gebhart/patrepeval huggingface dataset:
Selective gas adsorption and separation in metal–organic frameworks (2009)

Adsorptive separation is very important in industry. Generally, the process uses porous solid materials such as zeolites, activated carbons, or silica gels as adsorbents. With an ever increasing need for a more efficient, energy-saving, and environmentally benign procedure for gas separation, adsorbents with tailored structures and tunable surface properties must be found. Metal-organic frameworks (MOFs), constructed by metal-containing nodes connected by organic bridges, are such a new type of porous materials. They are promising candidates as adsorbents for gas separations due to their large surface areas, adjustable pore sizes and controllable properties, as well as acceptable thermal stability. This critical review starts with a brief introduction to gas separation and purification based on selective adsorption, followed by a review of gas selective adsorption in rigid and flexible MOFs. Based on possible mechanisms, selective adsorptions observed in MOFs are classified, and primary relationships between adsorption properties and framework features are analyzed. As a specific example of tailor-made MOFs, mesh-adjustable molecular sieves are emphasized and the underlying working mechanism elucidated. In addition to the experimental aspect, theoretical investigations from adsorption equilibrium to diffusion dynamics via molecular simulations are also briefly reviewed. Furthermore, gas separations in MOFs, including the molecular sieving effect, kinetic separation, the quantum sieving effect for H2/D2 separation, and MOF-based membranes are also summarized (227 references).
Lightweight server support for browser-based CSRF protection (2013)

Cross-Site Request Forgery (CSRF) attacks are one of the top threats on the web today. These attacks exploit ambient authority in browsers (eg cookies, HTTP authentication state), turning them into confused deputies and causing undesired side effects on vulnerable web sites. Existing defenses against CSRFs fall short in their coverage and/or ease of deployment. In this paper, we present a browser/server solution, Allowed Referrer Lists (ARLs), that addresses the root cause of CSRFs and removes ambient authority for participating web sites that want to be resilient to CSRF attacks. Our solution is easy for web sites to adopt and does not affect any functionality on non-participating sites. We have implemented our design in Firefox and have evaluated it with real-world sites. We found that ARLs successfully block CSRF attacks, are simpler to implement than existing defenses, and do not significantly impact browser performance.
Probabilistic Models for Inference about Identity (2011)

Many face recognition algorithms use "distance-based" methods: Feature vectors are extracted from each face and distances in feature space are compared to determine matches. In this paper, we argue for a fundamentally different approach. We consider each image as having been generated from several underlying causes, some of which are due to identity (latent identity variables, or LIVs) and some of which are not. In recognition, we evaluate the probability that two faces have the same underlying identity cause. We make these ideas concrete by developing a series of novel generative models which incorporate both within-individual and between-individual variation. We consider both the linear case, where signal and noise are represented by a subspace, and the nonlinear case, where an arbitrary face manifold can be described and noise is position-dependent. We also develop a "tied" version of the algorithm that allows explicit comparison of faces across quite different viewing conditions. We demonstrate that our model produces results that are comparable to or better than the state of the art for both frontal face recognition and face recognition under varying pose.
When Machine Learning Meets Blockchain: A Decentralized, Privacy-preserving and Secure Design (2018)

With the onset of the big data era, designing efficient and effective machine learning algorithms to analyze large-scale data is in dire need. In practice, data is typically generated by multiple parties and stored in a geographically distributed manner, which spurs the study of distributed machine learning. Traditional master-worker type of distributed machine learning algorithms assumes a trusted central server and focuses on the privacy issue in linear learning models, while privacy in nonlinear learning models and security issues are not well studied. To address these issues, in this paper, we explore the blockchain technique to propose a decentralized privacy-preserving and secure machine learning system, called LearningChain, by considering a general (linear or nonlinear) learning model and without a trusted central server. Specifically, we design a decentralized Stochastic Gradient Descent (SGD) algorithm to learn a general predictive model over the blockchain. In decentralized SGD, we develop differential privacy based schemes to protect each party’s data privacy, and propose an l-nearest aggregation algorithm to protect the system from potential Byzantine attacks. We also conduct theoretical analysis on the privacy and security of the proposed LearningChain. Finally, we implement LearningChain on Etheurum and demonstrate its efficiency and effectiveness through extensive experiments.
A fast and flexible implementation of parallel model combination (2002)

