bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ambipolar and non-ambipolar diffusion in an rf plasma source containing a magnetic filter
Authors: Lafleur T. , Aanesland A. 
Published: June 2014

By placing a magnetic filter across a rectangular plasma source (closed at one end with a ceramic plate and an rf antenna, and terminated at the opposite end by a grounded grid), we experimentally investigate the effect of conducting and insulating source walls on the nature of the plasma diffusion phenomena. The use of a magnetic filter creates a unique plasma, characterized by a high upstream electron temperature (Teu∼5 eV) near the rf antenna and a low downstream electron temperature (Ted∼1 eV) near the grid, which more clearly demonstrates the role of the source wall materials. For conducting walls a net ion current to ground is measured on the grid, and the plasma potential is determined by a mean electron temperature within the source. For insulating walls the plasma potential is determined by the downstream electron temperature (i.e., Vp∼5.2Ted in argon), and the net current to the grid is exactly zero. Furthermore, by inserting a small additional upstream conductor (that can be made floating or grounded through an external circuit switch), we demonstrate that the plasma potential can be controlled and set to a low (Vp∼5.2Ted), or high (Vp∼5.2Teu) value.
Functional recovery with recombinant human IGF1 treatment in a mouse model of Rett Syndrome
Authors: Castro Jorge , Garcia Rodrigo I. , Kwok Showming , Banerjee Abhishek , Petravicz Jeremy , Woodson Jonathan , Mellios Nikolaos , Tropea Daniela , Sur Mriganka 
Published: June 2014

SignificanceRett Syndrome is a devastating neurodevelopmental disorder that arises from mutations in the methyl-CpG binding protein 2 (MeCP2) gene and has no presently available treatment. We show that levels of insulin-like growth factor-1 (IGF1) are reduced in male and femaleMecp2mutant mice. Treating male knockout mice with recombinant human IGF1 (rhIGF1) improves a range of physiological symptoms and behaviors, increases excitatory transmission and synapse density in cortical neurons, and up-regulates molecular signals underlying these deficits. Treating symptomatic female heterozygous mice also improves a range of physiological and behavioral symptoms and normalizes maturation of cortical circuits. These findings demonstrate that rhIGF1 corrects functional, structural, and molecular mechanisms downstream of MeCP2 and may be an effective therapeutic for Rett Syndrome.
Actin-binding protein 1 links B-cell antigen receptors to negative signaling pathways
Authors: Seeley-Fallen Margaret K. , Liu Lisa J. , Shapiro Melanie R. , Onabajo Olusegun O. , Palaniyandi Senthilkumar , Zhu Xiaoping , Tan Tse-Hua , Upadhyaya Arpita , Song Wenxia 
Published: June 2014

SignificanceB cells are the major mediators of humoral immunity, producing antibody to aid in the elimination of pathogens. B cells signal through their membrane receptors, resulting in transcriptional modification for the maintenance of B-cell survival, proliferation, and antibody production. B-cell receptor (BCR) signaling is tightly regulated, and elevated or sustained BCR signals lead to loss of B-cell tolerance and subsequent autoimmunity. This study reveals that the adaptor molecule Abp1 negatively regulates development of marginal zone and spontaneous germinal center B cells, as well as autoantibody production. As a link between the actin cytoskeleton and BCR signaling, Abp1 assists BCR signal attenuation by promoting BCR central cluster formation, as well as recruitment of inhibitory signaling molecules to BCR signalosomes.
Archean komatiite volcanism controlled by the evolution of early continents
Authors: Mole David R. , Fiorentini Marco L. , Thebaud Nicolas , Cassidy Kevin F. , McCuaig T. Campbell , Kirkland Christopher L. , Romano Sandra S. , Doublier Michael P. , Belousova Elena A. , Barnes Stephen J. , Miller John 
Published: June 2014

