Últimos itens adicionados do Acervo: Proceedings Nature

Nature é uma das mais prestigiosas e antigas revistas científicas do mundo: sua primeira edição é de 4 de novembro de 1869. Entre as inúmeras descobertas científicas publicadas na Nature estão a dos raios X, da estrutura em dupla hélice do ADN e o buraco na camada de ozônio.

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‣ Detecting differential usage of exons from RNA-Seq data

Simon Anders; Alejandro Reyes; Wolfgang Huber
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package.

‣ Donor mesenchymal stem cells trigger chronic graft-versus-host disease following minor antigen-mismatched bone marrow transplantation

Yoko Ogawa; Satoru Morikawa; Hideyuki Okano; Yo Mabuchi; Sadafumi Suzuki; Tomonori Yaguchi; Saori Yaguchi; Takaaki Inaba; Shinichiro Okamoto; Yutaka Kawakami; Kazuo Tsubota; Shigeto Shimmura; Yumi Matsuzaki
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Chronic graft-versus-host disease (cGVHD) is a complication after minor antigen mismatched bone marrow transplantation (BMT) characterized by an autoimmune-type reaction in various organs. Aberration in T cell regulation is involved, with donor mesenchymal stem cells (MSCs) playing a possible role in immunomodulation. In a minor-antigen mismatched mouse BMT model, transplantation of mismatched, but not syngeneic MSCs triggered the onset of cGVHD, and was associated with fibrosis, increased IL-6 secretion, decreased Foxp3+ regulatory T cells and increased Th17 in the peripheral blood. Mismatched MSCs alone were sufficient to induce cGVHD, while removal of donor MSCs rescued mice from cGVHD. RAG2 knockout recipient mice did not suffer cGVHD, indicating that host T cells were involved. Residual host-derived T cells were significantly higher in cGVHD patients compared to non-cGVHD patients. In conclusion, donor MSCs react with residual host T cells to trigger the progression of cGVHD.

‣ Historical temporal trends in groundwater levels from British Columbia, Canada

Sierra Rayne; Kaya Forest
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
A time trend study of groundwater monitoring well levels was conducted in British Columbia, Canada. Trend data was available for a total of 210 groundwater monitoring well stations throughout the province with end-of-month water levels over the period of record. Significant temporal trends in groundwater levels were found at 67 stations (40.4% of all stations amenable to statistical examination, and 31.9% of all available stations). Of these 67 stations, 10 had increasing groundwater level trends and the remaining 57 had declining groundwater level trends. Thus, 34.3% of stations with a sufficiently long time series for analysis displayed declining groundwater level trends, while 6.0% have increasing trends, and 59.6% of these stations appear to have no significant temporal variation in groundwater levels. Geographic distinctions in groundwater level time trends are difficult to make owing to the unbalanced distribution of monitoring sites throughout the province. Based on percentages of total stations with a sufficiently long monitoring record for statistical analysis, it appears that the semi-arid Thompson/Nicola and Okanagan zones of British Columbia are most likely to have declining groundwater levels. Overall, a substantial proportion of groundwater monitoring wells in British Columbia - which have been operated with varying record lengths dating from recent installations to sites with records back to the 1950s - are exhibiting declining levels. At a significant number of other sites in the monitoring network...

‣ Oxidative Stress and Mitochondrial Injury in Chronic Multisymptom Conditions: From Gulf War Illness to Autism Spectrum Disorder

Beatrice A. Golomb
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Background: Overlapping chronic multisymptom illnesses (CMI) include Chronic Fatigue Syndrome (CFS), fibromyalgia, irritable bowel syndrome, multiple chemical sensitivity, and Gulf War illness (GWI), and subsets of autism spectrum disorder (ASD). GWI entails a more circumscribed set of experiences that may provide insights of relevance to overlapping conditions. Objectives: To consolidate evidence regarding a role for oxidative stress and mitochondrial dysfunction (OSMD), as primary mediators in CMI, using GWI as a departure point. Methods: Exposure relations, character, timecourse and multiplicity of symptoms, and objective correlates of GWI are compared to expectation for OSMD. Objective correlates of OSMD in GWI and overlapping conditions are examined. Discussion: OSMD is an expected consequence of known GWI exposures; is compatible with symptom characteristics observed; and accords with objective markers and health conditions linked to GWI, extending to autoimmune disease and infection. Emergent triangulating evidence directly supports OSMD in multisymptom “overlap” CMI conditions, with similarities to, and diagnosed at elevated rates in, GWI, suggesting a common role in each. Conclusions: GWI is compatible with a paradigm by which uncompensated exposure to oxidative/nitrative stressors accompanies and triggers mitochondrial dysfunction...

