gebhart/patrepeval huggingface dataset:
Depth versus Breadth in Convolutional Polar Codes (2018)

Polar codes were introduced in 2009 by Arikan as the first efficient encoding and decoding scheme that is capacity achieving for symmetric binary-input memoryless channels. Recently, this code family was extended by replacing the block-structured polarization step of polar codes by a convolutional structure. This article presents a numerical exploration of this so-called convolutional polar codes family to find efficient generalizations of polar codes, both in terms of decoding speed and decoding error probability. The main conclusion drawn from our study is that increasing the convolution depth is more efficient than increasing the polarization kernel's breadth as previously explored.
Inhibition of Tropoelastin Expression by 1, 25-Dihydroxyvitamin D 3 (1991)

Elastin production is modulated by steroid hormones and is dependent on calcium. Because vitamin D3 is involved in the regulation of calcium metabolism and influences the expression of various extracellular matrix proteins, we investigated whether vitamin D3 influences tropoelastin expression. Three elastin-producing, bovine cell types, auricular chondroblasts, nuchal ligament fibroblasts and arterial smooth muscle cells, were treated with the principal active metabolite of vitamin D3, 1,25-dihydroxyvitamin D3 (1,25[OH]2D3), and with 24,25 dihydroxyvitamin D3 (24,25[OH]2D3). Tropoelastin levels in culture media and cell layers, as measured by an enzyme-linked immunoassay, decreased in a dose and exposure dependent manner after treatment with 1,25(OH)2D3; 24,25(OH)2D3 had no effect on tropoelastin production relative to solvent-treated controls. The maximal effective dose of 1,25(OH)2D3 was 10(-7) M for 48 hr, which resulted in a severalfold reduction of tropoelastin production, and decreased tropoelastin levels were detected at 8 hr after treatment. Reduction of tropoelastin protein production was paralleled by a decrease of equal magnitude in the steady-state levels of tropoelastin mRNA. Vitamin D3 metabolites had no effect on DNA or total protein synthesis. These results suggest that vitamin D3 may be an important modulator of elastin expression.
Pharmacy Practice and Education in Latvia (2018)

The Pharmacy Education in Europe (PHARMINE) project studied pharmacy practice and education in the European Union (EU) member states. The work was carried out using an electronic survey forwarded to selected pharmacy representatives at community and hospital pharmacies, in the pharmacy industry and at drug authorities. The surveys of the individual member states are now being published as reference documents for students and staff interested in research on pharmacy education in the EU, and in mobility. This paper presents the results of the PHARMINE project on pharmacy practice and education in Estonia. In this paper, we examine the harmonisation of practice and education in Estonia with EU norms. Community pharmacies in Estonia provide traditional and extended services, of which influenza vaccination, the evaluation of the risk of diabetes, and medication use review have been introduced recently. Pharmacists (in Estonian <i>proviisor</i>) study at the University of Tartu for five years and graduate with a Master of Pharmacy (MSc Pharm) degree. A pharmacist can be the owner of a pharmacy, or work as a pharmacy manager or chief pharmacist in either a community or a hospital pharmacy. Assistant pharmacists (in Estonian <i>farmatseut</i>) study at the Tallinn Health Care College for 3 years; after graduation, they are mainly employed in community pharmacies. The University of Tartu is the only university in Estonia providing higher education in pharmacy at university level. The pharmacy curriculum is an integrated (bachelor followed by master), pharmaceutical product-oriented study programme. It was last updated in 2019. On that occasion, several changes were made such as the introduction of competency-based modules; novel methods in education and training based on the constructive alignment and the restructuring of the six-month traineeship. Several new courses focus on the concepts of clinical pharmacy and on patient-centred communication. In the current pharmacy curriculum, there is a balance between chemical and medical subjects. The traineeship is provided for six months at a community and/or hospital pharmacy in the 5th year. Currently, the pharmacy curriculum at the University of Tartu does not offer specialization in subjects such as hospital or industrial pharmacy.
Inducing Social Self-Sorting in Organic Cages to Tune the Shape of the Internal Cavity (2020)

