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"Fodor"
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Ethnic subjectivity in intergenerational memory narratives : politics of the untold
\"In this interdisciplinary study, Mâonika Fodor explores how intergenerational memory narratives embedded in own stories impact ethnic subjectivity construction. Working with thematically selected life experiences from interviews conducted with second-and later-generation European-Americans, Fodor demonstrates how the storytellers position themselves in a range of social, cultural, and political discourses to claim or disclaim ethnicity as part of their subjectivity. Tying narrative content, structural, and performance analysis to the sociological and sociolinguistic concepts of \"symbolic capital\" and \"investment,\" Fodor unpacks the changing levels of identifying with one's ancestral ethnic heritage and its potential to carry meaning for later generation descendants. In doing so, she reveals the shared features of identification among individuals through narrative meaning-making, which may be the basis of real or imagined, heterolocal discourse community formation and sustained ethnic subjectivity. The narrative analysis demonstrates how the cohesive force among members of the community is the shared knowledge of story frames and the personalized retelling of these. Ethnic Subjectivity in Intergenerational Memory Narratives draws on inherited, often moving, personal experiences that offers new insights into the so far largely unexplored terrain of the narrative structure of intergenerationally transferred memory retellings, that will be of great interest to students and scholars of ethnic studies, migration and identity studies\"-- Provided by publisher.
Book
Combinatorial labeling of single cells for gene expression cytometry
To understand why cells differ from each other, we need to understand which genes are transcribed at a single-cell level. Several methods measure messenger RNA (mRNA) expression in single cells, but most are limited to relatively low numbers of cells or genes. Fan et al. labeled each mRNA molecule in a cell with both a cellular barcode and a molecular barcode. Further analysis did not then require single-cell technologies. Instead, the labeled mRNA from all cells was pooled, amplified, and sequenced, and the gene expression profile of individual cells was reconstructed based on the barcodes. The technique successfully revealed heterogeneity across several thousand blood cells. Science , this issue 10.1126/science.1258367 A simple approach allows gene expression analysis of a large collection of cells by stochastic barcoding of cells and sequencing. We present a technically simple approach for gene expression cytometry combining next-generation sequencing with stochastic barcoding of single cells. A combinatorial library of beads bearing cell- and molecular-barcoding capture probes is used to uniquely label transcripts and reconstruct the digital gene expression profile of thousands of individual cells in a single experiment without the need for robotics or automation. We applied the technology to dissect the human hematopoietic system and to characterize heterogeneous response to in vitro stimulation. High sensitivity is demonstrated by detection of low-abundance transcripts and rare cells. Under current implementation, the technique can analyze a few thousand cells simultaneously and can readily scale to 10,000s or 100,000s of cells.
Journal Article
A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters
We explore the microbiota of 18 body sites in over 200 individuals using sequences amplified V1-V3 and the V3-V5 small subunit ribosomal RNA (16S) hypervariable regions as part of the NIH Common Fund Human Microbiome Project. The body sites with the greatest number of core OTUs, defined as OTUs shared amongst 95% or more of the individuals, were the oral sites (saliva, tongue, cheek, gums, and throat) followed by the nose, stool, and skin, while the vaginal sites had the fewest number of OTUs shared across subjects. We found that commonalities between samples based on taxonomy could sometimes belie variability at the sub-genus OTU level. This was particularly apparent in the mouth where a given genus can be present in many different oral sites, but the sub-genus OTUs show very distinct site selection, and in the vaginal sites, which are consistently dominated by the Lactobacillus genus but have distinctly different sub-genus V1-V3 OTU populations across subjects. Different body sites show approximately a ten-fold difference in estimated microbial richness, with stool samples having the highest estimated richness, followed by the mouth, throat and gums, then by the skin, nasal and vaginal sites. Richness as measured by the V1-V3 primers was consistently higher than richness measured by V3-V5. We also show that when such a large cohort is analyzed at the genus level, most subjects fit the stool \"enterotype\" profile, but other subjects are intermediate, blurring the distinction between the enterotypes. When analyzed at the finer-scale, OTU level, there was little or no segregation into stool enterotypes, but in the vagina distinct biotypes were apparent. Finally, we note that even OTUs present in nearly every subject, or that dominate in some samples, showed orders of magnitude variation in relative abundance emphasizing the highly variable nature across individuals.
Journal Article
Dissipation controls transport and phase transitions in active fluids: mobility, diffusion and biased ensembles
Active fluids operate by constantly dissipating energy at the particle level to perform a directed motion, yielding dynamics and phases without any equilibrium equivalent. The emerging behaviors have been studied extensively, yet deciphering how local energy fluxes control the collective phenomena is still largely an open challenge. We provide generic relations between the activity-induced dissipation and the transport properties of an internal tracer. By exploiting a mapping between active fluctuations and disordered driving, our results reveal how the local dissipation, at the basis of self-propulsion, constrains internal transport by reducing the mobility and the diffusion of particles. Then, we employ techniques of large deviations to investigate how interactions are affected when varying dissipation. This leads us to shed light on a microscopic mechanism to promote clustering at low dissipation, and we also show the existence of collective motion at high dissipation. Overall, these results illustrate how tuning dissipation provides an alternative route to phase transitions in active fluids.