Significance
Komatiites are rare, ultra-high-temperature (∼1,600 °C) lavas that were erupted in large volumes 3.5–1.5 bya but only very rarely since. They are the signature rock type of a hotter early Earth. However, the hottest, most extensive komatiites have a very restricted distribution in particular linear belts within preserved Archean crust. This study used a combination of different radiogenic isotopes to map the boundaries of Archean microcontinents in space and time, identifying the microplates that form the building blocks of Precambrian cratons. Isotopic mapping demonstrates that the major komatiite belts are located along these crustal boundaries. Subsequently, the evolution of the early continents controlled the location and extent of major volcanic events, crustal heat flow, and major ore deposit provinces.
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in
Arabidopsis
Authors: Para Alessia , Li Ying , Marshall-Colón Amy , Varala Kranthi , Francoeur Nancy J. , Moran Tara M. , Edwards Molly B. , Hackley Christopher , Bargmann Bastiaan O. R. , Birnbaum Kenneth D. , McCombie W. Richard , Krouk Gabriel , Coruzzi Gloria M. 
Published: June 2014

Significance
Cellular signals evoke rapid and broad changes in gene regulatory networks. To uncover these network dynamics, we developed an approach able to monitor primary targets of a transcription factor (TF) based solely on gene regulation, in the absence of detectable binding. This enabled us to follow the transient propagation of a nitrogen (N) nutrient signal as a direct impact of the master TF Basic Leucine Zipper 1 (bZIP1). Unexpectedly, the largest class of primary targets that exhibit transient associations with bZIP1 is uniquely relevant to the rapid and dynamic propagation of the N signal. Our ability to uncover this transient network architecture has revealed the “dark matter” of dynamic N nutrient signaling in plants that has previously eluded detection.
Water resources transfers through Chinese interprovincial and foreign food trade
Authors: Dalin Carole , Hanasaki Naota , Qiu Huanguang , Mauzerall Denise L. , Rodriguez-Iturbe Ignacio 
Published: June 2014

Significance
China’s fast socioeconomic growth increasingly strains national water resources, notably through rising urbanization and meat demand. Agriculture is located mainly in the dry north, where irrigation largely relies on groundwater reserves. This paper analyzes the role of international and interprovincial food trade in China’s national agricultural water-use and food supply. We combine a hydrological model with a trade model to quantify the volumes of irrigation and rainfall water transferred between provinces and other countries through agricultural trade. We find that China’s dry, irrigation-intensive provinces tend to export food commodities to wetter places, and identify specific provinces and products showing high potential for irrigation productivity enhancements. These findings are essential to inform sound policies aimed at improving agricultural sustainability in China.
Dissipative self-assembly of particles interacting through time-oscillatory potentials
Authors: Tagliazucchi Mario , Weiss Emily A. , Szleifer Igal 
Published: June 2014

Significance
Dissipative self-assembly is the organization of a system requiring continuous input of energy to the system from its environment. Dissipative self-assembly is ubiquitous in biology, where it leads to structures unavailable in equilibrium conditions and to complex dynamical behavior. There are, however, only a few synthetic examples of this phenomenon. This work proposes a method for dissipative self-assembly through the oscillations of the interaction potentials. As an example, a mixture of pH-responsive particles subjected to fast pH oscillations self-assembles into different nonequilibrium structures that cannot be obtained in equilibrium at fixed pH. This result shows that nontrivial dissipative structures can be formed by periodic oscillation of the forces among particles and reveals a novel strategy to create far-from-equilibrium self-organized structures.
STAT1-induced ASPP2 transcription identifies a link between neuroinflammation, cell polarity, and tumor suppression
Authors: Turnquist Casmir , Wang Yihua , Severson David T. , Zhong Shan , Sun Bin , Ma Jingyi , Constantinescu Stefan N. , Ansorge Olaf , Stolp Helen B. , Molnár Zoltán , Szele Francis G. , Lu Xin 
Published: June 2014

SignificanceTwo of the most debilitating and scientifically challenging diseases of the 21st century are cancer and neurodegeneration. Although cancer results from excessive cell growth, neurodegeneration is a consequence of excessive cell loss. Dysfunction of the same key regulators, including oncogenes and tumor suppressors, may cause both diseases. We report that LPS and IFN induce apoptosis-stimulating protein of p53 with signature sequences of ankyrin repeat-, SH3 domain-, and proline-rich region-containing protein 2 (ASPP2) transcription through a signal transducer and activator of transcription 1 (STAT1) -dependent but NF-κB RELA/p65-independent pathway and that ASPP2 mediates LPS-induced apoptosis. Thus, the identified STAT1/ASPP2 pathway reveals an important function of ASPP2 in the cellular response to inflammation and infection and connects neuroinflammation to cell polarity and tumor suppression.
When recognition memory is independent of hippocampal function
Authors: Smith Christine N. , Jeneson Annette , Frascino Jennifer C. , Kirwan C. Brock , Hopkins Ramona O. , Squire Larry R. 
Published: June 2014

