gebhart/patrepeval huggingface dataset:
Simultaneous prediction of protein folding and docking at high resolution (2009)

Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large alpha-helical bundles, interlocking beta sandwiches, and interleaved alpha/beta motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift information, accurate models can be obtained consistently for symmetric complexes with as many as 192 total amino acids; a blind prediction was within 1 A rmsd of the traditionally determined NMR structure, and fit independently collected RDC data equally well. Together, these results show that the Rosetta "fold-and-dock" protocol can produce models of homo-oligomeric complexes with near-atomic-level accuracy and should be useful for crystallographic phasing and the rapid determination of the structures of multimers with limited NMR information.
A System-Theoretic Approach to Bandwidth Estimation (2009)

This paper presents a new foundational approach to reason about available bandwidth estimation as the analysis of a min-plus linear system. The available bandwidth of a link or complete path is expressed in terms of a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">service curve</i> , which is a function that appears in the network calculus to express the service available to a traffic flow. The service curve is estimated based on measurements of a sequence of probing packets or passive measurements of a sample path of arrivals. It is shown that existing bandwidth estimation methods can be derived in the min-plus algebra of the network calculus, thus providing further mathematical justification for these methods. Principal difficulties of estimating available bandwidth from measurements of network probes are related to potential nonlinearities of the underlying network. When networks are viewed as systems that operate either in a linear or in a nonlinear regime, it is argued that probing schemes extract the most information at a point when the network crosses from a linear to a nonlinear regime. Experiments on the Emulab testbed at the University of Utah, Salt Lake City, evaluate the robustness of the system-theoretic interpretation of networks in practice. Multinode experiments evaluate how well the convolution operation of the min-plus algebra provides estimates for the available bandwidth of a path from estimates of individual links.
Incidence and level of aflatoxin contamination in imported foods which were inspected by the Official Method of Japan (1990)

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Applying Deep Learning and Vector Representation for Software Vulnerabilities Detection (2018)

This paper 1 addresses a problem of vulnerability detection in software represented as assembly code. An extended approach to the vulnerability detection problem is proposed. This work concentrates on improvement of neural network-based approach described in previous works of authors. The authors propose to include the morphology of instructions in vector representations. The bidirectional recurrent neural network is used with access to the execution traces of the program. This has significantly improved the vulnerability detecting accuracy.
Oxidation of sulfur dioxide to sulfur trioxide over honeycomb DeNoxing catalysts (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation of sulfur dioxide to sulfur trioxide over honeycomb DeNoxing catalystsJiri Svachula, Louis J. Alemany, Natale Ferlazzo, Pio Forzatti, Enrico Tronconi, and Fiorenzo BreganiCite this: Ind. Eng. Chem. Res. 1993, 32, 5, 826–834Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ie00017a009https://doi.org/10.1021/ie00017a009research-articleACS PublicationsRequest reuse permissionsArticle Views2214Altmetric-Citations113LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Revisiting loxapine: a systematic review (2015)

Loxapine is an antipsychotic used in psychiatry for over 40 years with a well-established profile. Loxapine is a dibenzoxazepine tricyclic antipsychotic agent, available for oral, intramuscular and inhalatory administration. In the light of the recent approval by the regulatory agencies of inhaled loxapine for use in the acute treatment of mild-to-moderate agitation in adults affected with schizophrenia or bipolar disorder, this article aims to critically review the available literature on loxapine, irrespective of its formulation. This review examines the efficacy and tolerability of the various formulations of loxapine in the treatment of agitation and aggression in patients affected with schizophrenia, bipolar disorder and other psychiatric conditions. A comprehensive and systematic literature search of PubMed/MEDLINE was conducted, and relevant pharmacodynamic and pharmacokinetic data was included. The findings from the literature were critically reviewed and synthesized. The available data suggests that the antipsychotic efficacy of loxapine is similar to the efficacy of other typical or atypical antipsychotics, with an adverse effects profile comparable to that of the typical antipsychotics at high doses for chronic treatment. As an acute treatment in agitation associated with schizophrenia or bipolar disorder, inhaled loxapine was developed as an innovative and rapid option which appears to be efficacious and tolerable.
Efficient general-purpose image compression with binary tree predictive coding (1997)

Binary tree predictive coding uses a noncausal, shape-adaptive predictor to decompose an image into a binary tree of prediction errors and zero blocks. Fast compression performance is comparable with Joint Photographers Expert Group (JPEG) for photographs, with Graphics Interchange Format (GIF) for graphics, and superior to the state of the art for composite images.
Improving the IEEE 802.15.4 Slotted CSMA/CA MAC for time-critical events in wireless sensor networks (2006)

