gebhart/patrepeval huggingface dataset:
Origin of Fast Ion Conduction in Li10GeP2S12, a Superionic Conductor (2016)

The discovery of additional sites has revealed important insights into the possibility of cross-channel ionic diffusion in Li10GeP2S12 (LGPS). Here, we present an ab initio study of a Li diffusion mechanism in LGPS. The presence of fractional occupancy for Li sites leads to different c channel population of Li and different local environment for Li hop both along the c-directional channels and in the ab plane. We perform a rigorous computation of the energy barriers with different population of Li and different environment of Li surrounding the c channels. It is found that the diffusion energy barrier in LGPS depends significantly on channel population, local environment, and the type of hop which leads to a range of relative diffusivity along different directions. A novel mechanism of correlated diffusion between the c channel and the ab plane is found with significantly low energy barrier. The relative frequency of occurrence of the novel hop mechanism critically controls the degree of anisotropy in LGPS. Moreover, low activation barrier associated with this hop leads to high diffusivity which is sustained even after repeated cycling due to the presence of cross-channel pathways.
Experimental characterization of the dispersive behavior in a uniaxial metamaterial around plasma frequency (2010)

In this paper, the dispersive behavior around the plasma frequency in a magnetically uniaxial metamaterial is experimentally investigated. We show by theoretical analysis, parameter retrieval and experiment that when material loss is considered, while the plasma frequency is defined by the frequency where the real part of permeability approaches zero, ultra fast phase velocity actually appears at a slightly lower frequency, due to the change of the dispersion diagram. Both parameter retrieval and experimental data show that within a narrow frequency band to the left of the plasma frequency, the inherent loss keeps finite and is much less than that in the corresponding resonant region. In a real metamaterial sample, an ultra fast phase velocity of 24,440 times the speed of light in free space is measured, and negative phase propagation due to the only negative permeability is observed. The existence of such ultra fast phase velocity with finite loss perfectly explains how the highly directivity antennas based on near-zero refractive index metamaterial work, and can be further used in other applications such as in-phase wave divider and coherent wave sources.
Preparation and Properties of Double-chain Bis (quaternary ammonium) Compounds (1993)

Two types of double-chain bis (N, N-dimethyl or N-benzyl-N-methyl quaternary ammonium) compounds each possessing two hydroxyl groups were easily prepared from the diepoxy compounds. The connecting group between the two quaternary ammonium head groups had significant effects on some surface-active properties, especially on the ability to lower surface tension and foam stability. The double-chain bisammonium compound bearing the shortest ether oxygen atom as a connecting component showed maximum foaming ability and foam stability. With increase in the length of the connecting group, the foam stability of these compounds decreased.
Silymarin retards collagen accumulation in early and advanced biliary fibrosis secondary to complete bile duct obliteration in rats (1997)

Silymarin (SIL), a standardized plant extract containing about 60% polyphenole silibinin, is used as a hepatoprotective agent. Its antifibrotic potential in chronic liver diseases has not been explored. Therefore, we applied SIL to adult Wistar rats that were subjected to complete bile duct occlusion (BDO) by injection of sodium amidotrizoate (Ethibloc). This treatment induces progressive portal fibrosis without significant inflammation. Rats with sham-operation that received SIL at 50 mg/kg/d (n = 10) and rats with BDO alone (n = 20) served as controls, whereas groups of 20 animals were fed SIL at a dose of 25 and 50 mg/kg/d during weeks 1 through 6 or doses of 50 mg/kg/d during weeks 4 through 6 of BDO. Animals were sacrificed after 6 weeks for determination of blood chemistries, total and relative liver collagen (as hydroxyproline [HYP]), and the serum aminoterminal propeptide of procollagen type III (PIIINP). BDO in untreated rats caused an almost ninefold increase in total liver collagen (16.1 +/- 3.1 vs. 1.8 +/- 0.4 mg HYP, P < .001). SIL at 50 mg/kg/d reduced total HYP by 30% to 35%, either when given from week 1 through 6 or from week 4 through 6 after BDO (10.6 +/- 2.7 and 10.2 +/- 3.9 mg HYP, both P < .01 vs. BDO alone), whereas 25 mg/kg/d were ineffective. Because SIL at 50 mg/kg/d also reduced the collagen content per gram of liver tissue, it acted as a true antifibrotic agent. The single value of PIIINP at killing paralleled the antifibrotic activity of SIL with 11.6 +/- 3.8 and 9.9 +/- 3.7 vs. 15.3 +/- 5.2 microg/L in both high-dose groups (P < .05 and P < .01, respectively, vs. rats with BDO alone). Except for a decreased alkaline phosphatase and a lower histological fibrosis score in the groups that received SIL, clinical-chemical parameters were not different among all groups with BDO. We therefore conclude that 1) BDO with Ethibloc is a suitable model to test for pure antifibrotic drugs because it induces progressive rat secondary biliary fibrosis without major inflammation; 2) oral SIL can ameliorate hepatic collagen accumulation even in advanced (biliary) fibrosis; and 3) PIIINP appears to be a suitable serum marker to monitor the inhibition of hepatic fibrogenesis in this model of biliary fibrosis.
Inhibitory Receptors Alter Natural Killer Cell Interactions with Target Cells Yet Allow Simultaneous Killing of Susceptible Targets (1999)

