gebhart/patrepeval huggingface dataset:
2-(Maleimidomethyl)-1,3-Dioxanes (MD): a Serum-Stable Self-hydrolysable Hydrophilic Alternative to Classical Maleimide Conjugation (2016)

The vast majority of antibody-drug conjugates (ADC) are prepared through amine-to-thiol conjugation. To date, N-Succinimidyl-4-(maleimidomethyl) cyclohexanecarboxylate (SMCC) has been one of the most frequently applied reagents for the preparation of ADC and other functional conjugates. However, SMCC-based conjugates suffer from limited stability in blood circulation and from a hydrophobic character of the linker, which may give rise to major pharmacokinetic implications. To address this issue, we have developed a heterobifunctional analogue of a SMCC reagent, i.e., sodium 4-(maleimidomethyl)-1,3-dioxane-5-carbonyl)oxy)-2,3,5,6- tetrafluorobenzenesulfonate (MDTF) for amine-to-thiol conjugation. By replacing the cyclohexyl ring in the SMCC structure with the 1,3-dioxane, we increased the hydrophilicity of the linker. A FRET probe based on MD linker was prepared and showed superior stability compared to the MCC linker in human plasma, as well as in a variety of aqueous buffers. A detailed investigation demonstrated an accelerated succinimide ring opening for MD linker, resulting in stabilized conjugates. Finally, the MDTF reagent was applied for the preparation of serum stable antibody-dye conjugate.
Minimus: a fast, lightweight genome assembler (2007)

We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.
Evolutionary conservation of domain-domain interactions (2006)

Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.
Calculating Restart States for Systems Modeled by Operations Using Supervisory Control Theory (2013)

This paper presents a supervisory control theory based offline method for calculating restart states in a manufacturing control system. Given these precalculated restart states, an operator can be given correct instructions for how to resynchronize the control system and the manufacturing resources during the online restart process. The proposed method enables restart after unforeseen errors. It is assumed that the control system is modeled by operations and that possible operation sequences emerge through dependencies between the operations. The paper shows how reexecution requirements may be included in the calculation to obtain a correct behavior for the restarted system. In addition, it is shown how to filter out restart states that require less effort for the operator during the online restart, and how to adapt the nominal production to always enable restart in desired restart states.
IMPROVED HIGH‐PERFORMANCE LIQUID CHROMATOGRAPHIC ANALYSIS OF 8‐METHOXYPSORALEN MONOADDUCTS and CROSS‐LINKS IN POLYNUCLEOTIDE, DNA, and CELLULAR SYSTEMS: ANALYSIS OF SPLIT‐DOSE PROTOCOLS (1993)

The distribution of 8-methoxypsoralen-thymidine photoadducts from polynucleotides, calf thymus DNA and mammalian cells treated with [3H]8-methoxypsoralen under a variety of irradiation conditions was determined using high-performance liquid chromatography and scintillation analysis. The split-dose protocol, with samples treated with 8-methoxypsoralen and low doses of long-wavelength UV radiation to generate monoadducts, washed to remove unreacted 8-methoxypsoralen, then irradiated further to convert the monoadducts to cross-links, was examined. The photoadduct distribution in the first step is dependent upon the UVA dose and the wavelength of the radiation, but it is relatively independent of 8-methoxypsoralen concentration. Low fluence and longer wavelengths generate mainly 4',5'-monoadducts, whereas higher fluences and shorter wavelengths yield more cross-links. The second irradiation step converts the 4',5'-monoadducts to cross-links as well as to 3,4-monoadducts. The overall yield of cross-links after the second irradiation step is not dependent upon the wavelength used in the first step. Cellular studies demonstrated that the split-dose protocol is applicable to mammalian systems. These results may affect the interpretation of mutagenesis studies based on the split-dose protocol, because the second step can convert 4',5'-monoadducts to both 3,4-monoadducts, the expected cross-links. Therefore, interpretations that link increases in mutagenicity after the second step in a split-dose study solely to cross-link formation may need re-examination.
Thermodynamic properties of transition metal compounds and coordination complexes: I. The heats of hydration of divalent cations in the series Ca<sup>2+</sup> ‐ Zn<sup>2+</sup> (1962)

