gebhart/patrepeval huggingface dataset:
Effects of additives on surfactant phase behavior relevant to bacteriorhodopsin crystallization (2006)

The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-beta-D-glucoside were investigated. Osmotic second virial coefficients (B(22)) were measured by self-interaction chromatography using a wide range of additives and precipitants, including polyethylene glycol (PEG) and heptane-1,2,3-triol (HT). In all cases, attractive protein-detergent complex (PDC) interactions were observed near the surfactant cloud point temperature, and there is a correlation between the surfactant cloud point temperatures and PDC B(22) values. Light scattering, isothermal titration calorimetry, and tensiometry reveal that although the underlying reasons for the patterns of interaction may be different for various combinations of precipitants and additives, surfactant phase behavior plays an important role in promoting crystallization. In most cases, solution conditions that led to crystallization fell within a similar range of slightly negative B(22) values, suggesting that weakly attractive interactions are important as they are for soluble proteins. However, the sensitivity of the cloud point temperatures and resultant coexistence curves varied significantly as a function of precipitant type, which suggests that different types of forces are involved in driving phase separation depending on the precipitant used.
Neonatal myosin in bovine and pig tensor tympani muscle fibres. (1991)

In previous studies of middle ear muscles, the classification of fibre types by histochemical methods was particularly difficult in the bovine and porcine tensor tympani muscle, suggesting the presence of immature fibres. We therefore reexamined the tensor tympani from pigs and cattle of various ages immunohistochemically, using a panel of antimyosin antibodies, including one (anti-NE) specific for neonatal and embryonic myosins. Fibres positive to anti-NE were found in tensor tympani in both species in all ages examined; only a few of these fibres reacted exclusively with this antibody; some also contained slow myosin and the majority also contained adult fast (type IIA) myosin. Furthermore, although the remaining fibres included some of the classical types I and IIA, the majority of them showed a mismatch between their histochemical and immunohistochemical profiles. The morphological appearance of the muscle, the widespread presence of neonatal myosin (often together with another myosin in the same fibre) and the persistence of this composition from birth to adulthood, could be explained by an incomplete development of the muscle fibres, resulting in a 'muscle' much better suited to the role of a ligament.
An in vitro thyroid function test without alcohol extraction. (1974)

A simplified method for performing a dual-function competitive binding test for assessing thyroid function without the need for ethanol extraction and separate addition of unextracted serum aliquots has been developed.
Peptidome characterization of ovarian cancer serum and the identification of tumor suppressive peptide ZYX36-58 (2020)

ZYX<sub>36-58,</sub> which was significantly down-regulated in the serum of ovarian cancer patients can significantly inhibit cell invasion, migration and promote apoptosis of ovarian cancer cells by binding and up-regulating TSP1 protein expression.
ChemInform Abstract: Convenient Method for Synthesis of Thiazolo[3,2‐a]pyrimidine Derivatives in a One‐Pot Procedure. (2011)

Abstract Careful α‐bromination of ketones with elemental bromine and direct addition of pyrimidine‐2‐thiones and triethylamine renders possible a direct two‐step one‐pot synthesis of the title compounds.
Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers (2008)

The phylogenetic relationships of Ig light chain (IGL) genes are difficult to resolve, because these genes are short and evolve relatively fast. Here, we classify the IGL sequences from 12 tetrapod species into three distinct groups (kappa, lambda, and sigma isotypes) using conserved amino acid residues, recombination signal sequences, and genomic organization of IGL genes as cladistic markers. From the distribution of the markers we conclude that the earliest extant tetrapods, the amphibians, possess three IGL isotypes: kappa, lambda, and sigma. Of these, two (kappa and lambda) are also found in reptiles and some mammals. The lambda isotype is found in all tetrapods tested to date, whereas the kappa isotype seems to have been lost at least in some birds and in the microbat. Conservation of the cladistic molecular markers suggests that they are associated with functional specialization of the three IGL isotypes. The genomic maps of IGL loci reveal multiple gene rearrangements that occurred in the evolution of tetrapod species. These rearrangements have resulted in interspecific variation of the genomic lengths of the IGL loci and the number and order of IGL constituent genes, but the overall organization of the IGL loci has not changed.
Supplementary Figures 1-3 from Platinum Sensitivity–Related Germline Polymorphism Discovered via a Cell-Based Approach and Analysis of Its Association with Outcome in Ovarian Cancer Patients (2023)

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The maize Hairy Sheath Frayed1 ( Hsf1 ) mutant alters leaf patterning through increased cytokinin signaling (2019)

