gebhart/patrepeval huggingface dataset:
Expression of the unique NCAM VASE exon is independently regulated in distinct tissues during development. (1990)

During development of the rat central nervous system, neural cell adhesion molecule (NCAM) mRNAs containing in the extracellular domain a 30-bp alternative exon, here named VASE, replace RNAs that lack this exon. The presence of this alternative exon between previously described exons 7 and 8 changes the predicted loop structure of the derived polypeptide from one resembling an immunoglobulin constant region domain to one resembling an immunoglobulin variable domain. This change could have significant effects on NCAM polypeptide function and cell-cell interaction. In this report we test multiple rat tissues for the presence of additional alternative exons at this position and also examine the regulation of splicing of the previously described exon. To sensitively examine alternative splicing, polymerase chain reactions (PCRs) with primers flanking the exon 7/exon 8 alternative splicing site were performed. Four categories of RNA samples were tested for new exons: whole brain from embryonic day 11 to adult, specific brain regions dissected from adult brain, clonal lines of neural cells in vitro, and muscle cells and tissues cultured in vitro and obtained by dissection. Within the limits of the PCR methodology, no evidence for any alternative exon other than the previously identified VASE was obtained. The regulation of expression of this exon was found to be complex and tissue specific. Expression of the 30-bp exon in the heart and nervous system was found to be regulated independently; a significant proportion of embryonic day 15 heart NCAM mRNAs contain VASE while only a very small amount of day 15 nervous system mRNAs contain VASE. Some adult central nervous system regions, notably the olfactory bulb and the peripheral nervous system structures adrenal gland and dorsal root ganglia, express NCAM which contains very little VASE. VASE is undetectable in NCAM PCR products from the olfactory epithelium. Other nervous system regions express significant quantities of NCAM both with and without VASE. Clonal cell lines in culture generally expressed very little VASE. These results indicate that a single alternative exon, VASE, is found in NCAM immunoglobulin-like loop 4 and that distinct tissues and nervous system regions regulate expression of VASE independently both during development and in adult animals.
Helicobacter Pylori-Related Gastric Histology Classification Using Support-Vector-Machine-Based Feature Selection (2008)

This study presents a computer-aided diagnosis system using sequential forward floating selection (SFFS) with support vector machine (SVM) to diagnose gastric histology of Helicobacter pylori (H. pylori) from endoscopic images. To achieve this goal, candidate image features associated with clinical symptoms are extracted from endoscopic images. With these candidate features, the SFFS method is applied to select feature subsets, which perform the best classification results under SVM with respect to different histological features. By using the classifiers obtained from the feature subsets, a new diagnosis system is implemented to provide physicians with H. pylori -related histological results from endoscopic images.
Orthoamides and iminium salts, LXXIII1. Contributions to the cleavage of carboxylic acid orthoamides – a new access to N,N,N‘,N‘-tetraalkyl-carboxamidinium salts (2012)

Orthoamides 7b-e of alkyne carboxylic acids are transformed by benzoyl chloride to give the corresponding amidinium chlorides 13b-f, which were isolated as the tetraphenylborates 14. The reaction of the orthoamide derivative of phenylpropiolic acid 7a with acetic acid anhydride results in the formation of the acylated ketene aminal 20. The orthoamide of propiolic acid 22 and chloroform react, affording the vinylogous guanidinium salt 24. By the hydrolysis of the orthoamide derivative of phenylpropiolic acid 7a the -keto-carboxylic acid amide 31A, which is in equilibrium with its enol form 31B, was obtained. Primary and secondary amines react with the phenylpropiolamidinium chloride 13a under conjugated addition, delivering vinylogous guanidinium salts 33.
Allosteric Regulation of Proteases (2008)

Allostery is a basic principle of control of enzymatic activities based on the interaction of a protein or small molecule at a site distinct from an enzyme's active center. Allosteric modulators represent an alternative approach to the design and synthesis of small-molecule activators or inhibitors of proteases and are therefore of wide interest for medicinal chemistry. The structural bases of some proteinaceous and small-molecule allosteric protease regulators have already been elucidated, indicating a general mechanism that might be exploitable for future rational design of small-molecule effectors.
Targeting the IL-1 family members in skin inflammation. (2010)

