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Showing papers by "Rutgers University published in 2005"


Journal ArticleDOI
Leslie McCall1
TL;DR: The authors argue that intersectionality is the most important theoretical contribution women's studies, in conjunction with related fields, has made so far, and they even say that intersectional is a central category of analysis in women’s studies, and that women are perhaps alone in the academy in the extent to which they have embraced intersectionality.
Abstract: Since critics first allegedthat feminism claimed tospeak universally for all women, feminist researchers havebeen acutely aware ofthe limitations of genderas a single analyticalcategory. In fact, feministsare perhaps alone in the academy in theextent to which theyhave embraced intersectionality – the relationshipsamong multiple dimensions andmodalities of social relations and subject formations – as itselfa central category ofanalysis. One could evensay that intersectionality isthe most important theoreticalcontribution that women’s studies,in conjunction with relatedfields, has made sofar.1

4,744 citations


Journal ArticleDOI
Takashi Matsumoto1, Jianzhong Wu1, Hiroyuki Kanamori1, Yuichi Katayose1  +262 moreInstitutions (25)
11 Aug 2005-Nature
TL;DR: A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.
Abstract: Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

3,423 citations


Journal ArticleDOI
TL;DR: Propagule pressure is proposed as a key element to understanding why some introduced populations fail to establish whereas others succeed and how the study of propagule pressure can provide an opportunity to tie together disparate research agendas within invasion ecology.
Abstract: Human-mediated species invasions are a significant component of current global environmental change. There is every indication that the rate at which locations are accumulating non-native species is accelerating as free trade and globalization advance. Thus, the need to incorporate predictive models in the assessment of invasion risk has become acute. However, finding elements of the invasion process that provide consistent explanatory power has proved elusive. Here, we propose propagule pressure as a key element to understanding why some introduced populations fail to establish whereas others succeed. In the process, we illustrate how the study of propagule pressure can provide an opportunity to tie together disparate research agendas within invasion ecology.

2,288 citations


Journal ArticleDOI
TL;DR: In this paper, the authors introduce a sublinear space data structure called the countmin sketch for summarizing data streams, which allows fundamental queries in data stream summarization such as point, range, and inner product queries to be approximately answered very quickly; in addition it can be applied to solve several important problems in data streams such as finding quantiles, frequent items, etc.

1,939 citations


Journal ArticleDOI
TL;DR: In this article, the authors introduce the current state of development in the application of ferroelectric thin films for electronic devices and discuss the physics relevant for the performance and failure of these devices.
Abstract: This review covers important advances in recent years in the physics of thin-film ferroelectric oxides, the strongest emphasis being on those aspects particular to ferroelectrics in thin-film form. The authors introduce the current state of development in the application of ferroelectric thin films for electronic devices and discuss the physics relevant for the performance and failure of these devices. Following this the review covers the enormous progress that has been made in the first-principles computational approach to understanding ferroelectrics. The authors then discuss in detail the important role that strain plays in determining the properties of epitaxial thin ferroelectric films. Finally, this review ends with a look at the emerging possibilities for nanoscale ferroelectrics, with particular emphasis on ferroelectrics in nonconventional nanoscale geometries.

1,908 citations


Journal ArticleDOI
TL;DR: Data Streams: Algorithms and Applications surveys the emerging area of algorithms for processing data streams and associated applications, which rely on metric embeddings, pseudo-random computations, sparse approximation theory and communication complexity.
Abstract: In the data stream scenario, input arrives very rapidly and there is limited memory to store the input. Algorithms have to work with one or few passes over the data, space less than linear in the input size or time significantly less than the input size. In the past few years, a new theory has emerged for reasoning about algorithms that work within these constraints on space, time, and number of passes. Some of the methods rely on metric embeddings, pseudo-random computations, sparse approximation theory and communication complexity. The applications for this scenario include IP network traffic analysis, mining text message streams and processing massive data sets in general. Researchers in Theoretical Computer Science, Databases, IP Networking and Computer Systems are working on the data stream challenges. This article is an overview and survey of data stream algorithmics and is an updated version of [1].