Abstract According to the ligand‐field theory the heat of hydration of a transition‐metal ion is the sum of an electrostatic interaction and a ligand‐field stabilization. An estimate of the latter can be deduced from the spectroscopic Δ‐value. If the experimental heats are corrected for the ligand‐field effects, a steady rise for the residual heats is observed going from Ti 2+ to Zn 2+ which is considered an argument for the validity of the theory. However, in the m.o. approximation the metal d‐electrons are either in the t 2g state (non‐bonding in the absence of π‐interaction) or in the antibonding e g state. Hence formally the transition‐metal hydrates can be considered as destabilized with respect to a hypothetical standard state which can be calculated, by making suitable corrections, with help of the spectroscopic Δ‐values. It is shown here that the values so obtained are numerically equal to those given by an empirical equation for cations with the inert gas configuration — (ΔH n ) = I + constant (I is the ionization energy for the formation of divalent cations).
Acid-Base Catalysis of Chiral Pd Complexes: Development of Novel Catalytic Asymmetric Reactions and Their Application to Synthesis of Drug Candidates (2006)

Using the unique character of the chiral Pd complexes 1 and 2, highly efficient catalytic asymmetric reactions have been developed. In contrast to conventional Pd(0)-catalyzed reactions, these complexes function as an acid-base catalyst. Thus active methine and methylene compounds were activated to form chiral palladium enolates, which underwent enantioselective carbon-carbon bond-forming reactions such as Michael reaction and Mannich-type reaction with up to 99% ee. Interestingly, these palladium enolates acted cooperatively with a strong protic acid, formed concomitantly during the formation of the enolates to activate electrophiles, thereby promoting the C-C bond-forming reaction. This palladium enolate chemistry was also applicable to electrophilic enantioselective fluorination reactions, and various carbonyl compounds including beta-ketoesters, beta-ketophosphonates, tert-butoxycarbonyl lactone/lactams, cyanoesters, and oxindole derivatives could be fluorinated in a highly enantioselective manner (up to 99% ee). Using this method, the catalytic enantioselective synthesis of BMS-204352, a promising anti-stroke agent, was achieved. In addition, the direct enantioselective conjugate addition of aromatic and aliphatic amines to alpha,beta-unsaturated carbonyl compound was successfully demonstrated. In this reaction, combined use of the Pd complex 2 having basic character and the amine salt was the key to success, allowing controlled generation of the nucleophilic free amine. This aza-Michael reaction was successfully applied to asymmetric synthesis of the CETP inhibitor torcetrapib.
Experience with Traits in the Xerox Star Workstation (1984)

The Xerox Star (8010) is an integrated office workstation. Its software is written in an object-oriented style. Often, different applications will impose slightly different requirements on nominally similar objects which they use. Customization of object definitions for different applications is achieved by attaching modifiers called traits to pre-existing object defintions. This paper describes the approach and recounts our experience with traits.
Investigation of the Kinetic Hydrate Inhibitor Performance of a Series of Copolymers of<i>N</i>-Vinyl Azacyclooctanone on Structure II Gas Hydrate (2013)

A series of copolymers of N-vinylazacyclooctanone (VACO) with more hydrophilic monomers, including the 5–7 ring N-vinyl lactams, N-vinyl-N-methyl acetamide (VIMA), and N-vinyl acetamide (NVA), have been synthesized. Their performance as kinetic hydrate inhibitors (KHIs) was compared to poly(N-vinylazacyclooctanone) (PVACO) homopolymer in high pressure rocking cells using a Structure II hydrate-forming natural gas mixture. The best 1:1 copolymer between any two of the four N-vinyl lactams was found to be for VP/VACO copolymer. 1:1 VACO/VIMA copolymers were also shown to be a superior KHI to PVACO, whereas copolymers of other ratios of these two monomers were less effective KHIs. 2-Butoxyethanol (BGE) was also found to be a good solvent and synergist for 1:1 VACO/VIMA copolymers. Finally, 1:1 N-vinyl lactam/NVA copolymers were shown to have worse KHI performance than the equivalent 1:1 N-vinyl lactam/VIMA copolymers at similar molecular weights.
The influence of statins on the free intracellular calcium concentration in human umbilical vein endothelial cells (2004)

