gebhart/patrepeval huggingface dataset:
Predicting genetic interactions from Boolean models of biological networks (2015)

Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. We describe a computational methodology allowing us to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. We classify the obtained interactions according to their class of epistasis, dependence on the chosen initial conditions and the phenotype. The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed.
Chest pathology detection using deep learning with non-medical training (2015)

In this work, we examine the strength of deep learning approaches for pathology detection in chest radiographs. Convolutional neural networks (CNN) deep architecture classification approaches have gained popularity due to their ability to learn mid and high level image representations. We explore the ability of CNN learned from a non-medical dataset to identify different types of pathologies in chest x-rays. We tested our algorithm on a 433 image dataset. The best performance was achieved using CNN and GIST features. We obtained an area under curve (AUC) of 0.87-0.94 for the different pathologies. The results demonstrate the feasibility of detecting pathology in chest x-rays using deep learning approaches based on non-medical learning. This is a first-of-its-kind experiment that shows that Deep learning with ImageNet, a large scale non-medical image database may be a good substitute to domain specific representations, which are yet to be available, for general medical image recognition tasks.
Design of a "minimAl" homeodomain: the N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure. (1994)

This report investigates the sequence specificity requirements for homeodomain structure and DNA binding activity by the design and synthesis of a "minimAl" homeodomain (for minimalist design and alanine scanning mutagenesis) which contains the consensus residues and in which all nonconsensus residues have been replaced with alanine. The murine homeodomain Msx served as the prototype for the minimAl homeodomain, Ala-Msx. We show that Ala-Msx binds to DNA specifically, albeit with lower affinity than Msx. A derivative of the minimAl homeodomain, Ala-Msx(NT), which contains a native rather than an alanine-substituted N-terminal arm, has similar DNA binding affinity as Msx. We show that the native N-terminal arm stabilizes the tertiary structure of the minimAl homeodomain. Although Ala-Msx resembles a molten-globule protein, the structure of Ala-Msx(NT) is similar to Msx. The requirement for an intact N-terminal arm is not unique to the minimAl homeodomain, since the N-terminal arm also promotes high-affinity binding activity and appropriate tertiary structure of Msx. Therefore, the homeodomain "scaffold" consists of consensus residues, which are sufficient for DNA recognition, and nonconsensus residues in the N-terminal arm, which are required for optimal DNA binding affinity and appropriate tertiary structure. MinimAl design provides a powerful strategy to probe homeodomain structure and function. This approach should be of general utility to study the sequence specificity requirements for structure and function of other DNA-binding domains.
A New and Useful Method for the Macrocyclization of Linear Peptides (2012)

A new and useful procedure for the macrocyclization of linear peptides is described. The natural amino acid side chains of tyrosine (phenol), lysine (alkylamine), and histidine (imidazole) react in an intramolecular fashion with a pendent pyridine-N-oxide-carboxamide, which is selectively activated by the phosphonium salt, PyBroP. The reaction is mild, rapid, and efficient with a potentially large substrate scope. Multiple examples are provided with full characterization and analyses, including a novel aza-variant of the C-O-D ring system of vancomycin.
A Bioelectric Controller for Computer Music Applications (1990)

This article is a description of a special purpose signal processing computer designed to acquire lowlevel neuroelectric and myoelectric signals, perform feature extraction on these signals, and then map the desired features to MIDI commands-all in real-time. The computer-called the Biomusecan be used as a biocontroller to augment normal musical instrument performance or as a direct nervous system, computer interface for musical composition and performance. Additionally, it could be used for paralyzed and movement impaired individuals as a means to regain the pleasures of music making. The concept of making musical sound from biological phenomena is not new. In fact, one of the earliest references to the idea of transforming a biological feature into musical sound appeared in an essay by the poet Rainer Maria Rilke in 1919 entitled The Primal Sound. In this essay, Rilke proposes creating a special stylus that could track the coronal suture of the skull and transduce the wave form into the primal sound, just as a phonograph needle recreated sound from the wavy imprint in a wax roll. In the poet's words:
Effectiveness of Patient Choice in Nonoperative vs Surgical Management of Pediatric Uncomplicated Acute Appendicitis (2015)

clinicaltrials.gov Identifier: NCT01718275.
Phase behavior of branched surfactants in oil and water (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase behavior of branched surfactants in oil and waterKlaus R. Wormuth and Stephen ZushmaCite this: Langmuir 1991, 7, 10, 2048–2053Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/la00058a014https://doi.org/10.1021/la00058a014research-articleACS PublicationsRequest reuse permissionsArticle Views774Altmetric-Citations31LEARN 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
IMIX Genome: Specification of Variable Packet Sizes for Additional Testing (2013)