ABSTRACT Leaf morphogenesis requires growth polarized along three axes - proximal-distal, medial-lateral and abaxial-adaxial. Grass leaves display a prominent proximal-distal (P-D) polarity consisting of a proximal sheath separated from the distal blade by the auricle and ligule. Although proper specification of the four segments is essential for normal morphology, our knowledge is incomplete regarding the mechanisms which influence P-D specification in monocots like maize ( Zea mays ). Here we report the identification of the gene underlying the semi-dominant, leaf patterning, maize mutant Hairy Sheath Frayed1 ( Hsf1 ). Hsf1 plants produce leaves with outgrowths consisting of proximal segments – sheath, auricle and ligule – emanating from the distal blade margin. Analysis of three independent Hsf1 alleles revealed gain-of-function missense mutations in the ligand binding domain of the maize cytokinin (CK) receptor Zea mays Histidine Kinase1 ( ZmHK1) gene. Biochemical analysis and structural modeling suggest the mutated residues near the CK binding pocket affect CK binding affinity. Treatment of wild type seedlings with exogenous CK phenocopied the Hsf1 leaf phenotypes. Results from expression and epistatic analyses indicated the Hsf1 mutant receptor appears to be hypersignaling. Our results demonstrate that hypersignaling of CK in incipient leaf primordia can reprogram developmental patterns in maize. Summary Increased cytokinin signaling in the maize Hairy Sheath Frayed1 mutant modifies leaf development leading to changes in pattering, growth and cell identity.
The Effect of Duloxetine on Painful Physical Symptoms in Depressed Patients (2004)

Treatment with duloxetine, 60 mg q.d., significantly reduced pain compared with placebo. Improvements in pain severity were attributable equally to the direct effect of duloxetine and to associated changes in depression severity. Improvement in painful physical symptoms was associated with higher remission rates even after accounting for improvement in core emotional symptoms.
Diagnostic Checking of Unobserved-Components Time Series Models (1992)

Diagnostic checking of the specification of time series models is normally carried out using the innovations—that is, the one-step-ahead prediction errors. In an unobserved-components model, other sets of residuals are available. These auxiliary residuals are estimators of the disturbances associated with the unobserved components. They can often yield information that is less apparent from the innovations, but they suffer from the disadvantage that they are serially correlated even in a correctly specified model with known parameters. This article shows how the properties of the auxiliary residuals may be obtained, how they are related to each other and to the innovations, and how they can be used to construct test statistics. Applications are presented showing how residuals can be used to detect and distinguish between outliers and structural change.
New Insights into Learning Algorithms and Datasets (2008)

We report on three distinct experiments that provide new valuable insights into learning algorithms and datasets. We first describe two effective meta-features that significantly impact the predictive accuracy of a broad range of learning algorithms. We then introduce a new efficient meta-feature that measures the degree of hardness (or difficulty) of datasets and show that it is highly linearly correlated with predictive accuracy. Finally, we use the notion of classifier output difference to cluster learning algorithms and show that learning algorithms from different model classes may demonstrate highly similar behaviors.
BRAKE SYSTEM REQUIREMENTS FOR PLATOONING ON AN AUTOMATED HIGHWAY (1995)

This paper presents a systematic procedure for adapting a nominal controller, designed while ignoring control saturation, to a higher- performance nonlinear controller that explicitly accounts for the saturating nonlinearities while guaranteeing stability. The performance of the nominal compensator without the saturations nominal compensator with saturation, error governor, and extended error governor is compared for a platoon of 15 cars.
Enterovirus infection morbidity and peculiarities of nonpolio enteroviruses circulation on some territories of Russia in 2017 (2018)

Aim: Characteristics of enterovirus infection morbidity and study of peculiarities of enterovirus circulation on some territories of Russia in 2017. Materials and methods: We investigated more than 5000 samples from the patients with enterovirus infection. The isolation and identification of enteroviruses were conducted by virological method and by partial sequencing of the genome region VP1. Phylogenic trees were constructed according to the method of Bayesian Monte Carlo Markov Chain. Results: Epidemic process and clinical picture of enterovirus infection were not the same on different territories. Peculiarities of the circulation of different types of enteroviruses on the territories were also different. In Saratov region 65% of cases were represented by enterovirus meningitis. In Murmansk region and in the Komi Republic enterovirus infection with exanthema prevailed, 95% and 60% correspondingly. In Saratov region enterovirus ECHO18 was the etiological agent of enterovirus meningitis. In Murmansk region and in the Komi Republic the cases were connected mainly with Coxsackieviruses A6. The strains of enterovirus ECHO18 were distributed to three clusters. The strains which provoked enterovirus meningitis in Saratov region belonged to cluster 3, they were formed separately from other strains of this enterovirus type and differed from the stains of ECHO18 which circulated in the North-West of Russia. The strains of Coxsackieviruses A6 identified in the North-West of Russia belonged to three sub-genotypes 5, 6, 8 of pandemic genotype of CoxsackievirusesA6. The majority of the strains belonged to sub-genotypes 6 and 8 which in 2017 dominated in the structure of Coxsackieviruses A6 in the North-West of Russia and in Russia. Conclusion: Epidemic peaks of enterovirus infection represented by different clinical forms of the disease were provoked by different types of enteroviruses. Enterovirus ECHO18 was the etiological agent of enterovirus meningitis. The main etiological factors of enterovirus infection with exanthema were Coxsackieviruses A6 of different sub-genotypes.
Photo-acoustic inversion in convex domains (2012)