1,598 citations


Proceedings Article
09 Jul 2005
TL;DR: This paper reports on the efforts to recognize user activity from accelerometer data and performance of base-level and meta-level classifiers, and Plurality Voting is found to perform consistently well across different settings.
Abstract: Activity recognition fits within the bigger framework of context awareness. In this paper, we report on our efforts to recognize user activity from accelerometer data. Activity recognition is formulated as a classification problem. Performance of base-level classifiers and meta-level classifiers is compared. Plurality Voting is found to perform consistently well across different settings.

1,561 citations


Book
01 Jan 2005
TL;DR: In this paper, the authors present a survey of basic mathematical foundations for data streaming systems, including basic mathematical ideas, basic algorithms, and basic algorithms and algorithms for data stream processing.
Abstract: 1 Introduction 2 Map 3 The Data Stream Phenomenon 4 Data Streaming: Formal Aspects 5 Foundations: Basic Mathematical Ideas 6 Foundations: Basic Algorithmic Techniques 7 Foundations: Summary 8 Streaming Systems 9 New Directions 10 Historic Notes 11 Concluding Remarks Acknowledgements References

1,506 citations


Journal ArticleDOI
13 Oct 2005-Nature
TL;DR: This work explores the known genome-wide interaction network to identify significant functional modules perturbed in response to an inflammatory stimulus and reveals that the human blood leukocyte response to acute systemic inflammation includes the transient dysregulation of leukocytes bioenergetics and modulation of translational machinery.
Abstract: Oligonucleotide and complementary DNA microarrays are being used to subclassify histologically similar tumours, monitor disease progress, and individualize treatment regimens1,2,3,4,5. However, extracting new biological insight from high-throughput genomic studies of human diseases is a challenge, limited by difficulties in recognizing and evaluating relevant biological processes from huge quantities of experimental data. Here we present a structured network knowledge-base approach to analyse genome-wide transcriptional responses in the context of known functional interrelationships among proteins, small molecules and phenotypes. This approach was used to analyse changes in blood leukocyte gene expression patterns in human subjects receiving an inflammatory stimulus (bacterial endotoxin). We explore the known genome-wide interaction network to identify significant functional modules perturbed in response to this stimulus. Our analysis reveals that the human blood leukocyte response to acute systemic inflammation includes the transient dysregulation of leukocyte bioenergetics and modulation of translational machinery. These findings provide insight into the regulation of global leukocyte activities as they relate to innate immune system tolerance and increased susceptibility to infection in humans.

1,397 citations


Proceedings ArticleDOI
25 May 2005
TL;DR: This paper proposes four different jamming attack models that can be used by an adversary to disable the operation of a wireless network, and evaluates their effectiveness in terms of how each method affects the ability of a Wireless node to send and receive packets.
Abstract: Wireless networks are built upon a shared medium that makes it easy for adversaries to launch jamming-style attacks. These attacks can be easily accomplished by an adversary emitting radio frequency signals that do not follow an underlying MAC protocol. Jamming attacks can severely interfere with the normal operation of wireless networks and, consequently, mechanisms are needed that can cope with jamming attacks. In this paper, we examine radio interference attacks from both sides of the issue: first, we study the problem of conducting radio interference attacks on wireless networks, and second we examine the critical issue of diagnosing the presence of jamming attacks. Specifically, we propose four different jamming attack models that can be used by an adversary to disable the operation of a wireless network, and evaluate their effectiveness in terms of how each method affects the ability of a wireless node to send and receive packets. We then discuss different measurements that serve as the basis for detecting a jamming attack, and explore scenarios where each measurement by itself is not enough to reliably classify the presence of a jamming attack. In particular, we observe that signal strength and carrier sensing time are unable to conclusively detect the presence of a jammer. Further, we observe that although by using packet delivery ratio we may differentiate between congested and jammed scenarios, we are nonetheless unable to conclude whether poor link utility is due to jamming or the mobility of nodes. The fact that no single measurement is sufficient for reliably classifying the presence of a jammer is an important observation, and necessitates the development of enhanced detection schemes that can remove ambiguity when detecting a jammer. To address this need, we propose two enhanced detection protocols that employ consistency checking. The first scheme employs signal strength measurements as a reactive consistency check for poor packet delivery ratios, while the second scheme employs location information to serve as the consistency check. Throughout our discussions, we examine the feasibility and effectiveness of jamming attacks and detection schemes using the MICA2 Mote platform.