Benchmarking methodologies have always relied on test conditions with
constant packet sizes, with the goal of understanding what network
device capability has been tested. Tests with a constant packet size
reveal device capabilities but differ significantly from the
conditions encountered in operational deployment, so additional tests
are sometimes conducted with a mixture of packet sizes, or IMIX
(Internet Mix). The mixture of sizes a networking device will
encounter is highly variable and depends on many factors. An IMIX
suited for one networking device and deployment will not be
appropriate for another. However, the mix of sizes may be known, and
the tester may be asked to augment the fixed-size tests. To address
this need and the perpetual goal of specifying repeatable test
conditions, this document defines a way to specify the exact repeating
sequence of packet sizes from the usual set of fixed sizes and from
other forms of mixed-size specification.
Towards QoS-Based Embedded Machine Learning (2022)

Due to various breakthroughs and advancements in machine learning and computer architectures, machine learning models are beginning to proliferate through embedded platforms. Some of these machine learning models cover a range of applications including computer vision, speech recognition, healthcare efficiency, industrial IoT, robotics and many more. However, there is a critical limitation in implementing ML algorithms efficiently on embedded platforms: the computational and memory expense of many machine learning models can make them unsuitable in resource-constrained environments. Therefore, to efficiently implement these memory-intensive and computationally expensive algorithms in an embedded computing environment, innovative resource management techniques are required at the hardware, software and system levels. To this end, we present a novel quality-of-service based resource allocation scheme that uses feedback control to adjust compute resources dynamically to cope with the varying and unpredictable workloads of ML applications while still maintaining an acceptable level of service to the user. To evaluate the feasibility of our approach we implemented a feedback control scheduling simulator that was used to analyze our framework under various simulated workloads. We also implemented our framework as a Linux kernel module running on a virtual machine as well as a Raspberry Pi 4 single board computer. Results illustrate that our approach was able to maintain a sufficient level of service without overloading the processor as well as providing an energy savings of almost 20% as compared to the native resource management in Linux.
Kinetic Study of Folding and Misfolding of Diacylglycerol Kinase in Model Membranes (2001)

Despite the relevance of membrane protein misfolding to a number of common diseases, our understanding of the folding and misfolding of membrane proteins lags well behind soluble proteins. Here, the overall kinetics of membrane insertion and folding of the homotrimeric integral membrane protein diacylglycerol kinase (DAGK) is addressed. DAGK was purified into lipid/detergent-free urea and guanidinium solutions and subjected to general structural characterization. In urea, the enzyme was observed to be monomeric but maintained considerable tertiary structure. In guanidinium, it was also monomeric but exhibited much less tertiary structure. Aliquots of these DAGK stock solutions were diluted 200-fold into lipid vesicles or into detergent/lipid mixed micelles, and the rates and efficiencies of folding/insertion were monitored. Reactions were also carried out in which micellar DAGK solutions were diluted into vesicular solutions. Productive insertion of DAGK from denaturant solutions into mixed micelles occurred much more rapidly than into lipid vesicles, suggesting that bilayer transversal represents the rate-limiting step for DAGK assembly in vesicles. The efficiency of productive folding/insertion into vesicles was highest in reactions initiated with micellar DAGK stock solutions (where DAGK maintains a nativelike fold and oligomeric state) and lowest in reactions starting with guanidinium stocks (where DAGK is an unfolded monomer). Moreover, the final ratio of irreversibly misfolded DAGK to reversibly misfolded enzyme was highest following reactions initiated with guanidinium stock solutions and lowest when micellar stocks were used. Finally, it was also observed that very low concentrations of detergents were able to both enhance the bilayer insertion rate and suppress misfolding.
Nucleation and growth of platelets in hydrogen-ion-implanted silicon (2005)

H ion implantation into crystalline Si is known to result in the precipitation of planar defects in the form of platelets. Hydrogen-platelet formation is critical to the process that allows controlled cleavage of Si along the plane of the platelets and subsequent transfer and integration of thinly sliced Si with other substrates. Here we show that H-platelet formation is controlled by the depth of the radiation-induced damage and then develop a model that considers the influence of stress to correctly predict platelet orientation and the depth at which platelet nucleation density is a maximum.
Bench-to-bedside review: Chloride in critical illness (2010)