The IL-1 family of cytokines comprises 11 proteins with pro- and anti-inflammatory functions that are mediated through an equally large group of receptors and coreceptors. Dysregulation of the IL-1 system may lead to diseases such as psoriasis, atopic dermatitis, contact dermatitis and cutaneous lupus erythematosus. These inflammatory skin conditions greatly affect quality of life and life expectancy, and their frequencies are increasing. However, treatment options for these diseases are unsatisfactory. This review briefly summarizes new findings, reported in the past 2 years, implicating IL-1 family members in skin inflammation. Furthermore, how the biological activities of the IL-1 family members may be inhibited is discussed.
An algorithm for maximizing target achievement in the stochastic knapsack problem with normal returns (1993)

We consider the stochastic linear knapsack problem in which costs are known with certainty but returns are independent, normally distributed random variables. The objective is to maximize the probability that the overall return equals or exceeds a specified target value. A previously proposed preference order dynamic programming-based algorithm has been shown to be potentially suboptimal. We offer an alternative hybrid DP/branch-and-bound algorithm that both guarantees optimality and significantly outperforms generating the set of Pareto optimal returns.© 1993 John Wiley & Sons, Inc.
Synthesis and Characterization of La<sub>0.8</sub>Sr<sub>0.2</sub>Ga<sub>0.8</sub>Mg<sub>0.2</sub>O<sub>3</sub><sub>-δ</sub> Nano-Particle by Aerosol Plasma Pyrolysis (2010)

Spherical La0.8Sr0.2Ga0.8Mg0.2O3-δ (LSGM) precursor powders were synthesized by aerosol plasma pyrolysis using an aqueous solution of metal nitrate. As-prepared powders obtained by this method were found to have a spherical morphology with a bimodal size distribution of nanosized (primary) and submicron-sized (secondary) particles. The average size of the primary particles was less than 100 nm. X-ray diffraction (XRD) patterns showed that as-prepared powders crystallized to LSGM and other phases. XRD revealed that LSGM pellets were crystallized to a perovskite structure after sintering at 1300 °C for 10 h.
Mail-Choosing the Best Method (1985)

The dispatch side of the mailing and/or sales departments of any organisation can save large sums of money each year if the personnel working in those departments keep an up-to-date check on the methods available for the dispatch of parcels and mail. While the information given here is accurate at the time of writing, readers must check to see the position at the time of reading — because the services change. If an organisation does not deliver its own parcels and mail it must choose from the alternatives and of these, those offered by the Post Office and British Rail are the most important.
Sustained High Prevalence of Chlamydia trachomatis Infections in Female Army Recruits (2003)

A study of 23,010 female Army recruits demonstrated that a high prevalence of C trachomatis was sustained during 4 years of observation. Year of study, young age, and being from the South were significant predictors of infection.
Liquid-Phase Epitaxy Growth of Gallium Phosphide by a Centrifugal Tipping Technique (1973)

A new growth technique for GaP single crystal material based on the liquid-phase epitaxial growth method is presented. This technique relies on centrifugal force to bring the saturated growth solution in contact with the substrate. The apparatus, referred to as the "centrifugal tipper," is described and its principles of operation are explained. Epitaxial layers, both n‐ and p‐ type, up to 100 µm thick, have been grown over a temperature range of 950°–1050°C. These layers exhibit good surface quality and variations in thickness of less than ±1 µm. A p‐type material with photoluminescence efficiency of 1.5% was produced. This new technique has demonstrated multislice capability for the growth of GaP light‐emitting diode material.
Using Hard Disks for Digital Preservation (2004)

The LOCKSS system is a tool librarians can use to preserve long-term access to content published on the web. It has three main functions. It collects the content by crawling the pub-lisher's web sites, it distributes the content by acting as a proxy for reader's browsers, and it preserves the content through a cooperative process of damage detection and repair. The system uses the hard disk holding the copy used for access as a preservation medium; the cooperative damage detection and repair mechanism eliminates the need for off-line backups on removable media. We describe the LOCKSS system as an example of the techniques needed to use hard disks as a medium for long-term preservation.
Human Saphenous Vein In Vitro Model for Studying the Action of Sclerosing Solutions (1993)