1,350 citations


Journal ArticleDOI
TL;DR: Forest transitions have occurred in two, sometimes overlapping circumstances: economic development and scarcity of forest products have prompted governments and landowners to plant trees in some fields as mentioned in this paper, and these transitions do little to conserve biodiversity, but they do sequester carbon and conserve soil, so governments should place a high priority on promoting them.
Abstract: Places experience forest transitions when declines in forest cover cease and recoveries in forest cover begin. Forest transitions have occurred in two, sometimes overlapping circumstances. In some places economic development has created enough non-farm jobs to pull farmers off of the land, thereby inducing the spontaneous regeneration of forests in old fields. In other places a scarcity of forest products has prompted governments and landowners to plant trees in some fields. The transitions do little to conserve biodiversity, but they do sequester carbon and conserve soil, so governments should place a high priority on promoting them. C 2005 Elsevier Ltd. All rights reserved.

Journal ArticleDOI
TL;DR: New views on how regulation of the migration of inflammatory cells to sites of tissue damage might guide therapeutic strategies for modulating the inflammatory response are discussed.

Journal ArticleDOI
TL;DR: Drug metabolizing enzymes (DMEs) play central roles in the metabolism, elimination and detoxification of xenobiotics and drugs introduced into the human body, and play crucial roles in response to many polycyclic aromatic hydrocarbon receptors and excretion.
Abstract: Drug metabolizing enzymes (DMEs) play central roles in the metabolism, elimination and detoxification of xenobiotics and drugs introduced into the human body. Most of the tissues and organs in our body are well equipped with diverse and various DMEs including phase I, phase II metabolizing enzymes and phase III transporters, which are present in abundance either at the basal unstimulated level, and/or are inducible at elevated level after exposure to xenobiotics. Recently, many important advances have been made in the mechanisms that regulate the expression of these drug metabolism genes. Various nuclear receptors including the aryl hydrocarbon receptor (AhR), orphan nuclear receptors, and nuclear factor-erythoroid 2 p45-related factor 2 (Nrf2) have been shown to be the key mediators of drug-induced changes in phase I, phase II metabolizing enzymes as well as phase III transporters involved in efflux mechanisms. For instance, the expression of CYP1 genes can be induced by AhR, which dimerizes with the AhR nuclear translocator (Arnt), in response to many polycyclic aromatic hydrocarbon (PAHs). Similarly, the steroid family of orphan nuclear receptors, the constitutive androstane receptor (CAR) and pregnane X receptor (PXR), both heterodimerize with the retinoid X receptor (RXR), are shown to transcriptionally activate the promoters of CYP2B and CYP3A gene expression by xenobiotics such as phenobarbital-like compounds (CAR) and dexamethasone and rifampin-type of agents (PXR). The peroxisome proliferator activated receptor (PPAR), which is one of the first characterized members of the nuclear hormone receptor, also dimerizes with RXR and has been shown to be activated by lipid lowering agent fibrate-type of compounds leading to transcriptional activation of the promoters on CYP4A gene. CYP7A was recognized as the first target gene of the liver X receptor (LXR), in which the elimination of cholesterol depends on CYP7A. Farnesoid X receptor (FXR) was identified as a bile acid receptor, and its activation results in the inhibition of hepatic acid biosynthesis and increased transport of bile acids from intestinal lumen to the liver, and CYP7A is one of its target genes. The transcriptional activation by these receptors upon binding to the promoters located at the 5-flanking region of these CYP genes generally leads to the induction of their mRNA gene expression. The physiological and the pharmacological implications of common partner of RXR for CAR, PXR, PPAR, LXR and FXR receptors largely remain unknown and are under intense investigations. For the phase II DMEs, phase II gene inducers such as the phenolic compounds butylated hydroxyanisol (BHA),tert-butylhydroquinone (tBHQ), green tea polyphenol (GTP), (-)-epigallocatechin-3-gallate (EGCG) and the isothiocyanates (PEITC, sulforaphane) generally appear to be electrophiles. They generally possess electrophilic-mediated stress response, resulting in the activation of bZIP transcription factors Nrf2 which dimerizes with Mafs and binds to the antioxidant/electrophile response element (ARE/EpRE) promoter, which is located in many phase II DMEs as well as many cellular defensive enzymes such as heme oxygenase-1 (HO-1), with the subsequent induction of the expression of these genes. Phase III transporters, for example, P-glycoprotein (P-gp), multidrug resistance-associated proteins (MRPs), and organic anion transporting polypeptide 2 (OATP2) are expressed in many tissues such as the liver, intestine, kidney, and brain, and play crucial roles in drug absorption, distribution, and excretion. The orphan nuclear receptors PXR and CAR have been shown to be involved in the regulation of these transporters. Along with phase I and phase II enzyme induction, pretreatment with several kinds of inducers has been shown to alter the expression of phase III transporters, and alter the excretion of xenobiotics, which implies that phase III transporters may also be similarly regulated in a coordinated fashion, and provides an important mean to protect the body from xenobiotics insults. It appears that in general, exposure to phase I, phase II and phase III gene inducers may trigger cellular “stress” response leading to the increase in their gene expression, which ultimately enhance the elimination and clearance of these xenobiotics and/or other “cellular stresses” including harmful reactive intermediates such as reactive oxygen species (ROS), so that the body will remove the “stress” expeditiously. Consequently, this homeostatic response of the body plays a central role in the protection of the body against “environmental” insults such as those elicited by exposure to xenobiotics.