The increase of resting [Ca2+]i after incubation with cerivastatin or fluvastatin may provide an explanation for the direct effects of statins on the endothelial-dependent vasodilatation and restoration of endothelial activity in vivo.
Inverse Solution for Bolt Preload Using Joint Surface Deformation (2013)

In this paper, an inverse bi-harmonic axisymmetric elasticity problem is solved by invoking measured out-of-plane surface deformation values at discrete locations around a preloaded bolt head, in order to calculate the under head contact stress and joint clamp load that would have caused that out-of-plane surface deformation. Solution of this type of inverse problem promises to improve the automation process of bolted joint system assembly, especially in critical and safety related applications. For example, a real-time optically measured joint surface deformation can be utilized for automating process control of bolted joint assembly in a reliable fashion. This would be a significant reliability improvement as compared to the commonly used method in mass production using torque-only control method in which there is wide scatter in the torque-tension correlation due to the normal scatter in frictional variables. Finite Element Analysis (FEA) method is used to validate the inverse problem solution provided in this paper.
Response to remarks regarding the optimal design and operation of helium refrigeration systems (2012)

Abstract
Biodegradation of 1,2,3-Trichloropropane to Valuable (S)-2,3-DCP Using a One-Pot Reaction System (2019)

1,2,3-trichloropropane (TCP) being one of the important environmental pollutants, has drawn significant concern due to its highly toxic and carcinogenic effects. In this study, we built a one-pot reaction system in which immobilized haloalkane dehalogenase (DhaA31) and halohydrin dehalognase (HheC) were used to catalyze the recalcitrant TCP to produce 2,3-dichloro-1-propanol (2,3-DCP) by removing epichlorohydrin (ECH). Since HheC displays a high R enantiopreference toward 2,3-DCP, the production of enantiopure (S)-2,3-DCP was expected. However, the enantioselective resolution of (R,S)-2,3-DCP by HheC was greatly inhibited by the circular reaction occurring between the product ECH and 1,3-dichloro-2-propanol (1.3-DCP). To resolve this problem, HZD-9 resin-based in situ product removal was implemented. Under the optimized conditions, TCP was completely consumed, resulting in optically pure (S)-2,3-DCP with enantiomer excess (e.e) > 99% and 40% yield (out of the 44% theoretical maximum). The scale-up resin-integrated reaction system was successfully carried out in 0.5 L batch reactor. Moreover, the system could be reused for 6 rounds with 64% of original activity retained, showing that it could be applied in the treatment of large volumes of liquid waste and producing enantiopure (S)-2,3-DCP.
Structure and function of the hematopoietic cancer niche focus on chronic lymphocytic leukemia (2012)

Chronic Lymphocytic Leukemia (CLL) is a B cell malignancy characterized by the accumulation of mature monoclonal CD5-positive B cells in the blood, secondary lymphoid tissues, and marrow. The infiltration of CLL cells in lymphoid tissues is a key element of disease pathogenesis. It is in such tissues that are found the microenvironments that provide CLL cells protection from spontaneous and/or drug-induced apoptosis. CLL cells actively shape their microenvironment by producing cytokines and chemokines, and by subverting normal accessory cells to promote leukemia-cell survival, proliferation, and escape from immune detection. In this review, we discuss how CLL cells disrupt the niches required for normal hematopoiesis or immune function and subvert normal cells in the microenvironment to support neoplastic cell growth and survival.
Facile Synthetic Access to Multisubstituted Benz[<i>f</i>]indenones and Their Application as Ligands to the First Synthesis of Group(IV) Metallocene Complexes (2003)

[reaction: see text] A very efficient method for the synthesis of benz[f]indenone derivatives was developed. This method allows the introduction of a variety of substituents to a molecule. The first zirconocene compound of benz[f]indene was synthesized.
Studies of biomolecular conformations and conformational dynamics by mass spectrometry (2002)