Significance
Hippocampal damage has been thought to impair memory for all domains of material (sounds, objects, words, odors). We investigated face recognition memory in patients with hippocampal lesions or large medial temporal lobe lesions. Recognition of novel faces was unequivocally intact in hippocampal patients but only at a short retention interval. Recognition memory for words, buildings, famous faces, and inverted faces was impaired. For medial temporal lobe patients, memory was impaired in all conditions. Ordinarily, recognition memory judgments depend on an association between study items and the study context. We suggest that face memory is spared because face processing is specialized (and holistic), and that participants can make recognition judgments without making explicit reference to the study context.
Clonal analysis reveals nerve-dependent and independent roles on mammalian hind limb tissue maintenance and regeneration
Authors: Rinkevich Yuval , Montoro Daniel T. , Muhonen Ethan , Walmsley Graham G. , Lo David , Hasegawa Masakazu , Januszyk Michael , Connolly Andrew J. , Weissman Irving L. , Longaker Michael T. 
Published: June 2014

Significance
In Urodeles, surgical denervation before limb amputation results in regeneration failure. Here we explored the dependency of the peripheral nervous system on tissue replacement in mammalian appendages by performing a comprehensive clonal analysis of hind limb tissues devoid of nerve supply. Our experiments uncover conserved phenotypes, which mimic clinical observations of patients with nerve damage resulting from spinal cord injury. Our system could be used to better understand both pathophysiology and treatment of patients with spinal cord injury.
A Patient Navigation Intervention for Drug-Involved Former Prison Inmates
Authors: Binswanger Ingrid A. , Whitley Elizabeth , Haffey Paul-Ryan , Mueller Shane R. , Min Sung-Joon 
Published: June 2014

Background: Former prison inmates experience high rates of hospitalizations and death during the transition from prison to the community, particularly from drug-related causes and early after release. The authors designed a randomized controlled trial (RCT) of patient navigation to reduce barriers to health care and hospitalizations for former prison inmates. Methods: Forty former prison inmates with a history of drug involvement were recruited and randomized within 15 days after prison release. Participants were randomized to receive 3 months of patient navigation (PN) with facilitated enrollment into an indigent care discount program (intervention) or facilitated enrollment into an indigent care discount program alone (control). Structured interviews were conducted at baseline, 3 months, and 6 months. Outcomes were measured as a change in self-reported barriers to care and as the rate of health service use per 100 person-days. Results: The mean number of reported barriers to care was reduced at 3 and 6 months in both groups. At 6 months, the rate of emergency department/urgent care visits per 100 person-days since baseline was 1.1 among intervention participants and 0.5 among control participants ( P = .04), whereas the rate of hospitalizations per 100 person-days was 0.2 in intervention participants and 0.6 in control participants ( P = .04). Conclusions: Recruitment of former inmates into an RCT of patient navigation was highly feasible, but follow-up was limited by rearrests. Results suggest a significantly lower rate of hospitalizations among navigation participants, although the rate of emergency department/urgent care visits was not improved. Patient navigation is a promising, pragmatic intervention that may be effective at reducing high-cost health care utilization in former prison inmates.
A genomic search approach to identify carbonyl reductases in Gluconobacter oxydans for enantioselective reduction of ketones
Authors: Chen Rong , Liu Xu , Lin Jinping , Wei Dongzhi 
Published: June 2014