Journal ArticleDOI
25 Aug 2005-Nature
TL;DR: It is shown that subinhibitory concentrations of aminoglycoside antibiotics induce biofilm formation in P. aeruginosa and Escherichia coli, and the molecular basis of this response includes alterations in the level of c-di-GMP.
Abstract: Biofilms are adherent aggregates of bacterial cells that form on biotic and abiotic surfaces, including human tissues. Biofilms resist antibiotic treatment and contribute to bacterial persistence in chronic infections. Hence, the elucidation of the mechanisms by which biofilms are formed may assist in the treatment of chronic infections, such as Pseudomonas aeruginosa in the airways of patients with cystic fibrosis. Here we show that subinhibitory concentrations of aminoglycoside antibiotics induce biofilm formation in P. aeruginosa and Escherichia coli. In P. aeruginosa, a gene, which we designated aminoglycoside response regulator (arr), was essential for this induction and contributed to biofilm-specific aminoglycoside resistance. The arr gene is predicted to encode an inner-membrane phosphodiesterase whose substrate is cyclic di-guanosine monophosphate (c-di-GMP)-a bacterial second messenger that regulates cell surface adhesiveness. We found that membranes from arr mutants had diminished c-di-GMP phosphodiesterase activity, and P. aeruginosa cells with a mutation changing a predicted catalytic residue of Arr were defective in their biofilm response to tobramycin. Furthermore, tobramycin-inducible biofilm formation was inhibited by exogenous GTP, which is known to inhibit c-di-GMP phosphodiesterase activity. Our results demonstrate that biofilm formation can be a specific, defensive reaction to the presence of antibiotics, and indicate that the molecular basis of this response includes alterations in the level of c-di-GMP.

Journal ArticleDOI
TL;DR: It is found that the level of subsidiary R&D depends on MNE group‐level and subsidiary‐level characteristics as well as locational factors, and that MNEs that grow through acquisition have more inter‐subsidiary R &D diversity.
Abstract: The determinants of R&D intensity differ between subsidiaries in a multinational enterprise (MNE). Previous literature suggests that whether a subsidiary achieves a competence-creating output mandate depends on the qualities of its location. R&D strategies in competence-creating subsidiaries are supply-driven while those in purely competence-exploiting subsidiaries are demand-driven. Using data on U.K. subsidiaries of non-U.K. MNEs, we find that the level of subsidiary R&D depends on MNE group-level and subsidiary-level characteristics as well as locational factors. The R&D of mandated subsidiaries rises with acquisition, but for non-mandated subsidiaries R&D falls upon acquisition. MNEs that grow through acquisition have more inter-subsidiary R&D diversity. Copyright © 2005 John Wiley & Sons, Ltd.

Journal ArticleDOI
TL;DR: An overview of the IMPACT molecular mechanics program is provided with an emphasis on recent developments and a description of its current functionality and a status report for the fixed charge and polarizable force fields is included.
Abstract: We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.