Inhibitory receptors expressed on natural killer (NK) cells abrogate positive signals upon binding corresponding major histocompatibility complex (MHC) class I molecules on various target cells. By directly micromanipulating the effector-target cell encounter using an optical tweezers system which allowed temporal and spatial control, we demonstrate that Ly49-MHC class I interactions prevent characteristic cellular responses in NK cells upon binding to target cells. Furthermore, using this system, we directly demonstrate that an NK cell already bound to a resistant target cell may simultaneously bind and kill a susceptible target cell. Thus, although Ly49-mediated inhibitory signals can prevent many types of effector responses, they do not globally inhibit cellular function, but rather the inhibitory signal is spatially restricted towards resistant targets.
Four additional members of the ras gene superfamily isolated by an oligonucleotide strategy: molecular cloning of YPT-related cDNAs from a rat brain library. (1987)

Several oligonucleotide mixtures corresponding to a 6-amino acid sequence that is strictly conserved in all the ras and ras-related proteins (from various organisms) were tested for their ability to hybridize to 11 cloned members of the ras gene superfamily. Among these mixtures, a combination of two sets of partially complementary oligomers were able to hybridize to all the tested sequences. To identify members of the ras superfamily, we screened a rat brain cDNA library with these probes and isolated four genes, denoted rab1, -2, -3, and -4, encoding proteins homologous to the yeast YPT protein. Amino acid homology scores with YPT range from 75% for rab1 to 37% for rab4, whereas the homologies with p21 ras and other ras-related proteins are approximately equal to 30%, and homologous residues were clustered in the regions involved in GTP/GDP binding. Another striking similarity shared by the rab and the other ras-related proteins is the conservation of at least one cysteine residue near the carboxyl-terminal end involved in the membrane binding of the ras proteins. rab1 is a mammalian homolog of the yeast YPT gene, and the four rab genes constitute an additional branch of the ras gene superfamily that to our knowledge has not been described in higher eukaryotes.
Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics (2012)

We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These vectors are generated from one of a finite number of Dirichlet mixture components each with different hyperparameters. Observed samples are generated through multinomial sampling. The mixture components cluster communities into distinct 'metacommunities', and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. The model can also deduce the impact of a treatment and be used for classification. We wrote software for the fitting of DMM models using the 'evidence framework' (http://code.google.com/p/microbedmm/). This includes the Laplace approximation of the model evidence. We applied the DMM model to human gut microbe genera frequencies from Obese and Lean twins. From the model evidence four clusters fit this data best. Two clusters were dominated by Bacteroides and were homogenous; two had a more variable community composition. We could not find a significant impact of body mass on community structure. However, Obese twins were more likely to derive from the high variance clusters. We propose that obesity is not associated with a distinct microbiota but increases the chance that an individual derives from a disturbed enterotype. This is an example of the 'Anna Karenina principle (AKP)' applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community.
Ultrahigh Responsivity Visible and Infrared Detection Using Silicon Nanowire Phototransistors (2010)

Nanowire photodetectors can perform exceptionally well due to their unique properties arising from the nanowire geometry. Here we report on the phenomenal responsivity and extended spectral range of scalable, vertically etched, silicon nanowire photodetector arrays defined by nanoimprint lithography. The high internal gain in these devices allows for detection at below room temperatures of subfemtowatt per micrometer visible illumination and picowatt infrared illumination resulting from band to surface state generation.
The Human Microbiome Project (2007)

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.
Towards good practice in large-scale learning for image classification (2012)

We propose a benchmark of several objective functions for large-scale image classification: we compare the one-vs-rest, multiclass, ranking and weighted average ranking SVMs. Using stochastic gradient descent optimization, we can scale the learning to millions of images and thousands of classes. Our experimental evaluation shows that ranking based algorithms do not outperform a one-vs-rest strategy and that the gap between the different algorithms reduces in case of high-dimensional data. We also show that for one-vs-rest, learning through cross-validation the optimal degree of imbalance between the positive and the negative samples can have a significant impact. Furthermore, early stopping can be used as an effective regularization strategy when training with stochastic gradient algorithms. Following these "good practices", we were able to improve the state-of-the-art on a large subset of 10K classes and 9M of images of lmageNet from 16.7% accuracy to 19.1%.
Human immunodeficiency virus-like, nonreplicating, gag-env particles assemble in a recombinant vaccinia virus expression system (1990)

