3,988 research outputs found
NPRF: A Neural Pseudo Relevance Feedback Framework for Ad-hoc Information Retrieval
Pseudo-relevance feedback (PRF) is commonly used to boost the performance of
traditional information retrieval (IR) models by using top-ranked documents to
identify and weight new query terms, thereby reducing the effect of
query-document vocabulary mismatches. While neural retrieval models have
recently demonstrated strong results for ad-hoc retrieval, combining them with
PRF is not straightforward due to incompatibilities between existing PRF
approaches and neural architectures. To bridge this gap, we propose an
end-to-end neural PRF framework that can be used with existing neural IR models
by embedding different neural models as building blocks. Extensive experiments
on two standard test collections confirm the effectiveness of the proposed NPRF
framework in improving the performance of two state-of-the-art neural IR
models.Comment: Full paper in EMNLP 201
PARADE: Passage Representation Aggregation for Document Reranking
We present PARADE, an end-to-end Transformer-based model that considers document-level context for document reranking. PARADE leverages passage-level relevance representations to predict a document relevance score, overcoming the limitations of previous approaches that perform inference on passages independently. Experiments on two ad-hoc retrieval benchmarks demonstrate PARADE's effectiveness over such methods. We conduct extensive analyses on PARADE's efficiency, highlighting several strategies for improving it. When combined with knowledge distillation, a PARADE model with 72\% fewer parameters achieves effectiveness competitive with previous approaches using BERT-Base. Our code is available at \url{https://github.com/canjiali/PARADE}
Maximally localized Wannier functions in LaMnO3 within PBE+U, hybrid functionals, and partially self-consistent GW: an efficient route to construct ab-initio tight-binding parameters for e_g perovskites
Using the newly developed VASP2WANNIER90 interface we have constructed
maximally localized Wannier functions (MLWFs) for the e_g states of the
prototypical Jahn-Teller magnetic perovskite LaMnO3 at different levels of
approximation for the exchange-correlation kernel. These include conventional
density functional theory (DFT) with and without additional on-site Hubbard U
term, hybrid-DFT, and partially self-consistent GW. By suitably mapping the
MLWFs onto an effective e_g tight-binding (TB) Hamiltonian we have computed a
complete set of TB parameters which should serve as guidance for more elaborate
treatments of correlation effects in effective Hamiltonian-based approaches.
The method-dependent changes of the calculated TB parameters and their
interplay with the electron-electron (el-el) interaction term are discussed and
interpreted. We discuss two alternative model parameterizations: one in which
the effects of the el-el interaction are implicitly incorporated in the
otherwise "noninteracting" TB parameters, and a second where we include an
explicit mean-field el-el interaction term in the TB Hamiltonian. Both models
yield a set of tabulated TB parameters which provide the band dispersion in
excellent agreement with the underlying ab initio and MLWF bands.Comment: 30 pages, 7 figure
A revision of Sanpasaurus yaoi Young, 1944 from the Early Jurassic of China, and its relevance to the early evolution of Sauropoda (Dinosauria)
© 2016 McPhee et al.
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. The attached file is the published version of the article
A proteasome-resistant fragment of NIK mediates oncogenic NF-ÎşB signaling in schwannomas
Schwannomas are common, highly morbid and medically untreatable tumors that can arise in patients with germ line as well as somatic mutations in neurofibromatosis type 2 (NF2). These mutations most commonly result in the loss of function of the NF2-encoded protein, Merlin. Little is known about how Merlin functions endogenously as a tumor suppressor and how its loss leads to oncogenic transformation in Schwann cells (SCs). Here, we identify nuclear factor kappa-light-chain-enhancer of activated B cells (NF-ÎşB)-inducing kinase (NIK) as a potential drug target driving NF-ÎşB signaling and Merlin-deficient schwannoma genesis. Using a genomic approach to profile aberrant tumor signaling pathways, we describe multiple upregulated NF-ÎşB signaling elements in human and murine schwannomas, leading us to identify a caspase-cleaved, proteasome-resistant NIK kinase domain fragment that amplifies pathogenic NF-ÎşB signaling. Lentiviral-mediated transduction of this NIK fragment into normal SCs promotes proliferation, survival, and adhesion while inducing schwannoma formation in a novel in vivo orthotopic transplant model. Furthermore, we describe an NF-ÎşB-potentiated hepatocyte growth factor (HGF) to MET proto-oncogene receptor tyrosine kinase (c-Met) autocrine feed-forward loop promoting SC proliferation. These innovative studies identify a novel signaling axis underlying schwannoma formation, revealing new and potentially druggable schwannoma vulnerabilities with future therapeutic potential