Journal ArticleDOI
TL;DR: In this paper, the ground-state structural and electronic properties of ferroelectric are calculated using density functional theory within the local spin-density approximation (LSDA) and the $\mathrm{LSDA}+U$ method.
Abstract: The ground-state structural and electronic properties of ferroelectric $\mathrm{Bi}\mathrm{Fe}{\mathrm{O}}_{3}$ are calculated using density functional theory within the local spin-density approximation (LSDA) and the $\mathrm{LSDA}+U$ method. The crystal structure is computed to be rhombohedral with space group $R3c$, and the electronic structure is found to be insulating and antiferromagnetic, both in excellent agreement with available experiments. A large ferroelectric polarization of $90--100\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{C}∕{\mathrm{cm}}^{2}$ is predicted, consistent with the large atomic displacements in the ferroelectric phase and with recent experimental reports, but differing by an order of magnitude from early experiments. One possible explanation is that the latter may have suffered from large leakage currents. However, both past and contemporary measurements are shown to be consistent with the modern theory of polarization, suggesting that the range of reported polarizations may instead correspond to distinct switching paths in structural space. Modern measurements on well-characterized bulk samples are required to confirm this interpretation.

Journal ArticleDOI
TL;DR: Clinically significant RLS is common (prevalence, 2.7%), is underdiagnosed, and significantly affects sleep and quality of life.
Abstract: Background Restless legs syndrome (RLS), a common sensorimotor disorder, has a wide range of severity from merely annoying to affecting sleep and quality of life severely enough to warrant medical treatment. Previous epidemiological studies, however, have failed to determine the prevalence of those with clinically significant RLS symptoms and to examine the life effects and medical experiences of this group. Methods A total of 16 202 adults (aged ≥18 years) were interviewed using validated diagnostic questions to determine the presence, frequency, and severity of RLS symptoms; respondents reporting RLS symptoms were asked about medical diagnoses and the impact of the disorder and completed the Short Form-36 Health Survey (SF-36). Criteria determined by RLS experts for medically significant RLS (frequency at least twice a week, distress at least moderate) defined “RLS sufferers” as a group most likely to warrant medical treatment. Results In all, 15 391 fully completed questionnaires were obtained; in the past year, RLS symptoms of any frequency were reported by 1114 (7.2%). Symptoms occurred at least weekly for 773 respondents (5.0%); they occurred at least 2 times per week and were reported as moderately or severely distressing by 416 (2.7%). Of those 416 (termed RLS sufferers), 337 (81.0%) reported discussing their symptoms with a primary care physician, and only 21 (6.2%) were given a diagnosis of RLS. The SF-36 scores for RLS sufferers were significantly below population norms, matching those of patients with other chronic medical conditions. Conclusion Clinically significant RLS is common (prevalence, 2.7%), is underdiagnosed, and significantly affects sleep and quality of life.

Journal ArticleDOI
11 Feb 2005-Science
TL;DR: It is shown that plant microRNAs (miRNAs) have a naturally occurring methyl group on the ribose of the last nucleotide, a new and crucial step in plant miRNA biogenesis and have profound implications in the function of miRNAs.
Abstract: Methylation on the base or the ribose is prevalent in eukaryotic ribosomal RNAs (rRNAs) and is thought to be crucial for ribosome biogenesis and function. Artificially introduced 2'-O-methyl groups in small interfering RNAs (siRNAs) can stabilize siRNAs in serum without affecting their activities in RNA interference in mammalian cells. Here, we show that plant microRNAs (miRNAs) have a naturally occurring methyl group on the ribose of the last nucleotide. Whereas methylation of rRNAs depends on guide RNAs, the methyltransferase protein HEN1 is sufficient to methylate miRNA/miRNA* duplexes. Our studies uncover a new and crucial step in plant miRNA biogenesis and have profound implications in the function of miRNAs.

Journal ArticleDOI
TL;DR: 35 years of empirical research on teacher expectations justifies the following conclusions: self-fulfilling prophecies in the classroom do occur, but these effects are typically small, they do not accumulate greatly across perceivers or over time, and they may be more likely to dissipate than accumulate.
Abstract: This article shows that 35 years of empirical research on teacher expectations justifies the following conclusions: (a) Self-fulfilling prophecies in the classroom do occur, but these effects are typically small, they do not accumulate greatly across perceivers or over time, and they may be more likely to dissipate than accumulate; (b) powerful self-fulfilling prophecies may selectively occur among students from stigmatized social groups; (c) whether self-fulfilling prophecies affect intelligence, and whether they in general do more harm than good, remains unclear, and (d) teacher expectations may predict student outcomes more because these expectations are accurate than because they are self-fulfilling. Implications for future research, the role of self-fulfilling prophecies in social problems, and perspectives emphasizing the power of erroneous beliefs to create social reality are discussed.