In photo-acoustics one has to reconstruct a function from its averages over spheres around points on the measurement surface. For special surfaces inversion formulas are known. In this paper we derive a formula for surfaces that bound smooth convex domains. It reconstructs the function modulo a smoothing integral operator. For special surfaces the integral operator vanishes, providing exact reconstruction.
Clinical and histopathological features of a lingual mucosal horn: First time described clinical case series (2019)

Lingual mucosal horns are diagnostically challenging variants of a non-viral lingual papilloma that can clinically mimic the cutaneous horn. Improved characterization of these rare variants is needed, as improper diagnosis may lead to inappropriate or delayed treatment. A case series of patients with lingual horns diagnosed and treated at two academic hospitals from 2008 to 2019, was performed along with a literature review. We have diagnosed and inventoried seven lingual mucosal horns. The clinical description reveals a unique white overgrowth located on the dorsal surface of the tongue, delevoping at expense of the filiform papillae, without any preferential site but always located forward of the V-shaped line. The lesions are firm but remain nevertheless flexible, movable, a few millimeters high, with a conical shape. The lingual mucosal horn is a conical overgrowth whose occurrence is extremely rare. The lingual mucosal horn is a non-viral papilloma, and differs from the cutaneous variant.
Interface Analysis of Composites Using AFM-Based Nanoscale IR and Mechanical Spectroscopy (2015)

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A Noise Source Module for In-Situ Noise Figure Measurements From DC to 50 GHz at Cryogenic Temperatures (2012)

This letter presents the design and performance of a noise source module for in-situ noise temperature measurements at cryogenic temperatures. The noise source module operates from DC up to 50 GHz and is suitable for measurements of noise temperatures as low as a few Kelvin, achieving a measurement accuracy of about <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\pm {1.2}~{\rm K}$</tex></formula> . The GaAs MMIC used in the module includes a well matched 50 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\Omega$</tex></formula> termination with better than 20 dB return loss, a heating element and an on-chip temperature sensor, hence the noise source module can directly be connected to the device under test (DUT) with no additional elements or transitions needed. The measurement can then be taken with standard noise measurement equipment. Noise temperatures as low as 13 K have been measured in Ka-band with this device. Due to the ease of use, the good matching, the extraordinary bandwidth and the less involved calibration technique, the noise source module outperforms the conventional measurement setup using a noise diode in conjunction with a cooled attenuator.
A hybrid method for service identification of SSL/TLS encrypted traffic (2016)

It is significant and helpful to analyze encrypted traffic for solution of the potential network security problem. As one of the most popular encryption protocol, SSL/TLS has provided useful support for various network security while the network traffic has become complex and diverse. However, most of research on SSL/TLS traffic is about protocol level, identification and classification of services in real time is required for the effective network traffic management. In this paper, we propose a hybrid method to identify and classify the service in real time. We first filter the HTTPS traffic with a machine learning algorithm C4.5 decision tree, then classify the services with random forest, and process the traffic data what we get. Experimental results have shown that the accuracy reach more than 95%.
The permian end catastrophe: an evidence for a broader phenomenon (2020)

It is well known that about 250 million years ago a huge catastrophe took place in our planet, with effects so big that about 95 % of the species disappeared in the process including sea animals. This event is called “the Permian extinction”. Other effects are also apparently connected to this event. This kind of event would require an extremely huge amount of energy. Since there is no evidence for an asteroid impact, the energy source should be searched inside the planet. Most importantly, it should show an energy source capable of producing such huge phenomenon. The aim of this paper is to propose a model to explain this extinction event and to show that there is evidence that this is a phenomenon that apparently happened several times not only in our planet but also in other Solar System bodies.
Oxidation behaviour of nanocrystalline Fe–Ni–Cr–Al alloy coatings (1999)

Nanocrystalline Fe–Ni–Cr–Al alloy coatings with ∼4 wt-%Al were produced using the unbalanced magnetron sputter deposition technique with a composite 310S stainless steel target embedded with aluminium plugs. The oxidation behaviour of the coatings was studied, during which complete external α-Al2O3 scales were formed. During isothermal oxidation tests at 950, 1000, and 1050°C, the oxidation kinetics followed an essentially parabolic rate law, and the oxidation constants were measured to be 2·06 × 10-3, 4·23 × 10-3, and 1·14 × 10-2 mg2 cm-4 h-1 respectively. During a cyclic oxidation test at 1000°C the α-Al2O3 scale showed good scale spallation resistance. The surface hardness of the coatings was measured with a Knoop indentor before and after oxidation. After oxidation, the coating surface hardness was still significantly higher than that of the uncoated specimen, demonstrating the potential this coating has in the improvement of high temperature erosion resistance.
Call for papers (2014)