Recommended from our members
Assembly of the algal CO2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif
Approximately one-third of the Earth's photosynthetic CO2 assimilation occurs in a pyrenoid, an organelle containing the CO2-fixing enzyme Rubisco. How constituent proteins are recruited to the pyrenoid and how the organelle's subcompartments-membrane tubules, a surrounding phase-separated Rubisco matrix, and a peripheral starch sheath-are held together is unknown. Using the model alga Chlamydomonas reinhardtii, we found that pyrenoid proteins share a sequence motif. We show that the motif is necessary and sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting. The presence of the Rubisco-binding motif on proteins that localize to the tubules and on proteins that localize to the matrix-starch sheath interface suggests that the motif holds the pyrenoid's three subcompartments together. Our findings advance our understanding of pyrenoid biogenesis and illustrate how a single protein motif can underlie the architecture of a complex multilayered phase-separated organelle
Two rapid assays for screening of patulin biodegradation
ArtĂculo sobre distintos ensayos para comprobar la biodegradaciĂłn de la patulinaThe mycotoxin patulin is produced by the blue
mould pathogen Penicillium expansum in rotting apples
during postharvest storage. Patulin is toxic to a wide range
of organisms, including humans, animals, fungi and bacteria.
Wash water from apple packing and processing
houses often harbours patulin and fungal spores, which can
contaminate the environment. Ubiquitous epiphytic yeasts,
such as Rhodosporidium kratochvilovae strain LS11 which
is a biocontrol agent of P. expansum in apples, have the
capacity to resist the toxicity of patulin and to biodegrade
it. Two non-toxic products are formed. One is desoxypatulinic
acid. The aim of the work was to develop rapid,
high-throughput bioassays for monitoring patulin degradation
in multiple samples. Escherichia coli was highly
sensitive to patulin, but insensitive to desoxypatulinic acid.
This was utilized to develop a detection test for patulin,
replacing time-consuming thin layer chromatography or
high-performance liquid chromatography. Two assays for patulin degradation were developed, one in liquid medium
and the other in semi-solid medium. Both assays allow the
contemporary screening of a large number of samples. The
liquid medium assay utilizes 96-well microtiter plates and
was optimized for using a minimum of patulin. The semisolid
medium assay has the added advantage of slowing
down the biodegradation, which allows the study and isolation
of transient degradation products. The two assays are
complementary and have several areas of utilization, from
screening a bank of microorganisms for biodegradation
ability to the study of biodegradation pathways
Chemopreventative celecoxib fails to prevent schwannoma formation or sensorineural hearing loss in genetically engineered murine model of neurofibromatosis type 2
Mutations in the tumor suppressor gene NF2 lead to Neurofibromatosis type 2 (NF2), a tumor predisposition syndrome characterized by the development of schwannomas, including bilateral vestibular schwannomas with complete penetrance. Recent work has implicated the importance of COX-2 in schwannoma growth. Using a genetically engineered murine model of NF2, we demonstrate that selective inhibition of COX-2 with celecoxib fails to prevent the spontaneous development of schwannomas or sensorineural hearing loss in vivo, despite elevated expression levels of COX-2 in Nf2-deficient tumor tissue. These results suggest that COX-2 is nonessential to schwannomagenesis and that the proposed tumor suppressive effects of NSAIDs on schwannomas may occur through COX-2 independent mechanisms
Fibrous Monolithic Ceramics
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66419/1/j.1151-2916.1997.tb03148.x.pd
Improvement of image quality of time-domain diffuse optical tomography with lp sparsity regularization
An lp (0 < p ≤ 1) sparsity regularization is applied to time-domain diffuse optical tomography with a gradient-based nonlinear optimization scheme to improve the spatial resolution and the robustness to noise. The expression of the lp sparsity regularization is reformulated as a differentiable function of a parameter to avoid the difficulty in calculating its gradient in the optimization process. The regularization parameter is selected by the L-curve method. Numerical experiments show that the lp sparsity regularization improves the spatial resolution and recovers the difference in the absorption coefficients between two targets, although a target with a small absorption coefficient may disappear due to the strong effect of the lp sparsity regularization when the value of p is too small. The lp sparsity regularization with small p values strongly localizes the target, and the reconstructed region of the target becomes smaller as the value of p decreases. A phantom experiment validates the numerical simulations
- …