital signs stabilized and lowering of dry weight was possible. In addition, X‐ray and cardiac diastolic failure on echocardiography improved. Taurine was effective for CHF patients on HDF in whom dry weight was difficult to control in spite of various medications.
The Empire of Home: Global Domestic Objects and The Female American (1767)
Authors: Smith Chloe Wigston 
Published: December 2015

AbstractThis article studies the representation of global domestic objects and the treatment of dress and domesticity in The Female American (1767). I argue that the novel's biracial heroine exploits portable goods, such as religious vestments, in her imperialist missionary scheme. This fictional re‐imagining of feminine material culture echoes, but remains distinct from, period examples of needlework and handicrafts that document knowledge of empire and colonisation. Whereas embroidery and novels often schooled women in the pleasures of domesticity, compelling their attention inwards, The Female American suggests a new model of heroic femininity that evades domestic gender ideologies.