&lt;p&gt;Many interesting target guest molecules have low symmetry, yet most methods for synthesising hosts result in highly symmetrical capsules. Methods of generating lower-symmetry pores are thus required to maximise the binding affinity in host-guest complexes. Here, we use mixtures of tetraaldehyde building blocks to access low-symmetry imine cages. Whether a low-energy cage is isolated can be correctly predicted from the thermodynamic preference observed in computational models. The stability of the observed structures depends on the geometrical match of the aldehyde building blocks. One bent aldehyde stands out as unable to assemble into high-symmetry cages—and the same aldehyde generates low-symmetry socially self-sorted cages when combined with a linear aldehyde. We exploit this finding to synthesise a family of low-symmetry cages containing heteroatoms, illustrating that pores of varying geometries and surface chemistries may be reliably accessed through computational prediction and self-sorting.&lt;/p&gt;
Technologies de l’hydrogène (2013)

Par une approche multidisciplinaire, combinant des approches de chimie de synthèse bio-inspirée et de chimie des protéines, des chercheurs du Collège de France, du CEA, du CNRS et de l’université Joseph-Fourier, en collaboration avec le Max-Planck Institut de Mülheim et l’université de Bochum, ont mis au point un réactif simple et efficace pour activer les hydrogénases, des métalloenzymes actuellement étudiées pour leurs applications comme catalyseurs dans des dispositifs de production d’hydr...
Interaction of lectins with Neisseria gonorrhoeae (1980)

Fifty-four strains of Neisseria gonorrhoeae were examined for their ability to be agglutinated by various lectins. Wheat germ agglutinin, ricin, soybean lectin, and peanut agglutinin agglutinated all strains tested. Dolichos biflorus, Sophora japonica, Maclura pomifera, Ulex Europaeus, Lens culinaris, Canavalia ensiformis, Phaseolus lunatus, and Bandeiraea simplicifolia BS I and BS II lectins either failed to agglutinate or agglutinated some strains but not others. Agglutination of gonococci by wheat germ agglutinin, ricin, and soybean lectin is sugar specific and most effectively inhibited by ligands known to interact with lectin combining sites. Lectin reactive groupings appear to be independent of antigenic determinants conferring Gc serogroup specificity. Interactions with wheat germ agglutinin and ricin suggest the occurrence of multiple beta-linked N-acetyl-D-glucosamine (D-GlcNAc) and beta-D-galactosyl (beta-D-Gal) units as common structural features of gonococcal cell envelope polysaccharide. Interactions with soybean agglutinin, peanut agglutinin, and Dolichos biflorus lectins suggest that alpha-N-acetyl-D-galactosamine (alpha-D-GalNAc) units and beta-D-Gal linked to GalNAc and (or) GlcNAc may also occur as structural features of the polysaccharide components of the cell envelope of some gonococci.
Abstract 4451: Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models (2020)

Abstract Cancer immunotherapies with anti-PD-1/PD-L1 checkpoint blockade antibodies have revolutionized the treatment of a wide variety of malignancies. However, immunotherapy is ineffective in a significant subset of patients, or eventually results in the development of resistance with relapsed disease. Therefore, the future of immuno-oncology is identification of new agents that can be combined to increase the depth and breadth of anti-PD-1/PD-L1 therapies. Local intratumoral delivery of messenger RNA (mRNA)-based immunotherapies provides an opportunity to stimulate innate and adaptive immune responses against tumors and modulate tumor microenvironment, while limiting the side-effects related to systemic administration of immuno-modulatory therapeutics. We examined the local immunotherapy of synthetic mRNAs encoding immunomodulatory cytokines (single chain interleukin-12 (IL-12), interferon alpha (IFN-α), granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-15 sushi(IL-15)) alone and in combination with anti-PD-1 antibodies across 12 syngeneic mouse tumor models representing a diverse range of murine tumor types. Single agent treatment with cytokine mRNAs resulted in a significant anti-tumor response in 8 out of 12 tumor models. Combining cytokine mRNA with systemic anti-PD-1 immunotherapy further improved the anti-tumor response and resulted in tumor growth inhibition in two additional models otherwise unresponsive to single agent treatments. Transcriptome and cytokine analyses have been performed to understand factors which determine sensitivity to single agent and combination treatments with cytokine mRNA and anti-PD-1 antibodies. In summary, the combination of local cytokine mRNA immunotherapy with immune checkpoint blockade demonstrated improvement in the anti-tumor activity in a range of preclinical cancer models representing different murine tumor types. Based on these and other data, clinical testing of cytokine encoding mRNA mixture has recently been initiated (NCT03871348). Citation Format: Natalia V. Malkova, Tatiana Tolstykh, Mikhail Levit, Joachim Theilhaber, Andrew Hebert, Kevin Atchison, Adalis Maisonet, Christian Hotz, Ugur Sahin, Alexei Protopopov, Jack Pollard, Sukhvinder Sidhu, Dmitri Wiederschain, Timothy R. Wagenaar. Combination of local mRNA immunotherapy with systemic immune checkpoint blockade demonstrates anti-tumor activity across a diverse range of preclinical syngeneic tumor models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4451.
Ozone Production in a Dielectric Barrier Discharge with Ultrasonic Irradiation (2011)