We report the assembly of human immunodeficiency virus (HIV)-like particles in African green monkey kidney cells coinfected with two recombinant vaccinia viruses, one carrying the HIV-1 gag and protease genes and the other the env gene. Biochemical analysis of particles sedimented from culture supernatants of doubly infected cells revealed that they were composed of gag proteins, primarily p24, as well as the env proteins gp120 and gp41. Thin-section immunoelectron microscopy showed that these particles were 100 to 120 nm in diameter, were characterized by the presence of cylindrical core structures, and displayed the mature gp120-gp41 complexes on their surfaces. Furthermore, thin-section immunoelectron microscopy analysis of infected cells showed that particle assembly and budding occurred at the plasma membrane. Nucleic acid hybridization suggested that the particles packaged only the gag mRNA but not the env mRNA. Therefore, the system we present is well suited for studies of HIV virion maturation. In addition, the HIV-like particles provide a novel and attractive approach for vaccine development.
Conserved cysteine and histidine residues in the putative zinc finger motif of the influenza A virus M1 protein are not critical for influenza virus replication (2003)

The influenza virus matrix protein (M1) possesses a cysteine and histidine (CCHH) motif in the helix 9 (H9) and adjacent region ((148)CATCEQIADSQHRSH(162)). The CCHH motif has been proposed as a putative zinc finger motif and zinc-binding activity has been implicated in virus uncoating as well as transcription inhibition and mRNA regulation. The function of the CCHH motif in the influenza virus life cycle was investigated by site-directed mutagenesis (alanine replacement) and by rescuing mutant viruses by reverse genetics. Mutant viruses containing an alanine replacement of the cysteine and histidine residues, either individually or in combination, were seen to exhibit wt phenotype in multiple virus growth cycles and plaque morphology. In addition, synthetic peptides containing the putative zinc finger motif did not inhibit virus replication in MDCK cells. However, mutation of Ala(155) in H9 was lethal for rescuing infectious virus. These data show that the CCHH motif does not provide a critical function in the influenza virus life cycle in cell culture and that the zinc-binding function may not be involved in virus biology. However, the lethal phenotype of the Ala(155) mutation shows that the H9 region of M1 provides some other critical function(s) in virus replication.
CLUE: cluster-based retrieval of images by unsupervised learning (2005)

In a typical content-based image retrieval (CBIR) system, target images (images in the database) are sorted by feature similarities with respect to the query. Similarities among target images are usually ignored. This paper introduces a new technique, cluster-based retrieval of images by unsupervised learning (CLUE), for improving user interaction with image retrieval systems by fully exploiting the similarity information. CLUE retrieves image clusters by applying a graph-theoretic clustering algorithm to a collection of images in the vicinity of the query. Clustering in CLUE is dynamic. In particular, clusters formed depend on which images are retrieved in response to the query. CLUE can be combined with any real-valued symmetric similarity measure (metric or nonmetric). Thus, it may be embedded in many current CBIR systems, including relevance feedback systems. The performance of an experimental image retrieval system using CLUE is evaluated on a database of around 60,000 images from COREL. Empirical results demonstrate improved performance compared with a CBIR system using the same image similarity measure. In addition, results on images returned by Google's Image Search reveal the potential of applying CLUE to real-world image data and integrating CLUE as a part of the interface for keyword-based image retrieval systems.
Proteoglycan-collagen interactions in intervertebral disc. A chondroitin sulphate proteoglycan associates with collagen fibrils in rabbit annulus fibrosus at the d-e bands (1986)

Rabbit annulus fibrosus and nucleus pulposus were analysed for hydroxyproline, chondroitin sulphate, keratan sulphate and dermatan sulphate. Tissue proteoglycans were stained for electron microscopy with Cupromeronic blue, used in the critical electrolyte concentration mode, with and without prior digestion by chondroitinase AC or ABC, hyaluronidase or keratanase. Collagen bands, a-e were demonstrated with UO2++. A chondroitin sulphate proteoglycan was found orthogonally associated with loosely packed collagen fibrils in annulus fibrosus at the d and e bands. The close metabolic and structural analogies with the dermatan sulphate proteoglycans previously shown to be located at collagen d-e bands in tendon, skin, etc. (Scott and Haigh (1985) Biosci. Rep. 5:71-81), are discussed. Tightly packed annulus collagen fibrils were surrounded by axially oriented proteoglycan filaments, mostly without specific locations.
Efficient representations and abstractions for quantifying and exploiting data reference locality (2001)