In beacon-enabled mode, IEEE 802.15.4 is ruled by the slotted CSMA/CA Medium Access Control (MAC) protocol. The standard slotted CSMA/CA mechanism does not provide any means of differentiated services to improve the quality of service for time-critical events (such as alarms, time slot reservation, PAN management messages etc.). In this paper, we present and discuss practical service differentiation mechanisms to improve the performance of slotted CSMA/CA for time-critical events, with only minor add-ons to the protocol. The contribution of our proposal is more practical than theoretical since our initial requirement is to leave the original algorithm of the slotted CSMA/CA unchanged, but rather tuning its parameters adequately according to the criticality of the messages. We present a simulation study based on an accurate model of the IEEE 802.15.4 MAC protocol, to evaluate the differentiated service strategies. Four scenarios with different settings of the slotted CSMA/CA parameters are defined. Each scenario is evaluated for FIFO and Priority Queuing. The impact of the hidden-node problem is also analyzed, and a solution to mitigate it is proposed.
Fast Boolean Matching with Don&#146;t Cares (2006)

This paper describes a fast Boolean matching algorithm which checks the containment relationship between an incompletely specified function and a completely specified function under permutation and negation on the input variables. The algorithm is designed for the pattern matching problem in technology mapping. It exploits functional symmetries of patterns and utilizes a compact data structure: binary permutation matrix. Using this matrix, nonmatching permutations and phase assignments can be pruned efficiently. All legal permutations and phase assignments, leading to a matching, can be obtained, as well. The experimental results on the MCNC benchmarks show that, compared with other Boolean matching approaches, our algorithm is at least 1,500 times faster for a common pattern abed + efgh and 58,000 times faster for another common pattern ab + cd + ef + gh. The matching speed for completely specified functions is also comparable to state-of-the-art matching algorithms.
Study of Aliphatic-Aromatic Copolyester Degradation in Sandy Soil and Its Ecotoxicological Impact (2010)

Degradation of poly[(1,4-butylene terephthalate)-co-(1,4-butylene adipate)] (Ecoflex, BTA) monofilaments (rods) in standardized sandy soil was investigated. Changes in the microstructure and chemical composition distribution of the degraded BTA samples were evaluated and changes in the pH and salinity of postdegradation soil, as well as the soil phytotoxicity impact of the degradation products, are reported. A macroscopic and microscopic evaluation of the surface of BTA rod samples after specified periods of incubation in standardized soil indicated erosion of the surface of BTA rods starting from the fourth month of their incubation, with almost total disintegration of the incubated BTA material observed after 22 months. However, the weight loss after this period of time was about 50% and only a minor change in the M(w) of the investigated BTA samples was observed, along with a slight increase in the dispersity (from an initial 2.75 up to 4.00 after 22 months of sample incubation). The multidetector SEC and ESI-MS analysis indicated retention of aromatic chain fragments in the low molar mass fraction of the incubated sample. Phytotoxicity studies revealed no visible damage, such as necrosis and chlorosis, or other inhibitory effects, in the following plants: radish, cres, and monocotyledonous oat, indicating that the degradation products of the investigated BTA copolyester are harmless to the tested plants.
DSM-III and the revolution in the classification of mental illness (2005)

A revolution occurred within the psychiatric profession in the early 1980s that rapidly transformed the theory and practice of mental health in the United States. In a very short period of time, mental illnesses were transformed from broad, etiologically defined entities that were continuous with normality to symptom-based, categorical diseases. The third edition of the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM-III) was responsible for this change. The paradigm shift in mental health diagnosis in the DSM-III was neither a product of growing scientific knowledge nor of increasing medicalization. Instead, its symptom-based diagnoses reflect a growing standardization of psychiatric diagnoses. This standardization was the product of many factors, including: (1) professional politics within the mental health community, (2) increased government involvement in mental health research and policymaking, (3) mounting pressure on psychiatrists from health insurers to demonstrate the effectiveness of their practices, and (4) the necessity of pharmaceutical companies to market their products to treat specific diseases. This article endeavors to explain the origins of DSM-III, the political struggles that generated it, and its long-term consequences for clinical diagnosis and treatment of mental disorders in the United States. © 2005 Wiley Periodicals, Inc.
Moiré bands in twisted double-layer graphene (2011)

A moiré pattern is formed when two copies of a periodic pattern are overlaid with a relative twist. We address the electronic structure of a twisted two-layer graphene system, showing that in its continuum Dirac model the moiré pattern periodicity leads to moiré Bloch bands. The two layers become more strongly coupled and the Dirac velocity crosses zero several times as the twist angle is reduced. For a discrete set of magic angles the velocity vanishes, the lowest moiré band flattens, and the Dirac-point density-of-states and the counterflow conductivity are strongly enhanced.
Loss Surfaces, Mode Connectivity, and Fast Ensembling of DNNs (2018)