Journal Article
High-precision scale setting in lattice QCD
A
bstract
Scale setting is of central importance in lattice QCD. It is required to predict dimensional quantities in physical units. Moreover, it determines the relative lattice spacings of computations performed at different values of the bare coupling, and this is needed for extrapolating results into the continuum. Thus, we calculate a new quantity,
w
0
, for setting the scale in lattice QCD, which is based on the Wilson flow like the scale
t
0
(M. Luscher,
JHEP
08 (2010) 071). It is cheap and straightforward to implement and compute. In particular, it does not involve the delicate fitting of correlation functions at asymptotic times. It typically can be determined on the few per-mil level. We compute its continuum extrapolated value in 2 + 1-flavor QCD for physical and non-physical pion and kaon masses, to allow for mass-independent scale setting even away from the physical mass point. We demonstrate its robustness by computing it with two very different actions (one of them with staggered, the other with Wilson fermions) and by showing that the results agree for physical quark masses in the continuum limit.
Journal Article
Simultaneous femoro-popliteal artery bypass and foot free flap for lower limb salvage: a 13-year follow-up
Critical limb ischemia (CLI) associated with lower extremity complex wounds is challenging for vascular and plastic surgeons. Despite a high risk of perioperative morbidity, complex reconstructive surgery in these patients is an alternative to primary major limb amputation. We present a patient with CLI and a complex foot wound treated with simultaneous femoro-popliteal arterial bypass and free flap for lower limb salvage. The 13-year follow-up showed good functional results.
Journal Article
Autonomous Engines Driven by Active Matter: Energetics and Design Principles
Because of its nonequilibrium character, active matter in a steady state can drive engines that autonomously deliver work against a constant mechanical force or torque. As a generic model for such an engine, we consider systems that contain one or several active components and a single passive one that is asymmetric in its geometrical shape or its interactions. Generally, one expects that such an asymmetry leads to a persistent, directed current in the passive component, which can be used for the extraction of work. We validate this expectation for a minimal model consisting of an active and a passive particle on a one-dimensional lattice. It leads us to identify thermodynamically consistent measures for the efficiency of the conversion of isotropic activity to directed work. For systems with continuous degrees of freedom, work cannot be extracted using a one-dimensional geometry under quite general conditions. In contrast, we put forward two-dimensional shapes of a movable passive obstacle that are best suited for the extraction of work, which we compare with analytical results for an idealized work-extraction mechanism. For a setting with many noninteracting active particles, we use a mean-field approach to calculate the power and the efficiency, which we validate by simulations. Surprisingly, this approach reveals that the interaction with the passive obstacle can mediate cooperativity between otherwise noninteracting active particles, which enhances the extracted power per active particle significantly.
Journal Article
The role of the pedicle omental flap in ruptured abdominal aortic aneurysm: a case report and literature review
A ruptured infrarenal abdominal aortic aneurysm (rAAA) is associated with an in-hospital mortality rate of 40% and an overall mortality rate of 60–80%. Open surgical repair for rAAA remains the principal method of treatment when endovascular repair is not available. Graft infection occurs in 1–4% of patients at 5 years, with a high incidence following emergency treatment. Other graft-related complications include pseudoaneurysm, graft occlusion and aorto-enteric fistula. This case report describes a 66-year-old male patient that was admitted to hospital complaining of intense abdominal pain, low blood pressure and tachycardia. He was diagnosed with a rAAA and treated using segmental resection of the abdominal aorta followed by reconstruction with a synthetic Dacron prosthesis. A pedicle omental flap was wrapped around the prosthetic graft and it was also used to fill the retroperitoneal cavity in order to reduce the risk of graft-related complications. Computed tomography angiography after 6 months showed good integration of the aortic prosthetic graft and the viability of the omental flap. In our opinion, vascular surgeons should consider the pedicle omental flap when they perform open surgical repair for rAAA in order to reduce the incidence of graft-related complications.
Journal Article
Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories
Background
Despite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition. In this study, we evaluated the performance of three commonly used metagenome prediction tools (PICRUSt, PICRUSt2, and Tax4Fun) by comparing the significance of the differential abundance of predicted functional gene profiles to those from shotgun metagenome sequencing across different environments.
Results
We selected 7 datasets of human, non-human animal, and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between predicted gene compositions and gene relative abundance measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the abundance of genes were permuted across samples. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of metagenome prediction tools. As an alternative, we compared the performance of genes predicted with PICRUSt, PICRUSt2, and Tax4Fun to sequenced metagenome genes in inference models associated with metadata within each dataset. With this approach, we found reasonable performance for human datasets, with the metagenome prediction tools performing better for inference on genes related to “housekeeping” functions. However, their performance degraded sharply outside of human datasets when used for inference.
Conclusion
We conclude that the utility of PICRUSt, PICRUSt2, and Tax4Fun for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted.
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Video abstract.
Journal Article