Chloride is the principal anion in the extracellular fluid and is the second main contributor to plasma tonicity. Its concentration is frequently abnormal in intensive care unit patients, often as a consequence of fluid therapy. Yet chloride has received less attention than any other ion in the critical care literature. New insights into its physiological roles have emerged together with progress in understanding the structures and functions of chloride channels. In clinical practice, interest in a physicochemical approach to acid-base physiology has directed renewed attention to chloride as a major determinant of acid-base status. It has also indirectly helped to generate interest in other possible effects of disorders of chloraemia. The present review summarizes key aspects of chloride physiology, including its channels, as well as the clinical relevance of disorders of chloraemia. The paper also highlights current knowledge on the impact of different types of intravenous fluids on chloride concentration and the potential effects of such changes on organ physiology. Finally, the review examines the potential intensive care unit practice implications of a better understanding of chloride.
Configuration of Proactive Operations, Administration, and Maintenance (OAM) Functions for MPLS-Based Transport Networks Using Label Switched Path (LSP) Ping (2016)

This specification describes the configuration of proactive MPLS-TP Operations, Administration, and Maintenance (OAM) functions for a given Label Switched Path (LSP) using a set of TLVs that are carried by the LSP Ping protocol.
Joint Pricing and Power Allocation for Dynamic Spectrum Access Networks with Stackelberg Game Model (2010)

In this work we study joint pricing and power allocation for Dynamic Spectrum Access (DSA) networks with Stackelberg game. In our model, Primary User (PU) is the game leader and jointly determines its power allocation (to guarantee its QoS requirement) and the interference price charged to Secondary User (SU) (to reap revenue). Meanwhile, SU is the game follower and determines its power demand in response to PU's decisions. We quantify PU's and SU's benefit from the channel sharing model by deriving the Stackelberg equilibrium. Our results show that PU's equilibrium profit is asymptotically upper bounded with its marginal power cost and rate requirement. A distributed algorithm is proposed to find the equilibrium. We also propose an incentive-compatible mechanism for PU and SU to keep the social welfare optimum cooperatively. We extend our Stackelberg game to the multiple SUs scenario, where the interference among SUs results in a noncooperative power demand subgame. We propose a low-complexity heuristic algorithm for PU to maximize its profit. Our results show that PU can benefit by selecting multiple SUs to share its channel if SUs' mutual interference is limited.
Promoting flowering, lateral shoot outgrowth, leaf development, and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T (FT)-like gene GhFT1 (2015)

FLOWERING LOCUS T (FT) encodes a mobile signal protein, recognized as major component of florigen, which has a central position in regulating flowering, and also plays important roles in various physiological aspects. A mode is recently emerging for the balance of indeterminate and determinate growth, which is controlled by the ratio of FT-like and TERMINAL FLOWER 1 (TFL1)-like gene activities, and has a strong influence on the floral transition and plant architecture. Orthologs of GhFT1 was previously isolated and characterized from Gossypium hirsutum. We demonstrated that ectopic overexpression of GhFT1 in tobacco, other than promoting flowering, promoted lateral shoot outgrowth at the base, induced more axillary bud at the axillae of rosette leaves, altered leaf morphology, increased chlorophyll content, had higher rate of photosynthesis and caused flowers abscission. Analysis of gene expression suggested that flower identity genes were significantly upregulated in transgenic plants. Further analysis of tobacco FT paralogs indicated that NtFT4, acting as flower inducer, was upregulated, whereas NtFT2 and NtFT3 as flower inhibitors were upregulated in transgenic plants under long-day conditions, but downregulated under short-day conditions. Our data suggests that sufficient level of transgenic cotton FT might disturb the balance of the endogenous tobacco FT paralogs of inducers and repressors and resulted in altered phenotype in transgenic tobacco, emphasizing the expanding roles of FT in regulating shoot architecture by advancing determine growth. Manipulating the ratio for indeterminate and determinate growth factors throughout FT-like and TFL1-like gene activity holds promise to improve plant architecture and enhance crop yield.
In vitro phosphorylation of ciliary dyneins by protein kinases from <i>Paramecium</i> (1993)

Paramecium dyneins were tested as substrates for phosphorylation by cAMP-dependent protein kinase, cGMP-dependent protein kinase, and two Ca(2+)-dependent protein kinases that were partially purified from Paramecium extracts. Only cAMP-dependent protein kinase caused significant phosphorylation. The major phosphorylated species was a 29 kDa protein that was present in both 22 S and 12 S dyneins; its phosphate-accepting activity peaked with 22 S dynein. In vitro phosphorylation was maximal at five minutes, then decreased. This decrease in phosphorylation was inhibited by the addition of vanadate or NaF. The 29 kDa protein was not phosphorylated by a heterologous cAMP-dependent protein kinase, the bovine catalytic subunit. Phosphorylation of dynein did not change its ATPase activity. In sucrose gradient fractions from the last step of dynein purification, phosphorylation by an endogenous kinase occurred. This phosphorylation could not be attributed to the small amounts of cAMP- and cGMP-dependent protein kinases known to be present, nor was it Ca(2+)-dependent. This previously uncharacterized ciliary protein kinase used casein as an in vitro substrate.
Effects of Preparation Methods on Properties of Nickel Catalyst (2003)