The year 2014 will see the debut of Neurology® Neuroimmunology & Neuroinflammation, a new online-only, open-access journal in the Neurology collection of publications. Many may ask whether we need a new biomedical journal. Our mission and vision statements embody why our answer is yes:
Abstract 4304: PPP1R1B-STARD3 fusion gene promotes gastric tumorigenesis through activation of PI3K/Akt signaling. (2013)

Abstract Fusion genes result from genomic aberrations such as translocation, amplification and rearrangement. They have the potential to be new targets for the diagnosis and therapeutics in several different types of cancers. To identify fusion genes in gastric cancer, we conducted RNA sequencing with 18 gastric cancer cell lines and 11 pairs of primary human gastric cancer tissues and their adjacent normal tissues. We identified PPP1R1B-STARD3 fusion gene and validated the expression of this fusion gene by Real-Time PCR in the expanded panel of the human gastric tissue samples. Interestingly, PPP1R1B-STRAD3 fusion gene was detected in approximately 30% of primary human gastric cancers, but not in adjacent matched normal gastric tissues. Overexpression of PPP1R1B-STARD3 in MKN-28 significantly increased cell proliferation and colony formation. This increased proliferation was mediated by activation of PI3K/Akt signaling. To confirm if the expression of PPP1R1B-STARD3 fusion gene affects the tumorigenic capacity of gastric cancer cells in vivo, we performed the xenograft assay with MKN-28 cells that stably express PPP1R1B-STARD3 fusion gene. Overexpression of the fusion gene enhanced the MKN-28 tumor growth in nude mice. Hence, PPP1R1B-STARD3 fusion gene overexpression gives growth advantage in vitro and in vivo. Taken together, these findings indicate that PPP1R1B-STRAD3 fusion gene increased cell proliferation through the activation of PI3K/Akt signaling in gastric cancer cells. Citation Format: Sun Mi Yun. PPP1R1B-STARD3 fusion gene promotes gastric tumorigenesis through activation of PI3K/Akt signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4304. doi:10.1158/1538-7445.AM2013-4304
Influence of silence duration distribution in perception of stop consonant clusters (1994)

The effects of the silence duration between two different stop consonants in /VC1–C2V/ tokens were examined. Earlier results using synthetic stimuli had shown that the decision boundary between hearing one and two stop consonants varied as a function of the range and frequency number of tokens) of the silent interval [B. H. Repp, Haskins Lab. Stat. Rep. Speech Res. SR-61, 151–165 (1980)]. Using real speech stimuli, The Repp (1980) experiment was replicated, showing that the results hold for individual subjects. Extending this result, the overall variance of the silence duration distribution was manipulated while maintaining the same mean, for two different distributions. The result shows that the overall variance does not significantly affect the boundary, and that listeners must be adapting to the mean silence duration. The final experiment examines this adaptation by presenting trials of sequential tokens to determine the relative weighting of the former token(s) on the judgment of the final token in the trial. The results of this experiment will be presented in relation to the adaptation process. Implications for adaptation in other durational cues, and influence of cue trading will be discussed. [Work supported by AFOSR.]
Flexible control of downloaded executable content (1999)

We present a security architecture that enables system and application a ccess control requirements to be enforced on applications composed from downloaded executable content. Downloaded executable content consists of messages downloaded from remote hosts that contain executables that run, upon receipt, on the downloading principal's machine. Unless restricted, this content can perform malicious actions, including accessing its downloading principal's private data and sending messages on this principal's behalf. Current security architectures for controlling downloaded executable content (e.g., JDK 1.2) enable specification of access control requirements for content based on its provider and identity. Since these access control requirements must cover every legal use of the class, they may include rights that are not necessary for a particular application of content. Therefore, using these systems, an application composed from downloaded executable content cannot enforce its access control requirements without the addition of application-specific security mechanisms. In this paper, we define an access control model with the following properties: (1) system administrators can define system access control requirements on applications and (2) application developers can use the same model to enforce application access control requirements without the need for ad hoc security mechanisms. This access control model uses features of role-based access control models to enable (1) specification of a single role that applies to multiple application instances; (2) selection of a content's access rights based on the content's application and role in the application; (3) consistency maintained between application state and content access rights; and (4) control of role administration. We detail a system architecture that uses this access control model to implement secure collaborative applications. Lastly, we describe an implementation of this architecture, called the Lava security architecture.