Abstract
The versatile carbonyl reductases from Gluconobacter oxydans in the enantioselective reduction of ketones to the corresponding alcohols were exploited by genome search approach. All purified enzymes showed activities toward the tested ketoesters with different activities. In the reduction of 4-phenyl-2-butanone with in situ NAD(P)H regeneration system, (S)-alcohol was obtained with an e.e. of up to 100% catalyzed by Gox0644. Under the same experimental condition, all enzymes catalyzed ethyl 4-chloroacetoacetate to give chiral products with an excellent e.e. of up to 99%, except Gox0644. Gox2036 had a strict requirement for NADH as the cofactor and showed excellent enantiospecificity in the synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate. For the reduction of ethyl 2-oxo-4-phenylbutyrate, excellent e.e. (&gt;99%) and high conversion (93.1%) were obtained by Gox0525, whereas the other enzymes showed relatively lower e.e. and conversions. Among them, Gox2036 and Gox0525 showed potentials in the synthesis of chiral alcohols as useful biocatalysts.
A multiobjective method for robust identification of bacterial small non-coding RNAs
Authors: Arnedo Javier , Romero-Zaliz Rocío , Zwir Igor , del Val Coral 
Published: June 2014

Abstract
Motivation: Small non-coding RNAs (sRNAs) have major roles in the post-transcriptional regulation in prokaryotes. The experimental validation of a relatively small number of sRNAs in few species requires developing computational algorithms capable of robustly encoding the available knowledge and using this knowledge to predict sRNAs within and across species.
Results: We present a novel methodology designed to identify bacterial sRNAs by incorporating the knowledge encoded by different sRNA prediction methods and optimally aggregating them as potential predictors. Because some of these methods emphasize specificity, whereas others emphasize sensitivity while detecting sRNAs, their optimal aggregation constitutes trade-off solutions between these two contradictory objectives that enhance their individual merits. Many non-redundant optimal aggregations uncovered by using multiobjective optimization techniques are then combined into a multiclassifier, which ensures robustness during detection and prediction even in genomes with distinct nucleotide composition. By training with sRNAs in Salmonella enterica Typhimurium, we were able to successfully predict sRNAs in Sinorhizobium meliloti , as well as in multiple and poorly annotated species. The proposed methodology, like a meta-analysis approach, may begin to lay a possible foundation for developing robust predictive methods across a wide spectrum of genomic variability.
Availability and implementation: Scripts created for the experimentation are available at http://m4m.ugr.es/SupInfo/sRNAOS/sRNAOSscripts.zip .
Contact: delval@decsai.ugr.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Resources partitioning by seabirds and their relationship with other consumers at and around a small tropical archipelago
Authors: Mancini Patrícia L. , Bugoni Leandro 
Published: June 2014

Abstract
Seabirds occupy a range of trophic levels in marine foodwebs, and as top predators, they potentially may compete with large fish for prey. Here, we examine trophic segregation among seabird species breeding on São Pedro and São Paulo Archipelago (SPSPA), in the tropical Atlantic Ocean, as well as the trophic relationships between the seabirds and pelagic fish. We used stable isotopes (δ15N, δ13C) combined with a conventional dietary analysis of brown booby (Sula leucogaster), brown noddy (Anous stolidus), and black noddy (Anous minutus) and also analysed stable isotopes in the muscles of tropical two-wing flying fish (Exocoetus volitans), blackfin tuna (Thunnus atlanticus), and common dolphinfish (Coryphaena hippurus). Brown boobies shared a similar trophic level with large predatory fish probably due to their intense consumption of flying fish, but seabirds are most likely not competing with blackfin tuna and common dolphinfish, despite relying on the same prey. Food resources seem to be abundant around SPSPA, minimizing competition. Despite relying mostly on two-wing flying fish, the three seabirds studied had non-overlapping trophic niches during the breeding period, with segregation apparently occurring by prey size. Sex-related trophic differences were not found, but age-related trophic segregation was observed in brown boobies and brown noddies. Overall, although seabirds and marine pelagic fish rely on the same prey species, the overlap in their trophic niches was limited, most likely due to an overabundant food resource, i.e. flying fish, a common prey of large predators in most pelagic tropical oceans.
Celiac Disease Genetics
Authors: Wijmenga Cisca , Gutierrez‐Achury Javier 
Published: June 2014