This paper studied the effects of preparation methods on the properties of nickel catalyst and analyzed the factors which influenced the activities of catalysts by the means of TPR and the measure of active surface area.The results showed that catalytic activity would be influenced by calcining temperature,calcining time and impregnation order.The results also indicated that the nickel oxide which was reduced at low temperature was the active center of reaction.
Factor-4 and 6 compression of cyclotomic subgroups of and (2010)

Abstract Bilinear pairings derived from supersingular elliptic curves of embedding degrees 4 and 6 over finite fields 𝔽 2 m and 𝔽 3 m , respectively, have been used to implement pairing-based cryptographic protocols. The pairing values lie in certain prime-order subgroups of the cyclotomic subgroups of orders 2 2 m + 1 and 3 2 m – 3 m + 1, respectively, of the multiplicative groups and . It was previously known how to compress the pairing values over characteristic two fields by a factor of 2, and the pairing values over characteristic three fields by a factor of 6. In this paper, we show how the pairing values over characteristic two fields can be compressed by a factor of 4. Moreover, we present and compare several algorithms for performing exponentiation in the prime-order subgroups using the compressed representations. In particular, in the case where the base is fixed, we expect to gain at least a 54% speed up over the fastest previously known exponentiation algorithm that uses factor-6 compressed representations.
Effect of heat shock protein 47 on collagen synthesis of keloid in vivo (2010)

Keloid is regarded as a fibroproliferative disorder with excessive accumulation of extracellular matrix. However, the molecular mechanism of keloid formation is not well understood and no treatment modality is consistently effective. Heat shock protein 47 (HSP47) is known as a collagen-specific molecular chaperone which plays a critical role in collagen biosynthesis. Results of our previous in vitro experiments demonstrated that HSP47 might be an important reason for excessive collagen accumulation in regard to keloid formation. Our objective is to investigate whether HSP47 has an influence on collagen metabolism in animal keloid models. The constructed plasmids, carrying HSP47-small hairpin RNA (shRNA), were transfected into animal keloid models, in comparison with the control groups. After transfection, the mRNA and protein expression of HSP47 and collage type I were detected by quantitative real-time PCR and Western blot. Both the mRNA and protein levels of HSP47 in animal keloid models were decreased dramatically after transfection of the HSP47- shRNA plasmid, in comparison with the control group. Following the down-regulation of HSP47, we found that the volume of animal keloid models and the major collagen expression were reduced correspondingly. Combining the results of our previous in vitro experiment results, we suggest that overexpression of HSP47 in keloid fibroblast cells could induce excessive collagen accumulation by enhancing collagen synthesis, which not only presents a possible mechanism of keloid formation, but also offers a therapeutic potential of RNA interference to HSP47 for the treatment of keloids and other fibroproliferative disorders.
Si-rich W silicide films composed of W-atom-encapsulated Si clusters deposited using gas-phase reactions of WF6 with SiH4 (2016)

We formed Si-rich W silicide films composed of Sin clusters, each of which encapsulates a W atom (WSi(n) clusters with 8 < n ≤ ∼ 12), by using a gas-phase reaction between WF6 and SiH4 in a hot-wall reactor. The hydrogenated WSi(n)H(x) clusters with reduced F concentration were synthesized in a heated gas phase and subsequently deposited on a substrate heated to 350-420 °C, where they dehydrogenated and coalesced into the film. Under a gas pressure of SiH4 high enough for the WSi(n)H(x) reactant to collide a sufficient number of times with SiH4 molecules before reaching the substrate, the resulting film was composed of WSi(n) clusters with a uniform n, which was determined by the gas temperature. The formed films were amorphous semiconductors with an optical gap of ∼0.8-1.5 eV and an electrical mobility gap of ∼0.05-0.12 eV, both of which increased as n increased from 8 to 12. We attribute this dependence to the reduction of randomness in the Si network as n increased, which decreased the densities of band tail states and localized states.
No beneficial effect of intrathecal methylprednisolone acetate in postherpetic neuralgia patients (2012)

Considering the absence of clinical benefits and the potential risks of the treatment, intrathecal administration of MPA is not recommended.