Journal ArticleDOI
TL;DR: A growing body of evidence suggests that biological mechanisms underlie a bidirectional link between mood disorders and many medical illnesses and there is evidence to suggest that mood disorders affect the course of medical illnesses.

Journal ArticleDOI
TL;DR: In this paper, a comparison of eight iron experiments shows that maximum Chl a, the maximum DIC removal, and the overall DIC/Fe efficiency all scale inversely with depth of the wind mixed layer (WML) defining the light environment.
Abstract: Comparison of eight iron experiments shows that maximum Chl a, the maximum DIC removal, and the overall DIC/Fe efficiency all scale inversely with depth of the wind mixed layer (WML) defining the light environment. Moreover, lateral patch dilution, sea surface irradiance, temperature, and grazing play additional roles. The Southern Ocean experiments were most influenced by very deep WMLs. In contrast, light conditions were most favorable during SEEDS and SERIES as well as during IronEx-2. The two extreme experiments, EisenEx and SEEDS, can be linked via EisenEx bottle incubations with shallower simulated WML depth. Large diatoms always benefit the most from Fe addition, where a remarkably small group of thriving diatom species is dominated by universal response of Pseudo-nitzschia spp. Significant response of these moderate (10–30 μm), medium (30–60 μm), and large (>60 μm) diatoms is consistent with growth physiology determined for single species in natural seawater. The minimum level of “dissolved” Fe (filtrate < 0.2 μm) maintained during an experiment determines the dominant diatom size class. However, this is further complicated by continuous transfer of original truly dissolved reduced Fe(II) into the colloidal pool, which may constitute some 75% of the “dissolved” pool. Depth integration of carbon inventory changes partly compensates the adverse effects of a deep WML due to its greater integration depths, decreasing the differences in responses between the eight experiments. About half of depth-integrated overall primary productivity is reflected in a decrease of DIC. The overall C/Fe efficiency of DIC uptake is DIC/Fe ∼ 5600 for all eight experiments. The increase of particulate organic carbon is about a quarter of the primary production, suggesting food web losses for the other three quarters. Replenishment of DIC by air/sea exchange tends to be a minor few percent of primary CO2 fixation but will continue well after observations have stopped. Export of carbon into deeper waters is difficult to assess and is until now firmly proven and quite modest in only two experiments.

Journal ArticleDOI
TL;DR: A large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenyation.
Abstract: mRNA polyadenylation is a critical cellular process in eukaryotes. It involves 3' end cleavage of nascent mRNAs and addition of the poly(A) tail, which plays important roles in many aspects of the cellular metabolism of mRNA. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. In this study, we surveyed genome regions containing cleavage sites [herein called poly(A) sites], for 13,942 human and 11,155 mouse genes. We found that a great proportion of human and mouse genes have alternative polyadenylation ( approximately 54 and 32%, respectively). The conservation of alternative polyadenylation type or polyadenylation configuration between human and mouse orthologs is statistically significant, indicating that alternative polyadenylation is widely employed by these two species to produce alternative gene transcripts. Genes belonging to several functional groups, indicated by their Gene Ontology annotations, are biased with respect to polyadenylation configuration. Many poly(A) sites harbor multiple cleavage sites (51.25% human and 46.97% mouse sites), leading to heterogeneous 3' end formation for transcripts. This implies that the cleavage process of polyadenylation is largely imprecise. Different types of poly(A) sites, with regard to their relative locations in a gene, are found to have distinct nucleotide composition in surrounding genomic regions. This large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenylation.

Journal ArticleDOI
TL;DR: The current status of supermassive black hole research, as seen from a purely observational standpoint, can be found in this article, where the authors present a review of the state of the art.
Abstract: This review discusses the current status of supermassive black hole research, as seen from a purely observational standpoint Since the early ‘90s, rapid technological advances, most notably the launch of the Hubble Space Telescope, the commissioning of the VLBA and improvements in near-infrared speckle imaging techniques, have not only given us incontrovertible proof of the existence of supermassive black holes, but have unveiled fundamental connections between the mass of the central singularity and the global properties of the host galaxy It is thanks to these observations that we are now, for the first time, in a position to understand the origin, evolution and cosmic relevance of these fascinating objects

Journal ArticleDOI
TL;DR: A new identification system for a trimer using three Arabic numerals, based on the alpha, beta and gamma chain numbers is introduced, which is introduced for laminin trimers.