In the post-genomic era, a wealth of structural information has been amassed for proteins from NMR and crystallography. However, static protein structures alone are not a sufficient description: knowledge of the dynamic nature of proteins is essential to understand their wide range of functions and behavior during the life cycle from synthesis to degradation. Furthermore, few proteins have the ability to act alone in the crowded cellular environment. Assemblies of multiple proteins governed by complex signaling pathways are often required for the tasks of target recognition, binding, transport, and function. Mass spectrometry has emerged over the past several years as a powerful tool to address many of these questions. Recent improvements in "soft" ionization techniques have enabled researchers to study proteins and biomolecular complexes, both directly and indirectly. Likewise, continuous improvements in instrumental design in recent years have resulted in a dramatic expansion of the m/z range and resolution, enabling observation of large multi-protein assemblies whose structures are retained in the gas phase. In this article, we discuss some of the mass spectrometric techniques applied to investigate the nature of the conformations and dynamical properties that govern protein function.
Enregistrement magnétique ultra-haute densité sur médias discrets à aimantation perpendiculaire (2007)

Patterned media is a potential new recording disk technology which can be used to increase the areal density in magnetic storage devices towards 1 Tbit/in2 and beyond. Patterned media allows circumventing the super-paramagnetic limit, which is expected to appear in conventional magnetic recording media at densities of the order of 300 Gb/in². Implementation of patterned media requires the fabrication of sub-50nm features over large areas at high-throughput manufacturing and low cost. In our approach, called pre-patterned media, isolated tracks of sub-100nm islands have been fabricated using nano-imprint technology, followed by sputtering deposition of a Co/Pt multilayer exhibiting a perpendicular-to-plane anisotropy. The recording performances on the pre-patterned magnetic structures have been studied with a contact tester using a high-resolution (~1nm) piezoelectric positioning stage and commercial giant magnetoresistive write/read heads. Bits with different lengths (BL), i.e. including a varying number of dots, have been written on the pattern. The synchronization requirements have been investigated along tracks of dots revealing a significant ‘‘write window,'' where islands can be written correctly, of about half the dot period. Moreover, the signal to noise ratio (SNR) has been calculated, by evaluating the correlation coefficients of the readback voltages of periodically written pseudo random bit sequences (PRBS). We conclude that the major sources of medium noise are the bit size fluctuations, bit amplitude and the jitter noise due to the substrate replication processes.
Keratan sulfate is a component of proteoglycans in the compressed region of adult bovine flexor tendon (1988)

A monoclonal antibody (ET-4-A-4) was used to identify keratan sulfate (KS) as a constituent of bovine flexor tendon. KS was present in at least 500-fold higher amounts in the fibrocartilaginous region of the tendon that is subjected to compressive forces in vivo (mean = 0.03% of tissue dry weight) than in the more proximal regions subjected only to tensional forces. The KS was associated with proteoglycans of three size categories that could be separated by Sepharose CL-4B chromatography. The largest proteoglycan (Vo) contained approximately 4% KS and was predominant in the surface region of the tendon subjected directly to compressive forces. A population of somewhat smaller molecules (Kav approximately equal to 0.3) contained less than or equal to 20% KS and proportionately less chondroitin sulfate (CS) or dermatan sulfate (DS). The KS chains of this population were not digested by keratanase. This population was dominant in tissue from the middle layer of the fibrocartilaginous region. A third population of small KS proteoglycans or fragments (Kav approximately equal to 0.6) comprised 40% of the KS found in the deepest layer of the compressed tendon region. This smaller component was independent of the small DS proteoglycans.
Chromium supplementation in impaired glucose tolerance of elderly: effects on blood glucose, plasma insulin, C-peptide and lipid levels (1992)