Ozone production has been investigated using an atmospheric pressure dielectric barrier discharge in pure O2 at room temperature with and without ultrasonic irradiation. It was driven at a frequency of either 15 kHz or ∼40 kHz. The ozone production was highly dependent on the O2 flow rate and the discharge power. Furthermore, powerful ultrasonic irradiation at a fundamental frequency of ∼30 kHz with the sound pressure level of ∼150 dB into the discharge can improve the ozone production efficiency, particularly when operated at the frequency of 15 kHz at the flow rate of 15 L/min.
Single Amino Acid Preferences for Specific Locations at Type-I α-Turns in Globular Proteins (1999)

Abstract Using both dihedral angles and hydrogen-bond definitions, 225 type-I α-turns were extracted from 125 analyzed proteins. The extracted α-turns were built up from 5% (1125) of the total amino acid residues (23286) found in the proteins. The type-I α-turn is an independent kind of secondary structural unit, although it has been frequently classified as (i, i+1) double β-turns. Both the nucleation of a helix with the type-I β-turn and its propagation with the repetitive addition of the type-I β-turn suggest that the origin of the helix in a globular protein might be the type-I β-turn. Single amino acid preferences for specific locations at type-I α-turns were compared to those at type-I β-turns and the ends of helices. The result indicates that the type-I α-turn, the type-I β-turn, and the helix are of similar kin. Similarities in the structure and amino acid preferences for specific locations among them suggest that the amino acid residues on defined positions along both turns could be properly assigned to the corresponding helix elements.
Silicon Photonic Modulators for High Speed Optical Analog Links (2017)

We discuss recent progress on the design of silicon photonic modulators for high speed digital and analog optical links and their implementation using advanced modulation formats (including PAM and DMT).
In Vitro Infection with Hepatitis B Virus Using Differentiated Human Serum Culture of Huh7.5-NTCP Cells without Requiring Dimethyl Sulfoxide (2021)

An estimated two billion people worldwide have been infected with hepatitis B virus (HBV). Despite the high infectivity of HBV in vivo, a lack of easily infectable in vitro culture systems hinders studies of HBV. Overexpression of the sodium taurocholate co-transporting polypeptide (NTCP) bile acid transporter in hepatoma cells improved infection efficiency. We report here a hepatoma cell culture system that does not require dimethyl sulfoxide (DMSO) for HBV infection. We overexpressed NTCP in Huh7.5 cells and allowed these cells to differentiate in a medium supplemented with human serum (HS) instead of fetal bovine serum (FBS). We show that human serum culture enhanced HBV infection in Huh7.5-NTCP cells, e.g., in HS cultures, HBV pgRNA levels were increased by as much as 200-fold in comparison with FBS cultures and 19-fold in comparison with FBS+DMSO cultures. Human serum culture increased levels of hepatocyte differentiation markers, such as albumin secretion, in Huh7.5-NTCP cells to similar levels found in primary human hepatocytes. N-glycosylation of NTCP induced by culture in human serum may contribute to viral entry. Our study demonstrates an in vitro HBV infection of Huh7.5-NTCP cells without the use of potentially toxic DMSO.
Gate-Bias-Induced Threshold Voltage Shifts in GaN FATFETs (2023)