The loss functions of deep neural networks are complex and their geometric properties are not well understood. We show that the optima of these complex loss functions are in fact connected by simple curves, over which training and test accuracy are nearly constant. We introduce a training procedure to discover these high-accuracy pathways between modes. Inspired by this new geometric insight, we also propose a new ensembling method entitled Fast Geometric Ensembling (FGE). Using FGE we can train high-performing ensembles in the time required to train a single model. We achieve improved performance compared to the recent state-of-the-art Snapshot Ensembles, on CIFAR-10, CIFAR-100, and ImageNet.
Fimbriae of <i>Bacteroides nodosus</i>: protein engineering of the structural subunit for the production of an exogenous peptide (1989)

The pattern of sequence variation between Bacteroides nodosus fimbrial subunits of different serotypes suggests a degree of flexibility, which might be exploited for protein engineering approaches for the expression of other peptides. We have tested this using the well-characterized peptide epitope from VP1 of foot-and-mouth disease virus (FMDV), residues 144-159: LRGDLQVLAQKVARTL (strain 01-BFS). Using bacterial codon usage, several oligonucleotides were designed for the substitution of this sequence internally at hypervariable regions of the fimbrial subunit (aligned for maximum homology), and for its addition at the carboxyterminus with a diglycine spacer as a flexible hinge. Following site-directed mutagenesis in phage M13, the modified genes were placed under PL promoter control and placed in a broad host range vector. Analysis of the variant proteins expressed in E. coli showed that these substitutions affected, to varying extents, recognition by both anti-fimbrial and anti-FMDV antibodies, indicating that hypervariable region 2 is a major antigenic determinant of the fimbrial subunit and that local stereochemical effects can influence antibody binding to the FMDV peptide antigenic determinant. In Pseudomonas aeruginosa, viable transformants could only be obtained with the mutant gene encoding the carboxy-terminal graft. These cells provided fimbrial preparations comprised of the modified subunit. This then constitutes the prototype for the development of a general expression system for the production of vaccine epitopes and other bioactive peptides. Furthermore, there is considerable scope for further modification of the system, for example by engineering specific chemical or protease cleavage sites for release of the grafted peptide. Alternatively, the fimbriae themselves may serve as a useful supramolecular carrier or adjuvant for immune provocation.
The use of loop inductances in signal integrity modeling (2002)

For many years, partial inductances have been used in circuit models for signal integrity. However, the author's experience has indicated that partial inductances have more drawbacks than benefits for such work. This paper describes these drawbacks, and proposes a different method of including inductive effects in signal integrity modeling, based on loop inductances. A discussion of the theory and an example are given.
Fast subspace methods for radar applications (1997)

Some problems of subspace methods are demonstrated by the two principle radar applications: resolution enhancement and interference suppression. We show that for real data a critical problem of subspace methods is the definition of the signal subspace. Channel errors result in a leakage of signal power into the noise eigenvalues. For resolution enhancement the optimum signal subspace dimension is close to the dimension without errors, because by this choice error effects can be reduced. A performance comparison of some current criteria to determine the subspace dimension is given. For interference suppression the error/leakage subspace must be included in the subspace. Real data experiments show, that projection methods are sensitive to the choice of the dimension of the jammer subspace. For this application 'weighted projections' show a much better performance. These 'weighted projections' can be effectively constructed from eigenvector-free subspace estimation methods.
Join sequence optimization in parallel query plans (2002)

We show an alternative way to optimize join sequences in a shared nothing architecture of the distributed relational DBMS HEAD. The hardware resources are also used for database independent applications in concurrency, for database access. To achieve a better hardware utilization we span a complete search space involving all intermediate shapes between left deep, right deep and bushy trees, but without join sequences including cartesian products. The approach is based on any combinatorial search engine and a complex cost function. The cost function involves the actual load of the processors, the network load, and the memory capacities. The new technique has free access to any join sequence in the whole search space. The approach is not restricted to acyclic join conditions.
Multiclass Brain Tissue Segmentation in 4D CT Using Convolutional Neural Networks (2019)