Journal ArticleDOI
TL;DR: The results suggest that romantic love uses subcortical reward and motivation systems to focus on a specific individual, that limbic cortical regions process individual emotion factors, and that there is localization heterogeneity for reward functions in the human brain.
Abstract: Early-stage romantic love can induce euphoria, is a cross-cultural phenomenon, and is possibly a developed form of a mammalian drive to pursue preferred mates. It has an important influence on social behaviors that have reproductive and genetic consequences. To determine which reward and motivation systems may be involved, we used functional magnetic resonance imaging and studied 10 women and 7 men who were intensely "in love" from 1 to 17 mo. Participants alternately viewed a photograph of their beloved and a photograph of a familiar individual, interspersed with a distraction-attention task. Group activation specific to the beloved under the two control conditions occurred in dopamine-rich areas associated with mammalian reward and motivation, namely the right ventral tegmental area and the right postero-dorsal body and medial caudate nucleus. Activation in the left ventral tegmental area was correlated with facial attractiveness scores. Activation in the right anteromedial caudate was correlated with questionnaire scores that quantified intensity of romantic passion. In the left insula-putamen-globus pallidus, activation correlated with trait affect intensity. The results suggest that romantic love uses subcortical reward and motivation systems to focus on a specific individual, that limbic cortical regions process individual emotion factors, and that there is localization heterogeneity for reward functions in the human brain.

Journal ArticleDOI
TL;DR: The conclusion follows that the liquid-like morphogenetic cell and tissue rearrangements of cell sorting, tissue spreading and segregation represent self-assembly processes guided by the diminution of adhesive-free energy as cells tend to maximize their mutual binding.

Journal ArticleDOI
TL;DR: This article discusses how TDDFT is much broader in scope, and yields predictions for many more properties, and discusses some of the challenges involved in making accurate predictions for these properties.
Abstract: Time-dependent density functional theory (TDDFT) is presently enjoying enormous popularity in quantum chemistry, as a useful tool for extracting electronic excited state energies. This article discusses how TDDFT is much broader in scope, and yields predictions for many more properties. We discuss some of the challenges involved in making accurate predictions for these properties.

Journal ArticleDOI
TL;DR: In this article, the authors review the mechanistic basis and assess the evidence that feedback occurs between plants and the soil and find that the evidence of feedback is strongest for plants growing in extreme environments and for plant-mutualist or plant-enemy interactions.
Abstract: ▪ Abstract Feedback between plants and the soil is frequently invoked on the basis of evidence of mutual effects. Feedback can operate through pathways involving soil physical properties, chemical and biogeochemical properties and processes, and biological properties, including the community composition of the microbiota and soil fauna. For each pathway, we review the mechanistic basis and assess the evidence that feedback occurs. We suggest that several properties of feedback systems (for example, their complexity, specificity, and strength relative to other ecological factors, as well as the temporal and spatial scales over which they operate) be considered. We find that the evidence of feedback is strongest for plants growing in extreme environments and for plant-mutualist or plant-enemy interactions. We conclude with recommendations for a more critical appraisal of feedback and for new directions of research. Let us not make arbitrary conjectures about the greatest matters. Heraclitus (1)

Journal ArticleDOI
TL;DR: This account incorporates recent ideas about emulators in the brain-mental simulations that run in parallel to the external events they simulate-to provide a mechanism by which motoric involvement could contribute to perception.
Abstract: Perceiving other people's behaviors activates imitative motor plans in the perceiver, but there is disagreement as to the function of this activation. In contrast to other recent proposals (e.g., that it subserves overt imitation, identification and understanding of actions, or working memory), here it is argued that imitative motor activation feeds back into the perceptual processing of conspecifics' behaviors, generating top-down expectations and predictions of the unfolding action. Furthermore, this account incorporates recent ideas about emulators in the brain-mental simulations that run in parallel to the external events they simulate-to provide a mechanism by which motoric involvement could contribute to perception. Evidence from a variety of literatures is brought to bear to support this account of perceiving human body movement.