With the growing processor-memory performance gap, understanding and optimizing a program's reference locality, and consequently, its cache performance, is becoming increasingly important. Unfortunately, current reference locality optimizations rely on heuristics and are fairly ad-hoc. In addition, while optimization technology for improving instruction cache performance is fairly mature (though heuristic-based), data cache optimizations are still at an early stage. We believe the primary reason for this imbalance is the lack of a suitable representation of a program's dynamic data reference behavior and a quantitative basis for understanding this behavior.
Dependency Analysis in Distributed Systems using Fault Injection: Application to Problem Determination in an e-commerce Environment (2001)

Distributed networked applications that are being deployed in enterprise settings, increasingly rely on a large number of heterogeneous hardware and software components for providing end-to-end services. In such settings, the issue of problem diagnosis becomes vitally important, in order to minimize system outages and improve system availability. This motivates interest in dependency characterization among the different components in distributed application environments. A promising approach for obtaining dynamic dependency information is the Active Dependency Discovery technique in which a dependency graph of e-commerce transactions on hardware and software components in the system is built by individually “perturbing” the system components during a testing phase and collecting measurements corresponding to the external behavior of the system. In this paper, we propose using fault injection as the perturbation tool for dynamic dependency discovery and problem determination. We describe a method for characterizing dependencies of transactions on the system resources in a typical e-commerce environment, and show how it can aid in problem diagnosis. The method is applied to an application server middleware platform, running end-user activity composed of TPC-W transactions. Representative fault models for such an environment, that can be used to construct the fault injection campaign, are also presented.
Long persistent and photo-stimulated luminescence in Cr3+-doped Zn–Ga–Sn–O phosphors for deep and reproducible tissue imaging (2014)

A phosphor with remarkable long persistent luminescence features, Zn3Ga2Sn1O8:0.5 Cr3+, suitable for deep and reproducible tissue imaging has been rationally designed and successfully fabricated. This phosphor shows bright and long persistent luminescence over 300 h in the near-infrared region, and permits an enabling long-term, reproducible, real-time and reliable structural imaging of deep tissues. Moreover, the revived luminescence and persistent luminescence under the excitation of near-infrared incoherent light are also demonstrated to reveal an optional multiplexed detection. This new luminescent indicator will allow repeatable visualization of the structural and functional processes in cells, tissues and other complex systems. In addition, multifarious and systematic investigations are successfully carried out to unravel the nature of traps and also to verify the rationality of the material design.
A novel hybrid heat sink using phase change materials for transient thermal management of electronics (2005)

A hybrid heat sink concept which combines passive and active cooling approaches is proposed. The hybrid heat sink is essentially a plate fin heat sink with the tip immersed in a phase change material (PCM). The exposed area of the fins dissipates heat during periods when high convective cooling is available. When the air cooling is reduced, the heat is absorbed by the PCM. The governing conservation equations are solved using a finite-volume method on orthogonal, rectangular grids. An enthalpy method is used for modeling the melting/re-solidification phenomena. Results from the analysis elucidate the thermal performance of these hybrid heat sinks. The improved performance of the hybrid heat sink compared to a finned heat sink (without a PCM) under identical conditions, is quantified. In order to reduce the computational time and aid in preliminary design, a one-dimensional fin equation is formulated which accounts for the simultaneous convective heat transfer from the finned surface and melting of the PCM at the tip. The influence of the location, amount, and type of PCM, as well as the fin thickness on the thermal performance of the hybrid heat sink is investigated. Simple guidelines are developed for preliminary design of these heat sinks.
OFDM With Iterative Blind Channel Estimation (2010)

A new blind channel estimation technique is presented for uncoded orthogonal frequency-division multiplexing (OFDM) systems. Instead of using pilots to sound the channel, a decision algorithm first makes primary estimates of the data symbol for each subcarrier based on a constrained linear minimum mean square error (MMSE) criterion. Then, these estimates are applied to optimal MMSE channel estimation. The technique requires only one value from the time–frequency correlation of the channel transfer function. Performance is evaluated by simulation so that comparison can be made with known optimal coherent/differential detection. Compared with known decision-directed Kalman-based estimation and two pilot-aided OFDM schemes (block pilots and comb pilots), the presented technique performs better for regions with mid to high signal-to-noise ratios (SNRs). Its robustness to the time variation of the channel is also quantified by simulation, showing only small degradation in performance relative to the quasistatic case of wireless local area network (WLAN) systems. Finally, the impact of covariance assumptions in the channel modeling is quantified using simulation, offering a feel for the performance with mismatch between the channel model and the receiver assumptions.
Boosting Brain Activity From the Outside In (2001)

A slew of recent clinical trials in the United States and abroad has indicated that repetitive transcranial magnetic stimulation (rTMS) can lift depression in some patients who are resistant to other types of therapy. A few studies have suggested that it can also ease symptoms of schizophrenia, obsessive-compulsive disorder, and Parkinson9s disease, although these findings aren9t as well established as those on depression. One recent study even shows that well-aimed rTMS can speed one9s ability to solve puzzles. But exactly how it works is a bit of a mystery.