The threshold voltage ( V TH ) stability in GaN fat field-effect transistors (FATFETs) with a large channel area of ∼6.2 × 10 4 μ m 2 was studied using drain current vs gate voltage ( I D – V G ) characteristics. Each measurement was found to positively shift the previous I D – V G curve, and V TH eventually saturated with increasing number of measurements. The saturated V TH was ∼0.8 V for measurements in which V G ranged from −10 to 25 V and was ∼8 V for measurements in which the V G ranged from −10 to 40 V. Moreover, the positive gate bias stress increased V TH to 12.3 V. These shifts of V TH can be explained by electron trapping; according to charge-pumping measurements, the traps cannot exist in the oxide or the oxide/ p -GaN interface but can exist near the surface region in p -GaN layers in GaN FATFETs. Scanning transmission electron microscopy and electron energy-loss spectroscopy analyses revealed the presence of oxygen within several atomic layers of p -GaN from the oxide/ p -GaN interface. This intermixed oxygen might be the origin of the n -type behavior of the p -GaN surface; furthermore, the oxygen is speculated to be related to the traps. Surprisingly, similar incorporated oxygen was observed even in the surface region of as-grown p -GaN layers.
4-Formyloxazole (2008)

[118994-84-6] C4H3NO2 (MW 97.07) InChI = 1S/C4H3NO2/c6-1-4-2-7-3-5-4/h1-3H InChIKey = JBWIIXBEPINWPB-UHFFFAOYSA-N (electrophilic reagent for incorporation of the 4-oxazolyl unit; aminomalondialdehyde synthetic equivalent) Alternate Names: 4-oxazolecarboxaldehyde; 1,3-oxazole-4-carboxaldehyde. Physical Data: white solid, mp 59–61 °C. Solubility: soluble in most organic solvents such as tetrahydrofuran. Sparingly soluble in water. Handling, Storage, and Precautions: handle and store under inert atmosphere. Incompatible with strong acids and bases, also oxidizing and reducing reagents. No toxicity or hazard data available. Store under nitrogen or argon to prevent oxidation. Form Supplied in: limited commercial availability as a solid. Analysis of Reagent Purity: 1H NMR and elemental analysis (C, H, N). Preparative Methods: can be prepared by partial reduction of ethyl 4-oxazolecarboxylate with diisobutylaluminum hydride in CH2Cl2.1 Alternatively, ethyl 4-oxazolecarboxylate may be reduced to 4-oxazolylmethanol using lithium triethylborohydride, and the alcohol oxidized to 4-formyloxazole by a Swern oxidation.2 Oxazole 4-carboxylic acid may be converted to oxazole 4-carboxylic acid chloride with SOCl2 and the acid chloride reduced to 4-formyloxazole with Pd/BaSO4 and H2.3 Purification: can be recrystallized from CH2Cl2/hexanes.1
Flow cytometric scoring of micronucleated erythrocytes: an efficient platform for assessing in vivo cytogenetic damage (2010)

The relative simplicity of the micronucleated erythrocyte endpoint has made it amenable to automated scoring approaches. Flow cytometry is one such scoring platform that has been employed successfully. This review describes the evolution and properties of flow cytometry-based scoring of micronucleated erythrocytes. The methodology has become widely applied to rodent blood specimens and the high throughput nature of the technology provides a number of advantages over manual microscopic scoring. For instance, the ability to efficiently survey many dose levels and many more cells per specimen relative to microscopy benefits studies that are designed to identify no observable effect levels or lowest observable effect levels. Furthermore, flow cytometry makes it practical to study species with low spontaneous reticulocyte (RET) counts and micronucleus (MN) frequencies, thereby facilitating integration of blood-based micronucleated reticulocyte (MN-RET) frequency measurements into experiments conducted across species of toxicological interest. This capability enhances genotoxicity assessments that have historically been made in dedicated MN tests performed in one species. Importantly, the feasibility of using MN-RET frequencies in blood from humans as an index of genetic damage in bone marrow opens a critical area of application that had not been practical previously. We conclude with recommendations for additional work that is needed to more fully realise the potential of flow cytometric in vivo MN scoring.
Radical Technology Meets Radical Application: An Interview with George Church (2019)

That's right-one of my many
AutoMate: A Dataset and Learning Approach for Automatic Mating of CAD Assemblies (2021)