In previous papers the use of parallel model combination (PMC) for noise robustness has been described. Various fast implementations have been proposed, though to date in order to compensate all the parameters of a system it has been necessary to perform Gaussian integration. This paper introduces an alternative method that can compensate all the parameters of the recognition system, whilst reducing the computational load of this task. Furthermore, the technique offers an additional degree of flexibility, as it allows the number of components to be chosen and optimised using standard iterative techniques. The new technique is referred to as data-driven PMC (DPMC). It is evaluated on the Resource Management database, with noise artificially added from the NOISEX-92 database. The performance of DPMC is found to be comparable to PMC, at a far lower computational cost. In complex noise environments, by more accurately modelling the noise source, using multiple components, and then reducing the number of components to the original number a slight improvement in performance is obtained.
Principal warps: thin-plate splines and the decomposition of deformations (1989)

The decomposition of deformations by principal warps is demonstrated. The method is extended to deal with curving edges between landmarks. This formulation is related to other applications of splines current in computer vision. How they might aid in the extraction of features for analysis, comparison, and diagnosis of biological and medical images in indicated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanistic studies on the interactions between poly(pyrrole) and organic vapors (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanistic studies on the interactions between poly(pyrrole) and organic vaporsJohn M. Charlesworth, Ashton C. Partridge, and Neil GarrardCite this: J. Phys. Chem. 1993, 97, 20, 5418–5423Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/j100122a038https://doi.org/10.1021/j100122a038research-articleACS PublicationsRequest reuse permissionsArticle Views294Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
A deep learning approach for generalized speech animation (2017)

We introduce a simple and effective deep learning approach to automatically generate natural looking speech animation that synchronizes to input speech. Our approach uses a sliding window predictor that learns arbitrary nonlinear mappings from phoneme label input sequences to mouth movements in a way that accurately captures natural motion and visual coarticulation effects. Our deep learning approach enjoys several attractive properties: it runs in real-time, requires minimal parameter tuning, generalizes well to novel input speech sequences, is easily edited to create stylized and emotional speech, and is compatible with existing animation retargeting approaches. One important focus of our work is to develop an effective approach for speech animation that can be easily integrated into existing production pipelines. We provide a detailed description of our end-to-end approach, including machine learning design decisions. Generalized speech animation results are demonstrated over a wide range of animation clips on a variety of characters and voices, including singing and foreign language input. Our approach can also generate on-demand speech animation in real-time from user speech input.
Evidence of a role for mesothelial cell-derived interleukin 8 in the pathogenesis of asbestos-induced pleurisy in rabbits. (1992)

Although acute asbestos-induced pleurisy is characterized by an influx of neutrophils, the identity of the factors that attract these cells to the pleural space and the source of the factors are unknown. We found that instillation of crocidolite asbestos into the pleural space of rabbits led to the appearance in pleural liquid of chemotactic activity for neutrophils, and that this chemotactic activity was inhibited significantly by a neutralizing antibody to human interleukin 8 (IL-8). Cultured rabbit pleural mesothelial cells incubated with crocidolite asbestos also released chemotactic activity for neutrophils, which was inhibited significantly by the anti-IL-8 antibody. To determine whether rabbit pleural mesothelial cells synthesize IL-8, we generated a probe for rabbit IL-8 mRNA by amplifying cDNA prepared from stimulated pleural mesothelial cells using the polymerase chain reaction (PCR) and primers based on homologous sequences in human and sheep IL-8 cDNAs. Homology-based PCR yielded a single cDNA fragment with a nucleotide sequence 88% identical to that of a corresponding region of human IL-8 cDNA. With the radiolabeled PCR product as a probe, we demonstrated rapid induction of IL-8 mRNA expression in pleural mesothelial cells exposed to asbestos. As expected, tumor necrosis factor-alpha also led to the appearance of IL-8 in the rabbit pleural space and stimulated cultured pleural mesothelial cells to synthesize and release IL-8. We conclude that asbestos directly stimulates pleural mesothelial cells to synthesize IL-8 and that mesothelial cell-derived IL-8 may play an important role in mediating asbestos-induced pleural inflammation.
Management of hepatitis C virus genotype 4 (2004)

Hepatitis C virus (HCV) genotype 4 is predominantly found in the Middle East and North Africa. Because most of the large randomized controlled trials of antiviral therapy for chronic hepatitis C were conducted in North America and Europe, little is known about management of patients with this particular genotype. Based on the available data, sustained virological response rates to interferon-based therapies appear to be intermediate between the relatively resistant HCV genotype 1 and the readily responsive genotypes 2 and 3. Several large prospective studies of pegylated interferon plus ribavirin combination therapy, the current gold-standard treatment, have recently been completed and will be reviewed.
Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches (2012)