Direct toxic effects of sclerosing agents may be compared in a constant, reproducible environment with this in vitro model.
Efficient Privacy-Preserving Matrix Factorization via Fully Homomorphic Encryption (2016)

Recommendation systems become popular in our daily life. It is well known that the more the release of users' personal data, the better the quality of recommendation. However, such services raise serious privacy concerns for users. In this paper, focusing on matrix factorization-based recommendation systems, we propose the first privacy-preserving matrix factorization using fully homomorphic encryption. On inputs of encrypted users' ratings, our protocol performs matrix factorization over the encrypted data and returns encrypted outputs so that the recommendation system knows nothing on rating values and resulting user/item profiles. It provides a way to obfuscate the number and list of items a user rated without harming the accuracy of recommendation, and additionally protects recommender's tuning parameters for business benefit and allows the recommender to optimize the parameters for quality of service. To overcome performance degradation caused by the use of fully homomorphic encryption, we introduce a novel data structure to perform computations over encrypted vectors, which are essential operations for matrix factorization, through secure 2-party computation in part. With the data structure, the proposed protocol requires dozens of times less computation cost over those of previous works. Our experiments on a personal computer with 3.4 GHz 6-cores 64 GB RAM show that the proposed protocol runs in 1.5 minutes per iteration. It is more efficient than Nikolaenko et al.'s work proposed in CCS 2013, in which it took about 170 minutes on two servers with 1.9 GHz 16-cores 128 GB RAM.
Advances in P/M Gear Materials (2002)

&lt;div class="htmlview paragraph"&gt;Powder Metallurgy is an efficient manufacturing process for the production of gearing and similar net shape components. Because of limitations arising from the inherent porosity and limited alloy systems available, the traditional uses for P/M gearing was in relatively low stress applications. The recent introduction of new compaction techniques and new alloy materials has produced P/M components with significantly higher yield and tensile strengths approaching the strength levels of wrought gearing materials. This paper will review the new P/M processes and materials and their suitability for gear type applications. Mechanical property comparisons will be made to the common automotive gearing materials including ductile and malleable cast irons and wrought low alloy steels.&lt;/div&gt;
Reducing C-terminal truncation mitigates synucleinopathy and neurodegeneration in a transgenic model of multiple system atrophy (2016)

Multiple system atrophy (MSA) is a sporadic orphan neurodegenerative disorder. No treatment is currently available to slow down the aggressive neurodegenerative process, and patients die within a few years after disease onset. The cytopathological hallmark of MSA is the accumulation of alpha-synuclein (α-syn) aggregates in affected oligodendrocytes. Several studies point to α-syn oligomerization and aggregation as a mediator of neurotoxicity in synucleinopathies including MSA. C-terminal truncation by the inflammatory protease caspase-1 has recently been implicated in the mechanisms that promote aggregation of α-syn in vitro and in neuronal cell models of α-syn toxicity. We present here an in vivo proof of concept of the ability of the caspase-1 inhibitor prodrug VX-765 to mitigate α-syn pathology and to mediate neuroprotection in proteolipid protein α-syn (PLP-SYN) mice, a transgenic mouse model of MSA. PLP-SYN and age-matched wild-type mice were treated for a period of 11 wk with VX-765 or placebo. VX-765 prevented motor deficits in PLP-SYN mice compared with placebo controls. More importantly, VX-765 was able to limit the progressive toxicity of α-syn aggregation by reducing its load in the striatum of PLP-SYN mice. Not only did VX-765 reduce truncated α-syn, but it also decreased its monomeric and oligomeric forms. Finally, VX-765 showed neuroprotective effects by preserving tyrosine hydroxylase-positive neurons in the substantia nigra of PLP-SYN mice. In conclusion, our results suggest that VX-765, a drug that was well tolerated in a 6 wk-long phase II trial in patients with epilepsy, is a promising candidate to achieve disease modification in synucleinopathies by limiting α-syn accumulation.
Manganese‐Catalyzed Oxidative Azidation of Cyclobutanols: Regiospecific Synthesis of Alkyl Azides by CC Bond Cleavage (2015)