4D CT imaging has a great potential for use in stroke workup. A fully convolutional neural network (CNN) for 3D multiclass segmentation in 4D CT is presented, which can be trained end-to-end from sparse 2D annotations. The CNN was trained and validated on 42 4D CT acquisitions of the brain of patients with suspicion of acute ischemic stroke. White matter, gray matter, cerebrospinal fluid, and vessels were annotated by two trained observers. The mean Dice coefficients, contour mean distances, and absolute volume differences were, respectively, 0.87 ± 0.04, 0.52 ± 0.47 mm, and 11.78 ± 9.55 % on a separate test set of five patients, which were similar to the average interobserver variability scores of 0.88 ± 0.03, 0.72 ± 0.93 mm, and 8.86 ± 7.65 % outperforming the current state of the art. The proposed method is, therefore, a promising deep neural network for multiclass segmentation in 4D spatiotemporal imaging data.
Measurement of methaemalbumin in plasma (1973)

Using the method of Chong and Owen (1967), the normal range of methaemalbumin in plasma was 0 to 0·6 mg/100 ml, expressed as milligrams of haematin per cent. Previous results, using the method of Shinowara and Walters (1963), reported a normal range of 0 to 8·0 mg/100 ml, but it was expressed as milligrams of haemoglobin percent. The conversion factor from the Shinowara method is as follows: mg haematin % = mg haemoglobin % × 0·04.
Diablo Promotes Apoptosis by Removing Miha/Xiap from Processed Caspase 9 (2001)

MIHA is an inhibitor of apoptosis protein (IAP) that can inhibit cell death by direct interaction with caspases, the effector proteases of apoptosis. DIABLO is a mammalian protein that can bind to IAPs and antagonize their antiapoptotic effect, a function analogous to that of the proapoptotic Drosophila molecules, Grim, Reaper, and HID. Here, we show that after UV radiation, MIHA prevented apoptosis by inhibiting caspase 9 and caspase 3 activation. Unlike Bcl-2, MIHA functioned after release of cytochrome c and DIABLO from the mitochondria and was able to bind to both processed caspase 9 and processed caspase 3 to prevent feedback activation of their zymogen forms. Once released into the cytosol, DIABLO bound to MIHA and disrupted its association with processed caspase 9, thereby allowing caspase 9 to activate caspase 3, resulting in apoptosis.
SIMULTANEOUS SPECTROPHOTOMETRIC DETERMINATION OF TERNARY MIXTURES OF TARTRAZINE, SUNSET YELLOW, AND PONCEAU 4R BY H-POINT STANDARD ADDITION METHOD (2001)

A simple UV spectrophotometric method has been developed for resolving ternary mixture of food colorants, Tartrazine, Sunset Yellow and Ponceau 4R, which are species with highly overlapped spectra, by using H-point standard addition method (HPSAM). In this method, the concentration of one colorant was calculated from overlapping spectra at two appropriate wavelengths, where the other two colorants were selected as interferents present the equal absorbance relationship. These wavelength pairs are generally easily found, and can be selected to give the most precise analytical results. This method was satisfactorily applied to determination of colorants of Tartrazine, Sunset Yellow and Ponceau 4R in synthetic ternary mixtures and several commercial products.
Exploration of a Multicapillary Column for Use in Elevated Speed Gas Chromatography (1997)

Abstract Elevated speed gas chromatography with a multicapillary column (MCC) was explored using mixtures of volatile alkanes and aromatic hydrocarbons with a 160 mm long MCC at 27°C. The van Deemter curves showed broad minima with volumetric flows from 10–60 mL/min (average linear velocities of 12–70 cm/s) and HETP values of 0.5–3 mm; corresponding retention times were 10–200 s. In comparison, a 2.89 m fused silica capillary column exhibited narrower minima with volumetric flows of 5–20 mL/min (average linear velocities of 105–418 cm/s) and HETP values of 2–70 mm; retention times were 10–60 s at 41°C. The MCC exhibited symmetry factors of ca. 1.3 at 10 ng and this rose to ca. 2.0 at 100 μ; greater loadings may be possible but were precluded here by limitations in the injector rather than the column. Comparison in the separation of volatiles in gasoline showed comparable performance with the conventional fused-silica capillary column. A first examination of the MCC suggests that major advantages exist with respect to low sensitivity in separation efficiency towards carrier gas flow rates and sample loading to at least 10 μg. The mechanical advantages of a MCC were also exploited revealing the simplicity of connecting it to other parts of a GC system.
Selective monoiodination of aromatic compounds with electrochemically generated I+ using micromixing (2006)

Selective monoiodination of aromatic compounds such as dimethoxybenzene has been successfully achieved with I+, which is generated by anodic oxidation of I2 in acetonitrile, using micromixing.
In vitro antibacterial activities of tigecycline in combination with other antimicrobial agents determined by chequerboard and time-kill kinetic analysis (2006)

The lack of antagonism seen with tigecycline combinations in both chequerboard and time-kill kinetic studies is an encouraging outcome, suggesting that tigecycline may prove to be effective in combination therapy as well as in monotherapy.