The internal ribosome entry site (IRES) in the hepatitis C virus (HCV) RNA genome is essential for the initiation of viral protein synthesis. IRES domains adopt well-defined folds that are potential targets for antiviral translation inhibitors. We have determined the three-dimensional structure of the IRES subdomain IIa in complex with a benzimidazole translation inhibitor at 2.2 Å resolution. Comparison to the structure of the unbound RNA in conjunction with studies of inhibitor binding to the target in solution demonstrate that the RNA undergoes a dramatic ligand-induced conformational adaptation to form a deep pocket that resembles the substrate binding sites in riboswitches. The presence of a well-defined ligand-binding pocket within the highly conserved IRES subdomain IIa holds promise for the development of unique anti-HCV drugs with a high barrier to resistance.
Analyzing the Human Microbiome: A “How To” guide for Physicians (2014)

The application of high-throughput next-generation sequencing to the analysis of the human microbiome has led to a shift in our understanding of the etiology of complex diseases. In consequence, a great deal of literature can now be found exploring this complex system, and reviewing recent findings. Observations of alterations in the intestinal microbiome associating with inflammatory bowel disease and other chronic conditions are well supported and have been widely accepted by the research community. Yet, it can be difficult to objectively evaluate the importance of these results, given the wide variety of methodologies applied by different groups in the field. The aim of this review is to focus attention on the basic principles involved in microbiome analyses, and to describe factors that may have an impact on the accurate interpretation of results.
Second-harmonic generation for studying structural motion of biological molecules in real time and space (2007)

SHG and sum-frequency generation (SFG) are surface-selective, nonlinear optical techniques whose ability to measure the average tilt angle of molecules on surfaces is well known in non-biological systems. By labeling molecules with a second-harmonic-active dye probe, SHG detection is extended to any biological molecule. The method has been used in previous work to detect biomolecules at an interface and their ligand-induced conformational changes. Here I demonstrate that SHG can be used to study structural motion quantitatively using a probe placed at a specific site (Cys-77) in adenylate kinase, a protein. The protein is also labeled non-site-specifically via amines. Labeled protein is absorbed to a surface and a baseline SH signal is measured. Upon introducing ATP, AMP or a specific inhibitor, AP(5)A, the baseline signal changes depending on the ligand and the labeling site. In particular, a substantial change in SH intensity is produced upon binding ATP to the amine-labeled protein, consistent with the X-ray crystal structures. In contrast, SHG polarization measurements are used to quantitatively determine that no rotation occurs at site Cys-77, in agreement with the lack of motion observed at this site in the X-ray crystal structures. A method for building a global map of conformational change in real time and space is proposed using a set of probes placed at different sites in a biomolecule. For this purpose, SH-active unnatural amino acids are attractive complements to exogenous labels.
An intelligent home using wireless location networks and real time messaging for patients with heart failure (2002)

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2003.
Antagonism of the Thromboxane‐Prostanoid Receptor is Cardioprotective against Right Ventricular Pressure Overload (2016)

Right ventricular (RV) failure is the primary cause of death in pulmonary arterial hypertension (PAH) and is a significant cause of morbidity and mortality in other forms of pulmonary hypertension. There are no approved therapies directed at preserving RV function. F-series and E-series isoprostanes are increased in heart failure and PAH, correlate to the severity of disease, and can signal through the thromboxane-prostanoid (TP) receptor, with effects from vasoconstriction to fibrosis. The goal of these studies was to determine whether blockade of the TP receptor with the antagonist CPI211 was beneficial therapeutically in PAH-induced RV dysfunction. Mice with RV dysfunction due to pressure overload by pulmonary artery banding (PAB) were given vehicle or CPI211. Two weeks after PAB, CPI211-treated mice were protected from fibrosis with pressure overload. Gene expression arrays and immunoblotting, quantitative histology and morphometry, and flow cytometric analysis were used to determine the mechanism of CPI211 protection. TP receptor inhibition caused a near normalization of fibrotic area, prevented cellular hypertrophy while allowing increased RV mass, increased expression of antifibrotic thrombospondin-4, and blocked induction of the profibrotic transforming growth factor β (TGF-β) pathway. A thromboxane synthase inhibitor or low-dose aspirin failed to replicate these results, which suggests that a ligand other than thromboxane mediates fibrosis through the TP receptor after pressure overload. This study suggests that TP receptor antagonism may improve RV adaptation in situations of pressure overload by decreasing fibrosis and TGF-β signaling.
De novolipogenesis in the liver in health and disease: more than just a shunting yard for glucose (2015)

Hepatic de novo lipogenesis (DNL) is the biochemical process of synthesising fatty acids from acetyl-CoA subunits that are produced from a number of different pathways within the cell, most commonly carbohydrate catabolism. In addition to glucose which most commonly supplies carbon units for DNL, fructose is also a profoundly lipogenic substrate that can drive DNL, important when considering the increasing use of fructose in corn syrup as a sweetener. In the context of disease, DNL is thought to contribute to the pathogenesis of non-alcoholic fatty liver disease, a common condition often associated with the metabolic syndrome and consequent insulin resistance. Whether DNL plays a significant role in the pathogenesis of insulin resistance is yet to be fully elucidated, but it may be that the prevalent products of this synthetic process induce some aspect of hepatic insulin resistance.
Link analysis, eigenvectors and stability (2001)