A novel, manganese-catalyzed oxidative azidation of cyclobutanols is described. A wide range of primary, secondary, and tertiary alkyl azides were generated in synthetically useful yields and exclusive regioselectivity. Aside from linear alkyl azides, otherwise elusive medium-sized cyclic azides were also readily prepared. Preliminary mechanistic studies reveal that the reaction likely proceeds by a radical-mediated C-C bond cleavage/C-N3 bond formation pathway.
Composite model-checking (2000)

There has been a surge of progress in automated verification methods based on state exploration. In areas like hardware design, these technologies are rapidly augmenting key phases of testing and validation. To date, one of the most successful of these methods has been symbolic model-checking, in which large finite-state machines are encoded into compact data structures such as Binary Decision Diagrams (BDDs), and are then checked for safety and liveness properties. However, these techniques have not realized the same success on software systems. One limitation is their inability to deal with infinite-state programs, even those with a single unbounded integer. A second problem is that of finding efficient representations for various variable types. We recently proposed a model-checker for integer-based systems that uses arithmetic constraints as the underlying state representation. While this approach easily verified some subtle, infinite-state concurrency problems, it proved inefficient in its treatment of boolean and (unordered) enumerated types—which are not efficiently representable using arithmetic constraints. In this article we present a new technique that combines the strengths of both BDD and arithmetic constraint representations. Our composite model merges multiple type-specific symbolic representations in a single model-checker. A system's transitions and fixpoint computations are encoded using both BDD (for boolean and enumerated types) and arithmetic constraints (for integers) representations, where the choice depends on the variable types. Our composite model-checking strategy can be extended to other symbolic representations provided that they support operations such as intersection, union, complement, equivalence checking, and relational image computation. We also present conservative approximation techniques for composite representations to address the undecidability of model-checking on infinite-state systems. We demonstrate the effectiveness of our approach by analyzing two example software specifications which include a mixture of booleans, integers, and enumerated types. One of them is a requirements specification for the control software of a nuclear reactor's cooling system, and the other one is a protocol specification.
DUB-ling down on the epigenetic regulation of cancer stem cells in glioblastoma (2023)

Glioblastoma (GBM) remains a challenge to effectively treat, due in part to cellular heterogeneity and therapeutic resistance, both of which are driven by self-renewing cancer stem cell (CSC) populations. 1 In addition to being driven by core pluripotency transcription factors and self-renewal signaling programs, CSCs possess a unique epigenetic state that drives self-renewal and suppresses differentiation programs. 2While much is known about how DNA methylation controls transcriptional programs, emerging evidence suggests that epigenetic regulation is more complex than initially appreciated, with RNA also capable of being methylated. 3N6-methyladenosine is a common reversible epigenetic modification on mRNA that determines RNA function and is essential for many tumorigenic processes, including the control of GBM CSCs. [4][5]5][6] Of the specific N6-methyladenosine demethylases, ALKBH5 (AlkB Homolog 5) has been implicated in many cancers, including GBM, where its expression is elevated in CSCs and drives their proliferation. 5While ALKBH5 appears to function upstream of many pro-tumorigenic programs, little is known about ALKBH5 regulation.Addressing this outstanding question was the focus of this manuscript by Chang et al. 7 The authors specifically focused on how ALKBH5 protein is stabilized by deubiquitylating enzymes (Fig. 1).In an initial screen of >40 deubiquitinases (DUBs), the addition of USP36 (Ubiquitin-Specific Peptidase 36) resulted in the highest expression of ALKBH5 protein, and USP36 was functionally validated to prevent the ubiquitination of ALKBH5.USP36 is well studied in the context of tumor cell proliferation via stabilization of c-myc and has previously been linked to GBM invasion and tumor growth via PRL1-mediated stabilization of Snail2. 8he authors observed expression of USP36 and ALKBH5 in GBM cell lines and CSCs, with generally higher expression of each in CSCs.The functional link between USP36 and ALKBH5 was first shown by the genetic reduction of USP36 via siRNA, which resulted in decreased protein stability of ALKBH5, and the opposite was observed with USP36 overexpression.Moreover, a catalytically dead USP36 phenocopied the reduction of ALKBH5.With evidence for this relationship between USP36 and ALKBH5, the authors assessed direct binding via immunoprecipitation studies.Direct binding between USP36 and ALKBH5 was confirmed, and domain mapping studies
Virtual Occupancy Grid Map for Submap-based Pose Graph SLAM and Planning in 3D Environments (2018)