‣ PROM Khad an efficient source of P to replace the costly chemical Phosphatic Fertilizer

DMR Sekhar; MK Katewa; MS Shaktawat
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The subsidy on phosphate fertilizers rose to an unacceptable level while alternate cost effective technologies are available. Fertilizer industry needs to develop innovative products using the recent advances in the agricultural sciences. Manure producing industries to be supplied rock phosphate mineral (at subsidized costs) as being supplied to chemical fertilizers industries suitable to produce PROM Khad (Phosphate Rich Organic Manure).

‣ Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates

Rodrick Wallace
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a 'biological renormalization' perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.

‣ Using TreeBASE from R

Carl Boettiger
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
I introduce an R package allowing programmatic access to the phylogenetic data in the TreeBASE archive and highlight why this is important.

‣ The Evolutionary Seesaw: Origins of biodiversity?

Carl Boettiger
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
I consider the problem of evolutionary branching in adaptive dynamics without applying the limits of separation of timescales between ecological and evolutionary processes. I derive expressions for the waiting time for a branching event to occur and survive in terms of both ecological and evolutionary parameters, and show how demographic stochasticity alone can result in the frequent failure of adaptive branching.

‣ Integrating Open Lab Notebooks with Online Databases

Carl Boettiger
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
My slides from a presentation and panel discussion on integrating open lab notebooks with online databases. A video archive of the presentation is available here: http://vimeo.com/20100632

‣ Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_

Hoi Shan Kwan; Chun Hang Au; Man Chun Wong; Jing Qin; Iris Sze Wai Kwok; Winnie Wing Yan Chum; Pui Ying Yip; Kin Sing Wong; Lei Li; Qian Li Huang; Wen Yan Nong
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups of _L. edodes_ genome sequence compared across genomes of several fungi including mushrooms identified gene families unique to mushroom-forming fungi. We used a mapping population of haploid basidiospores of dikaryon L54 for genetic linkage analysis. High-quality variations such as single nucleotide polymorphisms, insertions, and deletions of the mapping population formed a high-density genetic linkage map. We compared the linkage map to the _L. edodes_ L54A genome sequence and located selected quantitative trait loci. The Shiitake community will benefit from these resources for genetic studies and breeding.

‣ Limits to the detection of early warning signals of population collapse

Carl Boettiger; Alan Hastings
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Background/Question/Methods The recog­ni­tion that ecosys­tems can undergo sud­den shifts to alter­nate, less desir­able sta­ble states has led to the desire to iden­tify early warn­ing signs of these impend­ing col­lapses. This search has been moti­vated by the math­e­mat­ics of bifur­ca­tions, in which sud­den shifts result not from direct per­tur­ba­tions to the state (i.e. the pop­u­la­tion abun­dance, through mech­a­nisms such as over-harvesting) but to a slowly chang­ing para­me­ter that impacts the sys­tem sta­bil­ity. While these col­lapses can­not be antic­i­pated by observ­ing only the mean dynam­ics (as described by a deter­min­is­tic model), signs of the impend­ing col­lapse are expressed in the ran­dom per­tur­ba­tions, or noise, inher­ent in real sys­tems. The math­e­mat­i­cal the­ory of early warn­ing signs exploits this fact by seek­ing to detect pat­terns such as “crit­i­cal slow­ing down” of these per­tur­ba­tions due to the grad­ual loss of sta­bil­ity which leads to a bifurcation. While much atten­tion has been given to empha­siz­ing the exis­tence both of sud­den col­lapses and of signs of crit­i­cal slow­ing down...

‣ Deterministic Separation of Cancer Cells from Blood at 10 mL/min

Kevin Loutherback; Joseph D'Silva; Liyu Liu; Amy Wu; Robert Austin; James Sturm
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Circulating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate, propagate and characterize viable CTCs and clusters. Here, we present a microfluidic device for mL/min flow rate, continuous-flow capture of viable CTCs from blood using deterministic lateral displacement arrays. We show here that a deterministic bump array can be designed such that it will isolate with efficiency greater than 85% CTCs over a large range in sizes from millimeter volume clinical blood samples in minutes, with no effect on cell vitality so that further culturing and analysis of the cells can be carried out.

‣ Universality of a mesenchymal transition signature in invasive solid cancers

Dimitris Anastassiou
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
In this brief communication, additional computational validation is provided consistent with the unifying hypothesis that a shared biological mechanism of mesenchymal transition, reflected by a precise gene expression signature, may be present in all types of solid cancers when they reach a particular stage of invasiveness.