Altogether twenty-six elderly subjects (aged 65-74 years) with persistent impaired glucose tolerance (World Health Organization (1985) criteria) identified in a population-based study, were randomly treated either with chromium-rich yeast (160 micrograms Cr/d) or with placebo for 6 months. The 24 h urinary Cr increased from 0.13 (SE 0.03) to 0.40 (SE 0.06) micrograms/d in the Cr group (n 13) but no change was found in the placebo group (n 11) (0.13 (SE 0.02) v. 0.11 (SE 0.02) micrograms/d). No significant change was observed in the oral glucose tolerance test (glucose dose 75 g; 0, 1 and 2 h blood glucose respectively): 5.3 (SE 0.1), 9.3 (SE 0.3), 8.2 (SE 0.3) mmol/l v. 5.0 (SE 0.1), 8.5 (SE 0.4), 7.3(SE 0.5) mmol/l in the Cr group; 4.9 (SE 0.2), 9.2 (SE 0.6), 8.1 (SE 0.3) mmol/l v. 4.8 (SE 0.2), 8.5 (SE 0.5), 7.0 (SE 0.6) mmol/l in the placebo group (baseline v. 6 months). Glycosylated haemoglobin, plasma insulin, C-peptide and apolipoprotein A1 and B levels remained unchanged, and no improvement was seen in serum total cholesterol (6.2 (SE 0.3) v. 6.4 (SE 0.3) mmol/l for the Cr group, 6.2 (SE 0.4) v. 6.5 (SE 0.3) mmol/l for the placebo group), high-density-lipoprotein-cholesterol (1.1 (SE 0.1) v. 1.2 (SE 0.1) mmol/l for the Cr group, 1.0 (SE 0.1) v. 1.1 (SE 0.1) mmol/l for the placebo group) or triacylglycerols (2.5 (SE 0.4) v. 2.0 (SE 0.4) mmol/l for the Cr group, 2.4 (SE 0.2) v. 2.5 (SE 0.2) mmol/l for the placebo group). The present results indicate that Cr supplementation does not improve glucose tolerance or serum lipid levels in elderly subjects with stable impaired glucose tolerance.
Dehalogenation Reactions by Means of Hexaethylditin. III. : Reactions with &alpha;-Keto Halides (1971)

The dehalogenation reaction of phenacyl bromide (I) and its related compounds by means of hexaethylditin (II) was found to give the following products : diphenacyl (III) and acetophenone (IV) from I ; isodidesyl (VII), didesyl (VIII), and deoxybenzoin (IX) from desyl bromide (VI). Irradiation of ultraviolet ray at a low temperature in these reactions mainly gave the dimerization products (III, VII, VIII), and the thermal reaction predominantly gave the hydrogenated products (IV, IX). The expected dimerization product (XVI) was not isolated from the reaction of α-bromo-α, α-diphenylacetophenone (XIV) with II, but a new compound (XV) having no carbonylgroup was obtained.
COLLABORATIVE VISUALIZATION IN MEDICINE (2000)

One of the biggest areas of scientific visualization (ViSC) application is Medicine: with the evolution of image acquisition techniques the capacity and fidelity of image diagnosis were extended. Due to the large number of medical exams that output images, several visualization systems have been developed dealing with specific problems in this area in the last few years. The growing of World Wide Web-based applications and the modern trend of cooperative work in scientific research gave rise to a new class of systems, the so-called collaborative visualization systems. This survey presents an overview of ViSC in Medicine emphasizing the different approaches for collaborative visualization, and discussing difficulties still found for its real utilization. Keywords: Interactive Visualization, Visualization of Medical Images, Collaborative Visualization. 1.
3D Evaluation of the Lamina Cribrosa with Swept-Source Optical Coherence Tomography in Normal Tension Glaucoma (2015)

Thus, our results indicate that the parameters of our newly developed method of measuring LC thickness with SS-OCT may provide useful and important data for glaucoma diagnosis and research.
Magnetic properties of fine Fe-. Beta. particles (1989)

The magnetic properties of fine Fe-{Beta} particles with different boron concentration and particle sizes are studied. The powders were prepared by reducing Fe-salts with NaBH/sub 4/ as a reducing agent in aqueous solution. The particle size ranged from 300-600A. X-ray diffraction patterns show that the particles are crystalline for boron concentrations less than 20 at% and amorphous for greater concentrations. The maximum coervicity and saturation magnetization obtained for these particles are approximately 1200 Oe and 160 emu/g at room temperature. The coercivities are about two orders of magnitude higher than the values reported for Fe-{Beta} metallic glasses and {alpha}-Fe.
Direct Probing by Laser Scanning of the Current Distribution and Inhomogeneity of Josephson Junctions (1983)

A laser-scanning technique capable of probing the local current density in Josephson junctions has been used to study the current distribution and inhomogeneity of both high-and poor-quality junctions. Results from a high-quality tunnel junction are in good qualitative agreement with theory. The technique is also shown to be useful to study superconduting-normal-superconducting structures and bridge-type weak links.