ABSTRACTIn the past few years there has been enormous progress in unraveling the genetic basis of celiac disease (CD). Apart from the well‐known association to HLA, there are currently 40 genomic loci associated to CD. Most of these loci show pleiotropic effects across many autoimmune diseases and highlight the importance of a dysregulated immune system in the predisposition to CD. It is still too early, however, to use genetics in clinical practice for predicting individual risk. The major challenge for the future is to translate genetic findings into a better understanding of the underlying disease mechanism and to design new ways to treat CD and prevent its development.
Is ‘Genocide’ an Anachronistic Concept for the Study of Early Modern Mass Killing?
Authors: Kiernan Ben 
Published: June 2014

AbstractIs it anachronistic to apply the term ‘genocide’, coined in 1943, to ancient or early modern mass killings, even to those that might fit the mid‐twentieth‐ century definition? Historians must analyse actions and events of the pre‐modern era in the context of cultural stipulations discussed at the time, and of knowledge paradigms then available. To assess people's actions by standards understood in that era, it is important to determine whether a pre‐modern understanding of the concept of genocide existed. Long before that term, earlier terms such as ‘general massacre’ conveyed similar meanings, along with four much older, related terms – holocaust, extermination, crimes against humanity, and war crimes – which also conveyed pre‐modern concepts of the crimes involved. This essay traces the historical lineage and usage of those terms in European and transnational contexts, and argues that conceptions of genocide long pre‐dated the coining of the term. Genocide did occur in early modern times, though it was neither normal practice nor universally permitted and often provoked dissent. The essay concludes that a grasp of the concept and its moral implications long preceded both our word for it and its 1950 legal codification as an international crime. The essay then critiques common misunderstandings of that legal definition: that it refers to the crime's effect rather than the perpetrator's intent; that it is too broad for historians to use; that only a state can commit genocide; that it must involve the participation of an entire ethnic group; and that it must be complete, not partial.
Violence on the Fringes: The Virginia (1622) and Amboyna (1623) Massacres
Authors: Games Alison 
Published: June 2014

AbstractTwo events, both labelled massacres by the English who suffered death at the hands of their rivals, took place within the space of a year on opposite sides of the globe and in widely different overseas contexts. The first episode took place in Virginia in March 1622, when Opechancanough and his soldiers killed one‐third of the English colonists in a surprise attack. The second episode transpired in February 1623 in the Spice Islands, when Dutch East India Company officials in Ambon suspected English East India Company employees of conspiring with Japanese soldiers to seize the trading post, interrogated and tried them, and executed twenty‐one men. This episode, known in England by 1624 as the ‘Amboyna massacre’, endured as a meaningful frame of reference well into the eighteenth century. This article explores the particular contexts of each episode and analyses what violence meant to different participants. It investigates how each event became a ‘massacre’ to survivors and to observers in England. In both Virginia and Amboyna, the English were victims, not perpetrators, of violence, and thus these events offer an opportunity to explore how victims of violence deployed their ordeals, in pamphlets, images, plays, and songs, to further their own ends. Labelled as massacres, these two episodes acquired a meaning apart from the actual course of events, helping the English to reassess their overseas goals, to re‐evaluate their prospects and to define themselves anew.
Introduction: Human Rights and the History of Violence in the EarlyBritish Empire
Authors: Kane Brendan 
Published: June 2014

AbstractSpecialists on early modern violence and on human rights history have much to gain through collaboration, or at least mutual awareness. Human rights historians are increasingly drawing on studies of early modern violence. However, as contended here, early modernists tend to approach the subject framed by their own geographical areas of interest. As such, we lack an overarching sense of violence and its meanings across the Tudor and Stuart realms and colonies, something that would be of great utility in understanding how developments in the early modern period relate to later ones. In the interests of promoting such broader investigation and comparison, the present essay briefly surveys important aspects of the approach to violence in the English, Irish and Atlantic historiographies, and in the literatures of massacre and of human rights. In doing so, it sets the essays included in this special edition in their historiographical contexts and highlights crucial interventions. It concludes with thoughts not only on how a more comprehensive understanding of violence in the early British empire might be of value to human rights historians, but how the new meta‐narrative of human rights history might spur greater comparative work amongst early modernists.