‣ Some Computational Aspects of Essential Properties of Evolution and Life

Hector Zenil; James A. R. Marshall
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
While evolution has inspired algorithmic methods of heuristic optimisation, little has been done in the way of using concepts of computation to advance our understanding of salient aspects of biological evolution. We argue that under reasonable assumptions, interesting conclusions can be drawn that are of relevance to behavioural evolution. We will focus on two important features of life--robustness and fitness optimisation--which, we will argue, are related to algorithmic probability and to the thermodynamics of computation, subjects that may be capable of explaining and modelling key features of living organisms, and which can be used in understanding and formulating algorithms of evolutionary computation.

‣ Non-viral delivery and optimized optogenetic stimulation of retinal ganglion cells led to behavioral restoration of vision

Ling Gu; Shivaranjani Shivalingaiah; Mathew Ficinski; Edward Wong; Samarendra Mohanty
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Stimulation of retinal neurons using optogenetics via use of chanelrhodopsin-2 (ChR2) has opened up a new direction for restoration of vision for treatment of retinitis pigmentosa (RP). Here, we report non-viral in-vivo electroporation of degenerated retina of adult RP-mice with ChR2-plasmids and subsequent in-vivo imaging of retina to confirm expression. Further, we demonstrate that in addition to efficient non-viral delivery of ChR2 to a specific retinal layer, threshold level of stimulation light needs to be delivered onto the retina for achieving successful behavioral outcome. Measurement of intensity of light reaching the retina of RP-mouse models along with geometrical optics simulation of light propagation in the eye is reported in order to determine the stimulating source position for optimal light delivery to the retina. The light-guided navigation of mice with ChR2 expressing retinal ganglion cells was found to be significantly improved over a long distance in correlation with stimulation intensity.

‣ Statistical analysis of network data and evolution on GPUs: High-performance statistical computing

Thomas W. Thorne; Michael P. H. Stumpf
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man's parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent developments in the generation of random numbers that address the specific requirements posed by GPUs and high-performance computing needs.

‣ In-group/out-group bias in contagious yawning

J. Ryan Porter; Steven M. Platek
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Bias for an in-group is a social phenomenon characterized by an affinity for one’s in-group over a perceived out-group. Activation in the amygdala, which is implicated in social and emotional processes, is increased when humans view other-race faces. This increase in activation is associated with implicit racial bias as indicated by scores on an implicit attitude test. Contagious yawning is a social process that appears to subserve empathic processes enabling the inferential modeling of the mental states of others and is exhibited in few species other than humans, including chimpanzees (Pan troglodytes), stumptail macaques (Macaca arctoides), dogs (Canis familiaris), and budgerigars (Melopsittacus undulatus). Despite these comparative data, little research has investigated intra-species variation in contagious yawning.

‣ A quantitative model for efficient construction of lentiviral vectors with a unique clone site

Gang Zhang; Anurag Tandon
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Lentiviral vectors (LVs) were a powerful tool for transgene expression in vivo and in vitro. However, the construction of LVs is of low efficiency, due to the large sizes and lack of proper clone sites. Therefore, it is critical to develop efficient strategies for cloning LVs. Here, we reported a combinatorial strategy to efficiently construct LVs using EGFP, hPlk2 wild type (WT) and mutant genes as inserts. Firstly, site-directed mutagenesis (SDM) was performed to create BamH I site for the inserts; secondly, pWPI LV was dephosphorylated after BamH I digestion; finally, the amounts and ratios of the insert and vector DNA were optimized to increase monomeric ligation. Our results showed that the total percentage of positive clones was approximately 51.3%±15.2%. Using this model, almost all the vectors could be constructed through two or three minipreps, therefore, our study provided an efficient quantitative model for constructing large-size vectors. This paper has since been published in Scientific Reports: Zhang, G. & Tandon, A. Quantitative assessment on the cloning efficiencies of lentiviral transfer vectors with a unique clone site. Sci. Rep. 2, 415; DOI:10.1038/srep00415 (2012)

‣ Range of motion in intervertebral joints: why we don’t trust DinoMorph

Michael P. Taylor
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Attempts to quantitatively reconstruct the range of motion of sauropod necks are intrinsically flawed because of ubiquitous distortion in preserved cervical vertebrae. This is true even for specimens that are usually considered particularly well preserved, such as the Carnegie Diplodocus and the Berlin Giraffatitan.

‣ Quantization makes relativity compatible with superluminal phenomena

Qi-Ren Zhang
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
News shocked the physicist society that neutrinos may move faster than light. Most physicists affirm that this is impossible, according to the well-established relativity. Some try to find a new theory other than relativity to explain the phenomena. In the following we show it may be explained within relativity, if the quantum theory is also taken into account.