In this paper, we propose a mapping approach that constructs a globally deformable virtual occupancy grid map (VOG-map) based on local submaps. Such a representation allows pose graph SLAM systems to correct globally accumulated drift via loop closures while maintaining free space information for the purpose of path planning. We demonstrate use of such a representation for implementing an underwater SLAM system in which the robot actively plans paths to generate accurate 3D scene reconstructions. We evaluate performance on simulated as well as real-world experiments. Our work furthers capabilities of mobile robots actively mapping and exploring unstructured, three dimensional environments.
Cohérence et polarisation de la lumière diffuse: le rôle des « coefficients croisés » de diffusion (2011)

International audience
Direct nuclear pumping of a Ne-N$sub 2$ laser (1976)

Direct nuclear pumping of a Ne-N$sub 2$ laser has been achieved with simultaneous output at two wavelengths (8629 and 9393 A) in atomic nitrogen. Pumping was achieved through bombardment of the gas by MeV ions generated when neutrons from a TRIGA reactor interact with a boron-10 coating on the inner wall of the laser cell. Pressure, concentration, threshold, and other parameters are presented. (AIP)
Calculation of the Auger line at the Si/SiO2 interface (1980)

The Auger line shape has been calculated for the surface of (100) silicon, using a semiempirical tight-binding slab model. Chemisorbed oxygen was considered by having the oxygen atom (or molecule) satisfy the double dangling bond of the surface atoms. The presence of the chemisorbed oxygen caused a shift of the outer-layer local density of states in such a manner to create additional structure in the N(E) distribution for the Auger transition. This structure correlates well with such structure reported recently by several experimental groups.
Dielectric and metallic nanosuspensions with tunable optical nonlinearities (2014)

We provide a brief report on our recent work on dielectric and metallic colloidal nanosuspensions with negative polarizability where we observed robust propagation of self-trapped light over a long distance. Our results open up new opportunities in developing soft-matter systems with tunable optical nonlinearities.
Filtering random noise from deterministic signals via data compression (1995)

We present a novel technique for the design of filters for random noise, leading to a class of filters called Occam filters. The essence of the technique is that when a lossy data compression algorithm is applied to a noisy signal with the allowed loss set equal to the noise strength, the loss and the noise tend to cancel rather than add. We give two illustrative applications of the technique to univariate signals. We also prove asymptotic convergence bounds on the effectiveness of Occam filters.
Electrophoretic Deposition of Gentamicin-Loaded Bioactive Glass/Chitosan Composite Coatings for Orthopaedic Implants (2014)

Despite their widespread application, metallic orthopaedic prosthesis failure still occurs because of lack of adequate bone-bonding and the incidence of post-surgery infections. The goal of this research was to develop multifunctional composite chitosan/Bioglass coatings loaded with gentamicin antibiotic as a suitable strategy to improve the surface properties of metallic implants. Electrophoretic deposition (EPD) was applied as a single-step technology to simultaneously deposit the biopolymer, bioactive glass particles, and the antibiotic on stainless steel substrate. The microstructure and composition of the coatings were characterized using SEM/EDX, XRD, FTIR, and TGA/DSC, respectively. The in vitro bioactivity of the coatings was demonstrated by formation of hydroxyapatite after immersion in simulated body fluid (SBF) in a short period of 2 days. High-performance liquid chromatography (HPLC) measurements indicated the release of 40% of the loaded gentamicin in phosphate buffered saline (PBS) within the first 5 days. The developed composite coating supported attachment and proliferation of MG-63 cells up to 10 days. Moreover, disc diffusion test showed improved bactericidal effect of gentamicin-loaded composite coatings against S. aureus compared to control non-gentamicin-loaded coatings.