Assembly modeling is a core task of computer aided design (CAD), comprising around one third of the work in a CAD workflow. Optimizing this process therefore represents a huge opportunity in the design of a CAD system, but current research of assembly based modeling is not directly applicable to modern CAD systems because it eschews the dominant data structure of modern CAD: parametric boundary representations (BREPs). CAD assembly modeling defines assemblies as a system of pairwise constraints, called mates, between parts, which are defined relative to BREP topology rather than in world coordinates common to existing work. We propose SB-GCN, a representation learning scheme on BREPs that retains the topological structure of parts, and use these learned representations to predict CAD type mates. To train our system, we compiled the first large scale dataset of BREP CAD assemblies, which we are releasing along with benchmark mate prediction tasks. Finally, we demonstrate the compatibility of our model with an existing commercial CAD system by building a tool that assists users in mate creation by suggesting mate completions, with 72.2% accuracy.
BIOTRANSFORMATION OF DEHYDROABIETIC ACID WITH MICROBIAL CELL CULTURES AND α-GLUCOSIDASE INHIBITORY ACTIVITY OF RESULTING METABOLITES (2014)

Dehydroabietic acid (DHA, 1 ), a natural occurring diterpene resin acid, is an abundant resin acid in conifers, representing a natural wood protectant. The aim of this study was to use microbial cell cultures as tools for modification of 1 in order to obtain value-added functional derivatives. A scaled-up biotransformation of 1 by filamentous fungus Cunninghamella elegans , Rhizopus stolonifer , Gibberella fujikuroi , and Cephalosporium aphidicola were conducted for the first time. Three hydroxylated metabolites; 1b-hydroxydehydroabietic acid ( 2 ); 15-hydroxy dehydroabietic acid ( 3 ); and 16-hydroxy dehydroabietic acid ( 4 ). The structure of the hydroxylated metabolites were elucidated by 1-D ( 1 H, 13 C) and 2-D NMR (COSY, HMBC, HMQC, NOESY) techniques and MS analyses. Dehydroabietic acid ( 1 ) and their transformed products 2 - 4 exhibited a promising α-Glucosidase inhibitory activity. Compound 1 showed 38 times more active than the standard α-Glucosidase inhibitor, deoxynojirimycin. Compound 1 and its transformed metabolites 2 - 4 also showed significant antibacterial activities. Keywords: Microbial transformation, Dehydroabietic acid, Antibacterial activities, α-Glucosidase.
Data from Combining Local Immunotoxins Targeting Mesothelin with CTLA-4 Blockade Synergistically Eradicates Murine Cancer by Promoting Anticancer Immunity (2023)

&lt;div&gt;Abstract&lt;p&gt;Immune checkpoint blockade using antibodies to cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) benefits a limited number of cancer patients. SS1P and LMB-100 are immunotoxins that target mesothelin. We observed delayed responses to SS1P in patients with mesothelioma suggesting that antitumor immunity was induced. Our goal was to stimulate antitumor immunity by combining SS1P or LMB-100 with anti–CTLA-4. We constructed a BALB/c breast cancer cell line expressing human mesothelin (66C14-M), which was implanted in one or two locations. SS1P or LMB-100 was injected directly into established tumors and anti–CTLA-4 administered i.p. In mice with two tumors, one tumor was injected with immunotoxin and the other was not. The complete regression rate was 86% for the injected tumors and 53% for the uninjetced tumors. No complete regressions occurred when drugs were given separately. In regressing tumors, dying and dead tumor cells were intermingled with PMNs and surrounded by a collar of admixed eosinophils and mononuclear cells. Tumor regression was associated with increased numbers of tumor-infiltrating CD8&lt;sup&gt;+&lt;/sup&gt; cells and blocked by administration of antibodies to CD8. Surviving mice were protected from tumor rechallenge by 66C14 cells not expressing mesothelin, indicating the development of antitumor immunity. The antitumor effect was abolished when a mutant noncytotoxic variant was used instead of LMB-100, showing that the antitumor response is not mediated by recognition of a foreign bacterial protein. Our findings support developing a therapy composed of immunotoxins and checkpoint inhibitors for patients. &lt;i&gt;Cancer Immunol Res; 5(8); 685–94. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
The Elbow Cache: A Power-Efficient Alternative to Highly Associative Caches (2003)

Increasing the associativity is a common way to reduce the performance-detrimental conflicts in a cache. From a dynamic cache power perspective this associativity comes at a high cost. In this paper we present miss ratio performance and dynamic power estimates for a skewed cache and also for the organization proposed in this paper, the elbow cache. We will show that by extending a skewed cache organization with a relocation strategy we can obtain a miss ratio that is comparable to the miss ratio of an 8-way set-associative cache, while consuming up to 48% less dynamic power.