The HITS and the PageRank algorithms are eigenvector methods for identifying &amp;quot;authoritative&amp;quot; or &amp;quot;influential&amp;quot; articles, given hyperlink or citation information. That such algorithms should give consistent answers is surely a desideratum, and in this paper, we address the question of when they can be expected to give stable rankings under small perturbations to the hyperlink patterns. Using tools from matrix perturbation theory and Markov chain theory, we provide conditions under which these methods are stable, and give specific examples of instability when these conditions are violated. We also briefly describe a modification to HITS that improves its stability. 1
Genotyping of Hepatitis C Virus Isolates using CLIP Sequencing (2000)

Determination of hepatitis C virus (HCV) genotypes and subtypes has become increasingly important for the clinical management and prognosis of HCV infections. The aim of the present study was to assess the specificity and reliability of a newly developed, commercially available HCV genotyping kit (TRUGENE HCV 5'NC genotyping kit). This technique utilizes PCR fragments previously generated by the diagnostic Roche AMPLICOR HCV test, which are subsequently subjected to simultaneous PCR amplification and direct sequencing (CLIP sequencing) of the 5' noncoding region (5'NCR). HCV isolates from 100 randomly chosen patients were genotyped by both the TRUGENE HCV 5'NC genotyping kit and DNA enzyme immunoassay (DEIA). Typing results obtained by both methods were in complete concordance in 91% of the cases. HCV RNA from the samples with discordant genotype assignment in both assays was additionally amplified with primers from the HCV core and NS5B regions. Phylogenetic analysis of the obtained sequences supported the results obtained from DEIA in six cases and CLIP sequencing in two cases. In the former six cases, the TRUGENE HCV 5'NC genotyping kit could not correctly differentiate between subtypes of genotypes 1 and 2 due to the high conservation of the 5'NCR. However, since there was not any misclassification between HCV genotypes 1 and non-1 types, the results obtained with this system are, in general, reliable and can be used in clinical practice. The TRUGENE HCV 5'NC genotyping kit in our hands proved to be a fast and convenient technique that might be an attractive option for HCV genotyping in laboratories already using the Roche AMPLICOR HCV test for diagnostic reverse transcription-PCR.
Low-dose computed tomography image restoration using previous normal-dose scan (2011)

For low-dose CT image restoration, the presented ndiNLM method is robust in preserving the spatial resolution and identifying the low-contrast structure. The authors can draw the conclusion that the presented ndiNLM algorithm may be useful for some clinical applications such as in perfusion imaging, radiotherapy, tumor surveillance, etc.
Channel-forming activity and channel size of the RTX toxins ApxI, ApxII, and ApxIII of Actinobacillus pleuropneumoniae (1996)

The determinants of the Actinobacillus pleuropneumoniae RTX toxins ApxI, ApxII, and ApxIII were expressed in an Escherichia coli strain. The toxins were concentrated from the supernatants of cell cultures. The addition of the toxins to the aqueous-phase-bathing lipid bilayer membranes resulted in an increase in the membrane conductance when membranes made of asolectin or phosphatidylethanolamine were used. The toxins were relatively inactive in membranes made of other lipids. The membrane activity (i.e., the number of channels formed at a given Apx concentration) was different for each of the three Apx toxins. That of ApxI, which has the strongest cytotoxic activity, was highest, followed by that of ApxIII and ApxII, which is the least cytotoxic. The conductance increases of ApxIII and ApxII were smaller by factors of 10 and 50, respectively, than that of ApxI under otherwise identical conditions. Single-channel experiments demonstrated that all three Apx toxins formed ion-permeable channels of different conductances. The major open state was approximately the same for the two hemolytic toxins ApxI and ApxII (540 and 620 pS in 0.15 M KCI), whereas the single-channel conductance of the nonhemolytic ApxIII was approximately one-fifth of that of the other two toxins (95 pS). Experiments with different salts suggested that the Apx channels of A. pleuropneumoniae were exclusively cation selective because of negative charges localized at the channel mouth. Analysis of the single-channel data using the Renkin correction factor suggested that the Apx toxins formed aqueous channels with different diameters for the three toxins. Pore-forming properties of the Apx toxins were compared with those of other RTX toxins. All of these toxins have common features and form channels that are transient but have different sizes as judged from the different single-channel conductances.